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Ptyctodontida

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{{Taxobox
| color = pink
| name = Ptyctodontida
| fossil_range = Early/Mid [[Silurian]] - Late [[Devonian]]
| status = {{StatusFossil}}
| regnum = [[Animal]]ia
| phylum = [[Chordate|Chordata]]
| subphylum = [[Vertebrate|Vertebrata]]
| infraphylum = [[Gnathostomata]]
| classis = [[Placodermi]]
| classis_authority = McCoy, 1848
| ordo = [[Ptyctodontida]] [[extinction|†]]<br />
| subdivision_ranks = [[Family (biology)|Familie]]s
| subdivision =

}}

The Ptyctodontids were a group of primitive, unarmoured placoderms. Their armor was reduced to small plates around the face and neck.

[[Category:Prehistoric fish]]
[[Category:Placoderms]]
{{fish-stub}}

Bothriolepis

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Pseudopetalithchyida

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Gemuendina stuertzi

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<div style="float:right;">
<table border="1" cellspacing="0" cellpadding="2">
<tr><th bgcolor="#CCCCCC">'''[[Placodermi]]'''</th></tr>
<tr><td>
*[[Domain]]: [[Eukarya]]
*[[Kingdom]]: [[Animalia]]
*[[Phylum]]: [[Chordata]]
*[[Subphylum]]: [[Vertebrata]]
*[[Infraphylum]]: [[Gnathostomata]]
*[[Class]]: '''[[Placodermi]]'''
</td></tr>
<tr><td>
'''Order:'''
*[[Rhenanida]] [[extinction|†]]<br />
</td></tr>
<tr><td>
'''Family:'''
*[[Asterosteidae]]
<tr><td>
'''Genus:'''
*'''''Gemuendina'''''
</td></tr>
<tr><td>
'''Species:'''
*'''''G. stuertzi'''''
</td></tr>
<tr><td>
Fossil_range:
Early [[Devonian]]
</td></tr>
</table>
</div>

'''''Gemuendina stuertzi''''' was an early [[placoderm]] of the order [[Rhenanida]], of the seas of Early [[Devonian]] Germany. ''Gemuendina'' resembled a scaly ray with a pair of staring eyes, a pug-nose, and an upturned mouth. This leads virtually all artists who reconstruct it to give the creature a quizzical, almost shocked expression.

Unlike most other placoderms, such as the [[Antiarcha| Antiarchs]], or the [[Arthrodira| Arthrodires]], ''Gemuendina'' and its three other known relatives had armor made up of a mosaic of unfused bony plates. Also unlike other placoderms, it did not have the characteristic tooth plates of placoderms. Instead, it had star-shaped tubercle scales that allowed it to pick out [[shellfish]] and [[echinoderms]] out of the sediment, and crush them.

==References==
Paleos Rhenanida [http://www.palaeos.com/Vertebrates/Units/Unit060/060.100.html#Rhenanida]

[[Category:Prehistoric fish]]
[[Category:Fish]]
[[Category:Placoderms]]

Stensioella heintzi

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Rhenanida

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Phyllolepida

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Petalichthyida

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Arthrodira

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Antiarchi

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Placodermi

Admin — Sat, 09 Sep 2006 05:22:41 GMT

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<div style="float:right;">
<table border="1" cellspacing="0" cellpadding="2">
<tr><th bgcolor="#CCCCCC">'''Placodermi'''</th></tr>
<tr><td>
*[[Domain]]: [[Eukarya]]
*[[Kingdom]]: [[Animalia]]
*[[Phylum]]: [[Chordata]]
*[[Subphylum]]: [[Vertebrata]]
*[[Infraphylum]]: [[Gnathostomata]]
*[[Class]]: '''Placodermi'''
</td></tr>
<tr><td>
'''Orders:'''
*[[Antiarchi]] [[extinction|†]]<br />
*[[Arthrodira]] †<br />
*[[Petalichthyida]] †<br />
*[[Phyllolepida]] †<br />
*[[Ptyctodontida]] †<br />
*[[Rhenanida]] †<br />
*[[Acanthothoraci]] †<br />
*?[[Stensioellida]] †<br />
*?[[Pseudopetalithchyida]] †
</td></tr>
<tr><td>
Fossil_range:
Early [[Silurian]] - Late [[Devonian]]
</td></tr>
</table>
</div>

The [[Class]] '''Placodermi''' is composed of a group of armoured [[prehistoric fish]]es known from [[fossil]]s dating from the late [[Silurian]] to the end of the [[Devonian]] Period. Their [[head]] and [[thorax]] were covered by articulated armoured plates and the rest of the body was scaled or naked. Placoderms were one of the first [[jaw]]ed [[fish]], their jaws likely evolving from the first of their [[gill]] arches. Starting with the the studies of Dr Erik Stensio, and supported by uncrushed fossils that preserve their 3-dimensional structures from the Gogo Reef formation in Australia, it is presumed that sharks share a common ancestry with placoderms.

The first identifiable placoderms evolved in the late [[Silurian]]; they disappeared in the [[Late Devonian extinction]]s. The first appearance of late [[Silurian]] placoderm fossils, in [[China]], show the fishes already differentiated into [[Antiarchi|Antiarchs]] and [[Arthrodira|Arthrodires]], along with the other, more primitive groups; apparently Placoderm diversity originated long before the Devonian, somewhere in the middle Silurian, though earlier fossils of basal Placodermi, have yet to be discovered in these particular strata.

Many placoderms, particularly the [[Rhenanida]], [[Petalichthyida]], [[Phyllolepida]], and [[Antiarchi]], were bottom-dwellers. As such, to paraphrase from what was said in Paleos, Placodermi has been popularly misinterpreted as being a tribe of bottom-feeding snails and garbage trucks, nevermind that the placoderms were the dominant vertebrate group during the Devonian. One must remember that the vast majority of placoderms were predators, many of which lived at or near the bottom. Many, primarily the [[Arthrodira]] were mid- to upperwater dwellers, and were active predators. The largest known arthrodire, ''[[Dunkleosteus telleri]]'', was an 8 to 11 meter long predator and was presumed to have a nearly worldwide distribution, as its remains have been found in Europe, North America and Morocco. Other, smaller arthrodires, such as ''[[Fallacosteus]]'' and ''[[Rolfosteus]]'' of Gogo, had streamlined, bullet-shaped head armor, strongly crediting the idea that many, if not most, arthrodires were active swimmers, rather than passive ambush-hunters whose armor practically anchored them to the seafloor.

It was originally thought that the placoderms went extinct due to competition from the first bony fish, as well as the early sharks, due to a combination of the supposed inherent superiority of the bony fish and sharks, as well as the presumed sluggishness of the placoderms themselves. Since then, though, as more accurate summaries of prehistoric organisms have been developed, it is now presumed that the last placoderms died out one by one as each of their ecological communities suffered due to the environmental catastrophes during the Devonian/Carboniferous extinction event.

The earliest studies of placoderms were published by [[Louis Agassiz]], in his five volumes on fossil fishes, 1833 – 1843. In those days, the placoderms were thought to be shelled jawless fish akin to ostracoderms. Some naturalists even suggested that they were shelled invertebrates, or even turtle-like vertebrates. The work of Dr. [[Erik Stensio]], at the [[Swedish Museum of Natural History]], Stockholm, from the late 1920s established the details of placoderm anatomy, and identified them as true jawed fishes related to [[shark]]s. He took fossil specimens with well-preserved skulls, and ground them away, one-tenth of a millimeter at a time. Between each grinding, he made an imprint in wax. Once the specimens had been completely ground away (and ironically, completely destroyed as a result), he made enlarged, three-dimensional models of the skulls in order to examine the anatomical details more thoroughly. Many other placoderm specialists suspected that Stensio was trying to shoehorn placoderms into a relationship with [[shark]]s, but with more [[fossil]] specimens found, especially the exceptionally well-preserved fossils from the Gogo Reef formation in Australia, Stensio's theory of sharks and placoderms as sister groups is accepted as fact.

== See also ==
*''[[Gemuendina stuertzi]]''
*''[[Bothriolepis]]''
==External links==
*[http://hoopermuseum.earthsci.carleton.ca/placoderms/first.html Annetta Markussen-Brown, "Devonian Armoured Fish" 2000]
*[http://www.ucmp.berkeley.edu/vertebrates/basalfish/placodermi.html Introduction to the Placodermi Extinct armored fishes with jaws]
*[http://www.btinternet.com/~vendian/FOSSILWEB/paleozoic_fish.htm PALAEOZOIC FOSSILS UK]
*[http://www.toyen.uio.no/palmus/galleri/montre/english/m_panserhai_e.htm Placoderms]
*[http://www.palaeos.com/Vertebrates/Units/Unit060/060.000.html Placodermi: Overview]
*[http://www.amonline.net.au/archive.cfm?id=1137]

[[Category:Prehistoric fish]]
[[Category:Fish]]
[[Category:Placoderms]]

Petalocrinus

Admin — Sat, 09 Sep 2006 05:22:02 GMT

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'''''Petalocrinus''''' was a [[genus]] of [[crinoids]] from the [[Silurian]]. They are extremely distinctive from most, if not all other crinoids, in that their arms were modified into relatively large, wedge-shaped plates that gave their owners a decidedly flower-like appearance. All though the genus did not live out the Silurian, it was quite successful, with at least 15 species found in the United States, China, and Sweden (primarily from Gotland).

''P. mirabilis'' is the type species, with specimens found in Iowa, British Columbia, and Yunnan province in China.

== Links ==

Reconstruction of ''P. mirabilis'' [http://www.deviantart.com/deviation/33783990/]

List of species [http://crinoid.gsajournals.org/crinoidmod/indexii?genus=PETALOCRINUS]

[[Category:Prehistoric invertebrates]]

Eotitanops

Admin — Sat, 09 Sep 2006 05:20:36 GMT

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Time

Bmeyers — Sat, 19 Aug 2006 21:53:58 GMT

Bmeyers:

== The Geological Time Scale ==

Scientists divide the Earth into a number of periods - the "Geological time-scale", according to the rock types and sort of fossils found in each one. These divisions are pretty arbitrary, like any man-made divisions, but they at least can serve as useful labels. So the Paleozoic, the era of "ancient life" is characterized by fossils of invertebrates, primitive tetrapods, etc; the Mesozoic or era of "middle life", by fossils of dinosaurs etc, and the Cenozoic or era of "recent life" by mammals and modern plants and invertebrates.

These eras are divided into periods, the system of which was established by the end of the last century. The periods are in turn divided into epochs, and the epochs are divided into ages called ages. (more on these subdivisions)

Scientists know these periods lasted for millions of years, because they can date them with a fair degree of accuracy according to the amount of radioactivity that occurs in the rocks. (see Radiometric Dating)

The Geological time-scale can also be used to define the major stages in the history of life on Earth. Often each era ends with a major extinction, which eliminates the dominant life forms of the time and paves the way for newcomers

== Precambrian ==

=== Hadean Era ===

This era begins with the formation of the Solar System and Earth, outgassing of first atmosphere and oceans, bombardment by left-over planetessimals and debris. The name says it all; a hellish period lasting some 760 million years, when the Earth was subject to frequent bombardment by comets, asteroids, and other planetary debris. At one point, early in this era the moon was formed when a Mars-sized body struck the original Earth, pulverizing both. Yet incredibly, the first primitive life emerged even at this early stage. This was an era characterized by extensive volcanism and formation of first continents. By the end of the Hadean, the Earth had an atmosphere (unbreathable to most organisms today), and oceans filled with prokaryote life evolution

=== Archean Era ===

Lasting more than twice as long as the Phanerozoic eon, the Archean was a time when diverse microbial life flourished in the primordial oceans, and the continental shields developed from volcanic activity. The reducing (anaerobic) atmosphere enabled archea (anaerobic microbes) to develop, and plate tectonics followed a regime of continental drift different to that of the Proterozoic and later. During this era, one type of organism, the Cyanobacteria (blue-green algae) produced oxygen as a metabolic by-product; the eventual build-up of this highly reactive gas was to eventually prove fatal to many life-forms, and converted the atmosphere from.

=== Proterozoic Era ===

The Proterozoic, which lasted even longer than the Archean Era, saw the atmosphere changes from reducing to oxygenated, driving the original anaerobic inhabitants of the Earth into a few restricted anoxic refuges and enabling the rise of aerobic life (both prokaryote and the more complex eukaryotic cell, which requires the high octane boost that oxygen enables.) Stromatolites (colonial cyanobacteria), which had appeared during the Archean, were common. The modern regime of continental drift began, and saw the formation of supercontinent of Rodinia, and several extensive ice ages. Late in the Proterozoic a runaway icehouse effect meant that the preceding warm conditions were replaced by a "Snowball Earth" with ice several kilometers deep covering the globe. Warming conditions saw the short-lived Edicarian biota and finally the appearance of first metazoa.

== Phanerozoic ==

=== Paleozoic Era ===

Early in the 300 million year history of the Paleozoic, atmospheric oxygen reached its present levels, generating the ozone shield that screens out ultraviolet radiation and allows complex life to live in the shallows and finally on land. This era witnessed the age of invertebrates, of fish, of tetrapods, and (during the Permian) reptiles. From the Silurian on, life emerged from the sea to colonize the land, and in the later Paleozoic pteridophyte and later gymnospermous plants flourished. The generally mild to tropical conditions with their warm shallow seas were interspersed with Ordovician and Permo-Carboniferous ice ages. Towards the end of the Paleozoic the continents clustered into the supercontinent of Pangea, and increasingly aridity meant the end of the great Carboniferous swamps and their unique flora and fauna. The Paleozoic was brought to an end by the end Permian mass-extinction, perhaps the most severe extinction the planet has seen.

=== Mesozoic Era ===

Lasting little more than half the duration of the Paleozoic, this was a spectacular time. The generalized archosaurian reptiles of the Triassic gave way to the dinosaurs, a terrestrial megafauna the like of which the Earth has not seen before or since. While dinosaurs dominated the land, diverse sea-reptiles ruled the oceans, and invertebrates, especially ammonites, were extremely diverse. Pterosaurs and later birds took to the sky. Mammals however remained small and insignificant. Climatic conditions remained warm and tropical worldwide. The supercontinent of Pangea broke up into Laurasia and Gondwana, with different dinosaurian faunas evolving on each. During this era modern forms of corals, insects, new fishes and finally flowering plants evolved. At the end of the Cretaceous period the dinosaurs and many other animals abruptly died out, quite likely the result of an asteroid impact and associated extensive volcanism (acid rain)

=== Cenozoic Era ===

With the extinction of the dinosaurs and the end of the Mesozoic, the mammals swiftly inherit the Earth. Archaic mammals co-existed with birds and modern reptiles and invertebrates. The current continents emerged, and the initial tropical conditions were replaced by a colder drier climate, possibly caused by the Himalayan uplift. The appearance of grass meant the rise of grazing mammals, and the cooler drier world allowed modern mammalian groups to evolve, along with other lineages now extinct and a few archaic hold-overs. Among the newcomers were the anthropoid apes that culminated in the australopithecine hominids of Africa. Decreasing temperatures and a polar landmass of Antarctica resulted in a new Ice Age. Most recently, in the blink of an eye geologically speaking, this era saw the rise of Man (Homo erectus, Neanderthal and Cro Magnon) and use of stone tools and fire, the extinction of Megafauna, and civilization and human activities that have transformed the globe, but at a cost of great environmental destruction.

Nectarian Era

Bmeyers — Sat, 19 Aug 2006 21:37:09 GMT

Bmeyers: initial copy the the Nectarian Era entry

== The Nectarian Era of the Hadean Eon: 3950 to 3850 million years ago ==

The Nectarian Era is named for the Mare Nectaris ("Sea of Nectar"), an old basin on the southwest part of the lunar Nearside. This region was formed approximately 3950 to 3850 Mya. The absolute dates vary considerably, but there is general agreement that the Nectarian was relatively short, lasting 75 to 100 My. The Nectaris Basin was created by the impact of perhaps thirteen large bodies within a region only 860 km wide. The current "best guess" is that these objects were derived from the breakup of the planet which produced the asteroid belt, a result of tidal stresses caused by a close approach to Jupiter. The basins of Nectarian age are the oldest surviving basins on the moon.

Given that the Earth has a substantially larger gravitational field, the effect of the Nectarian bombardment on the Earth was probably severe. Almost nothing from this era remains on Earth, so the geology is somewhat speculative. However, by churning and heating the outer regions of the Earth, these impacts would have promoted the density sorting that eventually produced "light" granite continents floating on the distinctly denser material of the mantle.

Embryophyta

Admin — Sat, 19 Aug 2006 19:18:27 GMT

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=== Bryophyta ===

Bryophyte Life Cycle If the mosses had not survived into the present, we would be forced to invent them as just the sort of intermediate we might expect between essentially aquatic algae and fully terrestrial plants. Mosses do have differentiated stems. Although these are generally only a few millimeters tall, they are still designed to provide mechanical support against gravity without help from water -- the first such structure in any kingdom. Bryophytes also have leaves. These are typically one cell thick and lack veins, although they may have a central thickening for support. Mosses also have rhizomes. These may have some function in extracting soil nutrients, although their primary function seems to be mechanical attachment to the substrate. Thus they are not true roots, but do approach that condition.

The bottom line is that, structurally, mosses really differ from rhyniophytes in only one aspect: mosses lack specialized vascular tissues. That alone is sufficient to explain the lack of big leaves, long stems, and true roots. This whole complex of characters is thus probably primitive. The other distinctive character of mosses is that the plant we normally observe is the haploid, gametophyte stage. But this character is shared with liverworts (basal embryophytes) and so is also probably plesiomorphic.

Curiously, in hornworts (also basal embryophytes) the sporophyte generation is dominant. In addition, it turns out that the leaves of moss probably evolved independently from the leaves of higher plants. So the relationships of the mosses and basal embryophytes are still uncertain. What really does seem to set mosses apart is their unique form of leaf. What really seems to unite mosses with higher plants is (a) the presence of stomata to control water loss and (b) meristem (apical growth) in the sporophyte generation. See, Friedman et al. (2004). Phylogenetically, we treat Bryophyta as Moss > Quercus.

=== Rhyniophtya ===

HorneophytonSee Rhyniophyta. That section covers the basal rhyniophytes, such as Horneophyton, which were the first real land plants. These probably evolved in the Ludlow and formed the stem group for all other land plants. Consequently, they are paraphyletic. Rather than abandoning this name and its rich history, we use it to mean all land plants. Our working phylogenetic definition is definition is Quercus > moss.

This group is characterized by the ability to reproduce without open water. Anatomically, in all rhyniophytes, the (diploid) sporophyte generation is dominant, and the sporophyte is branched. For this reason, the taxon is often referred to as the Polysporangiophytes. In addition, the archegonium develops inside the body of the plant, rather than being superficial as in mosses and most basal embryophytes. Kenrick & Crane (1997).

Horneophyton and a few other basal forms lack tracheids. That is, they are avascular plants. However, almost all other rhyniophytes have some development of specialized vascular tissues. The most basal tracheid type, present in most stem rhyniophytes, appears to be the S-type tracheid.

=== Lycophytina ===

The Lycophytina includes the lycopods, zosterophylls, and related forms, including (probably) a number of plants often treated as basal rhyniophytes, such as Baragwanathia. Kenrick & Crane (1997). Since they are a complex group and are treated extensively elsewhere, we will defer discussion to a revision of the existing materials.
Euphyllophytina

The clade that unites oak trees and ferns is Euphyllophytina = Quercus + Equisetum. The two complementary stem clades are Moniliformopsida and Spermatophytata. Euphyllophytines are characterized (Kenrick & Crane, 1997) by monopodial or pseudomonopodial branching, helical arrangement of branches, small, pinnule-like vegetative branches, the branch apex is recurved or coiled, paired sporangia which split open along one side through a single slit, and radially-alligned xylem in the larger axes. Only early euphyllophytines have P-type tracheids. Kenrick & Crane identified this clade based entirely on morphological characters. However, Euphytophytina has also been recovered, with essentially the same structure, using ssu rDNA. Duff & Nickrent (1999).

=== Moniliformopses ===

Psilotum nudumThe Moniliformopses are the horsetails and ferns, including the Psilotidae (whisk ferns). They are closely related to the seed plants. Pryer et al. (2001). So, for example, they exhibit apical growth (meristem) in both sporophyte and gametophyte generations. They have well-developed roots megaphyllous leaves and the vascular system needed to make use of both. However, both may have been evolved independently of higher plants. Friedman et al. (2004). In addition, Moniliformopses lack a complete vascular cambium, and growth of xylem is restricted to lobes of the primary xylem strand.

Since this is a new clade -- discovered, for all practical purposes, by Preyer's group, we have little to say about Moniliformopses as a taxon, and defer discussion to a fuller consideration of its three component parts. The Psilotidae are the most basal, followed by the horsetails, then the remainder of the ferns.

We apply a crown group defiition to Moniliformopses: Equisetum + ferns.

=== Spermatophytata ===

PsilophytonThe clade that unites oaks and lycopsids is Euphyllophytina. The two complementary stem clades are Lycopsida and Spermatophytata = Quercus > Lepidodendron. A second way to look at Spermatophytata is as the stem group leading to angiosperms. It includes Trimerophyta and the progymnosperms, in fact everything up to and including the seed plants (Spermatopsida). However, we will only be concerned with the more basal forms for now. A third way of considering Spermatophytata is as the seed plants. However, this applies only to living forms. The basal Trimerophyta and their immediate descendants (assuming Trimerophyta is paraphyletic) lacked seeds, true leaves, or even, perhaps, roots. It is quite likely that virtually all the important land plant adaptations were independently developed in the moniliformopsid and spermatophytate lineages.

What seems to have set Spermatophytata apart quite early is not, in fact, the development of seeds, but the evolution of a full vascular cambium which permitted secondary growth. Early plants with apical growth were able to use that trait to grow taller and (a) get more sunlight (b) shade their competition and (c) have a better shot at spore dispersal. However, supporting a long stalk is much easier with a wider central column. Less derived groups either had no way to do this, or developed lateral lobes of the apical meristem. The latter worked, but required the tree to grow wide before it grew tall. The evolution of a complete vascular cambium permitted the tree to grow just wide enough to suit its height -- growing continuously wider as it grew tall.

The evolution of seeds follwed this innovation. Seeds are embryonic sporophytes, held in a sort of metabolic stasis and provided with enough food to get started once their growth has been re-stared by exposure to suitable growing conditions. Well adapted seeds combined sexual reproduction with spore-like wide dispersal and so made the alternation of generations obsolete. However, early seeds, which might lack these refinements, probably evolved on tall trees which gave any sort of propagule a head start in dispersal.

The Spermatophytata are the stem group for our next major division, the Spermatopsida.

[[Chlorobionta|Back to Chlorobionta]]

The Diversity of Plants

Admin — Sat, 19 Aug 2006 19:15:59 GMT

Admin:

== The Diversity of Plants ==

We will cover the higher taxa of lower plants in two blocks: Chlorobionta and Embryophyta. The prasinophytes (basalmost chlorobionts), chlorophytes and charophytes are essentially algae, which normally impinge on our consciousness just long enough to apply a little wasabi and shoyu. Arigato, and next I'll have ni unagi, kudasai. Don't try that with an embryophyte. There's a differnce between sushi and soba. Embryophytes are mostly land plants, and it was the ability of plants to live on land that allowed all the other branches of life to live on land as well. In fact, only the plants can really be said to have adapted to land. With few exceptions, the rest of life simply adapted to plants.

=== Chlorobionta ===

Halosphaera viridisThe general characteristics of the green plants are touched on above. The purpose of this section is to introduce the prasinophytes. These are a paraphyletic group of green algae which radiate from the base of the Chlorobionta. Most are photosynthetic flagellates. In addition, the prasinophytes are the only mixotropic plants, i.e., they obtain food both by photosynthesis and phagotrophy. This is, presumably, how they obtained chloroplasts in the first place.

The phycomate prasinophytes (those with large, thick-walled floating stages, or "phycomata") have received special attention because of their extremely long fossil record. Phycomata are known as acritarchs well into Proterozoic time. One genus (Tasmanites) dates back to 600 Mya. Javaux et al. (2004) have turned up an entire menagerie of forms from the Mesoproterozoic, and even beyond (at least 1500 Mya), which are almost certainly eukaryotic and could well be prasinophytes, or somewhat stemward of the plants. They cannot be too distantly related, as the presence of thick organic walls, with extreme resistance to degradation, seems to be a trait of the plant-chromist lineage. One of these in particular, Leiosphaeridia crassa, from the c. 1460 Mya Roper Fm. of northern Australia, is being investigated as a possible green alga. Interestingly, in Recent or merely Paleozoic forms, these relatively large, thick-walled morphs are associated with moderately anoxic conditions and nutrient exhaustion during algal blooms.

=== Chlorophyta ===

UlvaWithin the Chlorobionta are two large clades making up the "green algae." The green algae, as currently conceived, have no formal taxonomic name. We will define the group as Quercus + Chlamydomonas. The corresponding stem clades are Chlorophyta (Chlamydomonas > Quercus) and Charophyta (Quercus > Chlamydomonas). "Chlorophyta" is also the old name for all green algae, so this is perhaps unnecessarily confusing. Tough luck. The ambiguity is now so embedded in the literature that there's nothing anyone can do about it.

The Chlorophyta have largely been delineated by molecular techniques, so it is a bit difficult to describe their characters. We know of two possible synapomorphies of the Chlorophyta. First, chlorophyte sexual forms bear paired apical flagellae usually separated by 180�, but sometimes at the same end. Second, they retain the nuclear envelope during mitosis. Indeed, chlorophytes seem to be distinguished by a variety of bizarre variations on the usually pedestrian theme of mitosis; however those variations are not entirely consistent within the group.

Like the land plant lineage, they tend to form large aggregates, with some tissue differentiation (primarily holdfasts and reproductive structures). They are very often found in terrestrial and fresh water environments, with a distinct preference for very cold environments, such as under snow cover, or even within Antarctic ice. Various species are important in forming symbiotic relationships with fungi, i.e., lichens. As with all green algae, chlorophytes tend to have a double cell wall -- an inner wall of cellulose and an outer gelatinous wall of protein, particularly pectin, known in higher plants as a marker for parenchyma. Starch stored in pyrenoids, located inside the chloroplasts.

=== Charophyta (= Streptophyta) ===

KlebsormidiumThe Charophyta are the other lineage of green algae, the group which includes the land plants. Karol et al. (2001). As mentioned above, our working definition is Quercus (oak) > Chlamydomonas. The Charophyta have recently been referred to as the Streptophyta, but the reasons given for this change in nomenclature are probably insufficient. Unfortunately, the name is also frequently, and wrongly, used in place of Charophycea or Charales to describe the stoneworts -- one of several distinct groups of charophytes.

The synapomorphies of the group are said to include the the dissolution of the nuclear membrane during mitosis and the presence of paired flagella (when flagella are present at all) directed perpendicularly to each other. In addition, the charophytes are strongly inclined toward growth as long filaments.

=== Embryophyta ===

LiverwortThe Embryophyta constitute the terrestrial or land plants, the first representatives of which appeared during the Silurian or possibly even the Middle or Late Ordovician period. The most primitive of these are nonvascular land plants, a group that classically includes liverworts (Hepatophyta / Hepaticopsida), hornworts (Anthocerotophyta / Antheroceratopsida) and mosses (Bryophyta). The majority of land plants however are included within the huge and diverse clade traditionally called Tracheophyta, or Vascular Pants, and which we will refer to as the Rhyniophyta.

We treat Embryophyta in a specialized sense, as Quercus + moss. This may be a mistake, as this definition probably excludes the liverworts (see image) and perhaps even the hornworts. Both of these groups have traditionally been thought of as embryophytes.

Embryophytes (including liverworts) have the following synapomorphies: 1) a life cycle with alternation of generations 2) apical cell growth (some kind of meristem-like growth organization), 3) cuticle (needed to control water loss on land), 4) antheridia (male gametophyte organs), and 5) archegonia (female gametophyte organs). The more derived embryophytes are vascular plants. Vascular plants have an elaborate system of conducting cells, consisting of xylem - in which water and minerals are transported) and phloem (in which carbohydrates are transported). This method of internal support enables them to stand and grow upright and pull up nutrients against the force of gravity. There are two developmental grades - those that reproduce by means of spores, and hence are dependent on water or extensive moisture (e.g. ferns), and those that reproduce by means of seeds (e.g. conifers and flowering plants). The most primitive forms reproduce by means of spores (haploid (1N) spores). They generally require a moist environment, because the flagellated sperm require water for fertilization.

The Embryophytes, then, are plants with an alternation of generations and some ability to live on land. The basal embryophytes were still not land plants, since they required, and still require, open water to propogate. As we define the Embryophyta, they split basally into mosses (Bryophyta) and land plants (Rhyniophyta). The Rhyniophytes two important groups: the Lycophytina (lycopods and the extinct zosterophylls) and the Euphyllophytina (ferns and seed plants).
Embryophyta

[[Chlorobionta|Back to Chlorobionta]]

Devonian Plant Evolution

Admin — Sat, 19 Aug 2006 18:53:49 GMT

Admin: /* The Carboniferous Period */

The development of plant root depth during the [[Devonian]] period marked a major shift in plant evolution and terrestrial ecosystems. Early Devonian plants such as the rhyniophytes, zosterophyllophytes and lycophytes have features such as vascular tissue, stomata, a cuticle to protect against drying, rhizoids, and sporangia at the tips of short lateral branches instead of terminal as in Cooksonia. These forms were small, non-rooted or shallowly rooted, lacked woody tissue and hence were unable to grow beyond the height of small bushes. These plants reproduced by means of spores, which requires a moist habitat. They were therefore confined to moist, lowland habitats, thus having little effect on their physical environment

The first shrub and tree-like plants, such as Progymnosperms and lycopsids, had evolved by the middle Devonian. By the late Devonian the first real trees, such as Archaeopteris ("ancient fern" - not to be confused with Archaeopteryx, "ancient wing", the first bird!), had appeared. Trees have special vascular systems to allow for water circulation and nutrient flow against the pull of gravity. At the very end of the Devonian seed-bearing (gymnosperm) plants appeared for the first time, breaking free of the dependence on moisture that limits spore-bearing (pteridophyte) plants. Along with these developments came the development of advanced root systems and the production of soils, increased weathering, and huge ecological feedback.

The black & white figure shows the increasing terrestrial plant root depth penetration with time during the Devonian, leading to increasing soil depth and weathering. "Rhyniophytes" are a basal radiation of land plants such as Aglaophyton or Horneophyton. Trimerophytes include such plants as Psilophyton. Lycophytes arrived in the Middle Devoinian. They originally appeared as low-lying herbaceous forms, such as Asteroxylon or Drepanophycus. Tree-sized lycopods (e.g., Lepidosigillaria and Cyclostigma) appeared by the end of the Middle Devonian. Progymnosperms, such as Tetraxylopteris, arose in the Frasnian. By the Famennian, Archaeopteris forests are common. At the very end of the Devonian, Archaeopteris is found together with early gymnosperms, such as Elkinsia and Moresnetia, and zygopierid ferns such as Rhacophyton.

=== The Carboniferous Period ===

Despite the origin of the seed habit, the majority of Carboniferous plants reproduced by spores. The moist swampy environments of the time provided a nurturing environment. Lycophytes (scale trees and club mosses), which had evolved as small plants during the late Silurian? or early Devonian, and diversified greatly during the succeeding Devonian period, continued and thrived throughout the Carboniferous, but being dependent on water and moist conditions, most died out with the increasing aridity at the end of the Paleozoic, only a few small ones making it through. Calamites and ferns were other spore-bearing plants that appeared during the Devonian and flourished during the following Carboniferous period.

[[Chlorobionta|Back to Chlorobionta]]

Evolution of Paleozoic Land Plants

Admin — Sat, 19 Aug 2006 18:50:38 GMT

Admin:

=== Green Algae ===

The Green Algae - the Chlorophyta and Charophyta - include a number of mostly aquatic forms, including some unicellauar and primitive colonial forms. and other multi-cellular types that however lack a true root system

They are very closely related to (and probably the ancestors of) the higher plants in the kingdom Plantae. Molecular and cellular similarities between green algae, particularly the charophytes, and land plants include the following:

(1) Both the green algae and plants have chlorophyll b and beta-carotene

(2) Green algae and plants both have special intracellular membranes (the thylakoid membranes) which contain the chlorophyll stacked into grana.

(3) Charophytes have a cellulose content of 20 to 25% of the cell wall, a composition similar to that of plants.

(4) Cell division in green algae is very similar to that of land plants. Both use microtubules to bring vesicles containing new material in to form the cell plate which will divide the cell into two.

(5) Nuclear genes and RNA are similar between charophytes and plants.

=== Plants Conquer the Land ===

The Early Devonian Rhynie Chert Flora - from Life Before Man by Zdenek V. Spinar, illustrated by Zdenek BurianIf the great evolutionary radiation of metazoa (multicellular animals) in the earliest Cambrian oceans was the first great dramatic even of the Phanerozoic era (indeed ushering in the Phanerozoic), the conquest of land by multicellular plants was the next, and of equal importance. Indeed, without the plants no animals would ever have been able to survive on land.

But whereas the Cambrian explosion was very rapid, in the order of perhaps 3 to 5 million years for the origin of all major phyla (and many others now extinct), the colonization of the land by vegetation was a much slower and more protracted. The reason for this is not hard to understand. Cambrian animals were moving into a favorable new environment with no competitors. Plants had to brave desiccation, extremes of temperature, and harsh ultra-violet radiation.

Enigmatic traces are known from the early and middle Ordovician, These are fossils of spores, cuticles, and tubes and don't reveal much about the structures or nature of these plants. All we can say is that these plants were probably of a bryophyte grade of evolution - small, non-vascular, and lacking morphological differentiation into roots, stems, and leaves, like modern mosses and liverworts.

The first unambiguous record of land plants is from the Silurian period. They were mostly small, primitive forms, dependent on the proximity of water, and with the most rudimentary stem and leaf structure.

A common middle Silurian to early Devonian plant is Cooksonia, which had dichotomous branching and terminal sporangia (spore cases) at the tips of its green leafless stems. It is not known whether Cooksonia was a proper vascular (tracheid-bearing) plant. True vascular plants evolved and began to diversify during the Latest Silurian and Early Devonian.

[[Chlorobionta|Back to Chlorobionta]]

Metazoa

Bmeyers3535 — Sat, 19 Aug 2006 02:32:25 GMT

Bmeyers3535: first load of the metazoa entry

== Metazoa: the Animals ==

LIFE (=Archaea?)
|--Eubacteria
`--Eukarya
|--Chlorobionta
`--+--Fungi
`--METAZOA
|--Porifera
`--+--+--Cnidaria
| `--Ctenophora
`--Bilateria
|--Deuterostomata
`--Protostomata

Quick Links to Major Animal Groups
Evolution of the Metazoa
Phylogenetic Organization of the Metazoa
Some Linnean Lists
Links

== Quick Links to Major Animal Groups ==

Archaeocyatha: enigmatic early reef builders.

Arthropods: insects, crustaceans, scorpions -- the most successful metazoans.

Brachiopoda: they look like mollusks, but they're not.

Bryozoa: advanced, encrusting reef-builders.

Chordata: mostly, the Vertebrates.

Cnidaria: Radiate animals -- jellyfish and corals.

Echinoderms: our cousins, the sea urchins, sand dollars, starfishes and so on.

Mollusca: clams, oysters, and the like.

Porifera: sponges.

"Procoelomates": sometimes bizarre worms near the root of the Bilateria.

Tardigrada: "water bears."

== Evolution of the Metazoa ==

Lodosiga from Barnes (1968)The Animal Kingdom (Metazoa) is usually considered to include multi-cellular, heterotrophic eukaryotes in which (unlike Plants) the cells are without cell walls. This includes basically everything from sponges and jellyfish to insects and vertebrates included under the heading of to be "Metazoa", and considered to have evolved from a single unicellular choanoflagellate ancestor, sometime during the Vendian period.

From a simple colonial choanoflagellate animals developed through increasing grades of specialization and complexity, first sponges, then coelenterates, and finally bilateral animals (possessing a head and front and rear). A recent interpretation of this monophyletic animal kingdom theory is the phylogenetic scheme of Wainright et al. 1993 shows choanoflagellates contained within the monophyletic assemblage Metazoa (= "animals"), and Fungi as the closest sister group to Metazoa.

The problem here is that although choanoflagellates seem clearly related to sponges, it is not clear how closely related sponges are to the rest of the Metazoa. It is also difficult to see how such a poorly organized organism as a sponge (essentially nothing but a glorified colonial protozoan) can develop into organisms with a proper body structure and internal organs. The most widely held theory seems to be that a colonial choanoflagellate evolved into a hollow spherical ball of cells, the blastula, which constitutes the earliest embryonic stage of development, and even occurs in sponges. The 'blastula model' of metazoan evolution goes all the way back to the famous 19th century German Darwinist Ernst Haskell.

Blastea hypothesis from Barnes (1968)However, it is not certain that such a blastaea animal ever even existed. The ontogeny recapitulates phylogeny theory championed by Haekel (according to which the growing embryo passes through all its past evolutionary stages - e.g. the early human fetus possesses gill slits and a tail), was enormously popular for some time, and incorporated into the late 19th century and early twentieth century esoteric and occult speculations of Blavatsky and Rudolph Steiner, and more recently, the "Up from Eden" transpersonal psychology of Ken Wilber, has been shown to have very little scientific basis, and in fact it is known that Haekel faked a number of his images, chopping up the embryos so they look more like how they should in his theory.

All we can say for certain is that some time during the late Proterozoic era an unknown protozoan (or protistan) organism developed into a tiny colonial form, which eventually became the common ancestor of the actual nature of this organism is not known, as it was soft-bodied and left no trace. It used to be thought that sponges evolved from a different single celled organism to higher animals (in which case the Metazoa are a polyphyletic taxon), but recent molecular phylogenetic evidence indicates this is not the case.

== Phylogenetic Organization of Metazoa ==

The base of the animal tree is moderately non-controversial. Animals are closely related to a particular type of protist, the choanoflagellates. The first metazoans were probably sponges, Porifera. Sponges are multicellular animals with specialized cell types, but no specialized tissues. The different cell types are intermingled, and one part of a sponge looks rather like another. The Porifera are probably paraphyletic. That is, all other animals are probably descended from something we would probably think of as a "sponge." In that sense, all animals may be members of the Porifera. However, we will use the term only as it applies to sponge-like animals. More generally, animals without strongly differentiated tissues are sometimes referred to as Parazoa, since there are probably animals other than sponges with this grade of organization, e.g., the Archaeocyatha and the Ediacaran fauna.

All animals with distinct tissue types are referred to as the Eumetazoa. Phylogenetically, we might define the Eumetazoa as the crown group uniting jellyfish and silverfish. The jellyfish lineage includes the Cnidaria (jellyfish, corals, etc.) and some related types. These animals, the Radiata, seem to have derived from a single common ancestor who was not in our direct line of descent. They all have tissues, but normally nothing much more complicated than "inside" (endoderm) and "outside" (ectoderm) tissues, with some level of front-to-back specialization. From an embryological standpoint, they do not undergo gastrulation, and they consequently lack mesoderm, a tissue type which characterizes all more derived animals. Most are radially symmetrical. That is, their body plan is based on a cylinder open at one end, with the open end serving both for ingesting food and eliminating waste.

All other animals are Bilateria. Bilaterians undergo gastrulation and possess mesoderm. Thus, they begin with three embryonic cell types. Furthermore, the are bilaterally symmetrical. In addition to a more complex inside-outside pattern of tissues and the ancestral front-to-back organization, they have a separate top and bottom. In many worm-like forms, this top-and-bottom asymmetry is not well developed on the outside. However, the internal organization generally involves distinct dorso-ventral organization, with , for example, muscles and circulatory structures located dorsally, and the gut and a major nerve chord located ventrally. Most (but not all) also have a separate mouth and anus, so that the flow of digestion is one way.

At this point, things become much less clear. There are three groups of Bilateria which show some internal cohesion. These are the Deuterostoma (including echinoderms and chordates), the Lophotrochozoa (including annelid worms and mollusks), and the Ecdysozoa (including arthropods). Each of these groups includes some of the "minor phyla" of animals. However, a large number of mostly worm-like groups are left out of this scheme; and their positions are sometimes too vague even to guess at.

Of the three main groups, the deuterostomes probably branched off earliest, but even this has been disputed. The term "protostome" is used a good deal, particularly in the older literature, to refer to the lophotrochozoans, ecdysozoans, and everyone else who exhibits a particular pattern of early embryonic development. For our purposes, we will treat the deuterostomes as the earliest-branching clade and use the term "protostome" to refer to the crown group of bugs + slugs (Ecdysozoa + Lophotrochozoa). Other than the most well-established members of the two protostome groups, all other animal phyla will be treated as Bilateria incertae sedis.

With that said, our tree looks like this:

METAZOA
|--Archaeocyatha
`--+--Porifera
`--EUMETAZOA (= jellyfish + silverfish)
|--RADIATA
| |--Cnidaria
| `--Ctenophora
`--BILATERIA (including "Procoelomates")
|--DEUTEROSTOMA
| |--Echinodermata
| `--Chordata
`--PROTOSTOMA? (= bugs + slugs)
|--LOPHOTROCHOZOA
| |--Annelida
| `--+--Mollusca
| `--Brachiopoda
`--ECDYSOZOA
|--Bryozoa ?
`--Arthropoda
|--Crustacea
`--Insecta

Most of the "Procoelomates" are probably below the deuterostome divergence, and some may be closer to mollusks than to arthropods. However, their relationships are so poorly known that we have "demoted" them to generalized bilaterians for the present.

ATW041229. Text public domain. No rights reserved.

== Some Linnean Lists ==

We often disparage Linnean lists. However, The phylogeny of this region is fairly unstable and includes a large number of unknown connections. Furthermore, most of the invertebrate literature still uses a Linnean scheme for higher-level classifications. Accordingly, it is useful to include two of these schemes as a point of reference. In the Linnean system the Animal Kingdom has traditionally been classified into about three dozen phyla, which have been grouped into larger categories:

Kingdom ANIMALIA - Develop from a blastula, cellular to organ-systems grade, food ingesting without chloroplasts, subdivided on grade of organization, symmetry, and coelomic development.

Subkingdom PARAZOA - Cellular (multi-cellular) grade, no tissues, organs, digestive tract or mouth.

Phylum Placozoa

Phylum Porifera - porous with one to many internal cavities lined with choanocytes; (the sponges).

Subkingdom EUMETAZOA - Tissue to organ-system grade, with mouth and digestive tract.

Branch RADIATA - Radial to modified radial symmetry, tissue grade organization with incipient organs, diploblastic, mesenchyme of ectodermal origin, digestive cavity the sole body cavity, no anus.

Phylum Cnidaria - Symmetry radial, biradial, or radio-bilateral, mouth usually encircled by tentacles armed with nematocysts; (the coelenterates, jellyfish).

Phylum Ctenophora - Symmetry biradial, eight radial rows of ciliated swimming plates, tentacles when present not encircling mouth, no nematocysts.

Branch BILATERIA - Primary bilateral symmetry, secondarily modified to pentameral or radial, organ-system grade of organization, most triploblastic with well-developed mesoderm of endodermal origin, most with body cavity other than the digestive cavity, anus typically present.

Grade ACOELOMATA - No coelom, region between digestive tract and body wall filled with mesenchyme or mesoderm, if segmented youngest segments nearest head.

Phylum Mesozoa

Phylum Platyhelminthes

Phylum Nemertina

Phylum Gnathostomulida

Grade PSEUDOCOELOMATA - Body cavity a pseudocoel (remnant of blastocoel, not lined with mesoderm on both sides), triploblastic.

Phylum Gastrotricha

Phylum Rotifera

Phylum Kinorhyncha

Phylum Acanthocephala

Phylum Entoprocta

Phylum Nematoda

Phylum Nematomorpha

Grade COELOMATA - With a true coelom and well-developed mesoderm.

Series PROTOSTOMATA - Blastopore becomes mouth, typically schizocoelous with spiral cleavage.

Phylum Bryozoa (Ectoprocta) - Colonial lophophorate, oligomerous.

Phylum Phoronida - Solitary lophophorate with worm-like (vermiform) body, oligomerous.

Phylum Brachiopoda - Solitary lophophorate with bivalve shell, oligomerous, enterocoelous.

Phylum Mollusca - Pseudometamerous, reduced coelom, visceral mass covered by a body fold, the mantle, which secretes a calcareous shell of one or more pieces.

Phylum Priapulida - Marine worms, some consider pseudocoelomate; no fossil record.

Phylum Sipuncula - Marine worms, amerous; no fossil record.

Phylum Echiura - Another amerous worm.

Phylum Annelida - Metamerous, segmented, vermiform, without jointed appendages.

Phylum Tardigrada - small (<2mm) worm-like, meiofaunal, no fossil record.

Phylum Pentostomata - "Tongue worms", parasitic, no fossil record. [note: now known to be a specialized side-branch of arthropods specialized side-branch of arthropods)

Phylum Onychophora - Metamerous, segmented, uniramous unsegmented appendages, waxy cuticle.

Phylum Arthropoda - Metamerous, segmented; uniramous or biramous jointed (segmented) appendages.

Series DEUTEROSTOMATA - Blastopore becomes anus, typically enterocoelous with radial cleavage, and oligomerous.

Phylum Pogonophora - "Beard worms", sessile deep-sea worms that build chitinous tubes, some large forms inhabit hydrothermal vents.

Phylum Echinodermata - With secondary, pentamerous radial symmetry; water vascular system; calcareous endoskeleton of mesodermal origin.

Phylum Chaetognatha - "Arrow worms" and conodonts; without gill slits or endoskeleton; "teeth" of calcium phosphate (apatite).

Phylum Hemichordata - With gill slits and nerve chord; no notochord.

Phylum Chordata - "Vertebrates"; gill slits, nerve chord and notochord; endoskeleton of mesodermal origin.

external link Modified from Margulis and Schwartz, 1982

Here's another, more recent scheme:

Kingdom Animalia
Subkingdom Radiata
Infrakingdom Spongiaria
Phylum Porifera
Infrakingdom Coelenterata
Phylum Cnidaria
Infrakingdom Placozoa
Subkingdom Myxozoa
Subkingdom Bilateria
Branch Protosomia
Infrakingdom Lophozoa
Phylum Bryozoa
Phylum Kamptozoa
Phylum Mollusca
Phylum Brachiopoda
Phylum Sipuncula
Phylum Annelida
Phylum Nemertina
Infrakingdom Chaetognathi
Phylum Chaetognatha
Infrakingdom Ecdysozoa
Phylum Arthropoda
Phylum Lobopoda
Phylum Nemathelminthes
Infrakingdom Platyzoa
Phylum Acanthognatha
Phylum Platyhelminthes
Branch Deuterostomia
Infrakingdom Coelomopora
Phylum Hemichordata
Phylum Echinodermata
Infrakingdom Chordonia
Phylum Urochorda
Phylum Chordata
Subkingdom Mesozoa

classification according to pdf document Cavalier-Smith, 1998

== Links ==

[http://www.ultranet.com/~jkimball/BiologyPages/I/Invertebrates.html The Invertebrate Animals] - John Kimbell - excellent overview

[http://www.interaktv.com/INVERTS/Inverttitl.html Checklist of the Invertebrates], Robert B. Hole, Jr.

[http://dragon.bionet.nsc.ru/szmn/Inverteb/Inverteb.htm Invertebrata] collection of the Siberian Zoological Museum

[http://www.ucmp.berkeley.edu/phyla/phyla.html Introduction] to the Metazoa</a></strong>

[http://animaldiversity.ummz.umich.edu/index.html Animal Diversity Web] University of Michigan Museum of Zoology's Animal Diversity Web

[http://www.teaching-biomed.man.ac.uk/bs1999/bs146/biodiversity/metadiv.htm Metazoan Diversity Homepage] by Graham Davison - see [http://www.teaching-biomed.man.ac.uk/bs1999/bs146/biodiversity/orirelpi.htm Prominent Metazoan Evolutionary Schemes and Components] - has diagrams showing the possible evolution and relationship of Metazoa (higher animals) from ancestral choanoflagellate forms - a number of figures on that page have been reproduced here

[http://sn2000.taxonomy.nl/Main/Classification/11166.htm Systema Naturae 2000 / Classification] - lists the various animal phyla, and when each division was first formally named and by who; an invaluable reference.

[http://www.il-st-acad-sci.org/ Illinois State Academy of Science]
[http://www.il-st-acad-sci.org/kingdoms.html The Kingdoms Project]
[http://www.il-st-acad-sci.org/kingdom/anim001.html The Animal Kingdom] at the ISAS

[http://www.ucmp.berkeley.edu/museum/75th/ab6.html Evaluating Multiple Hypotheses for the Origin of Bilateral Animals] by Allen G. Collins. (abstract, the complete essay with diagrams is on a poster)

[http://project.bio.iastate.edu/Articulation/ISU/Freshman/Biol_201/Outlines/chp29.html Chapter 29] - the Animal Kingdom - overview of the main phyla, in notational form

[http://www.langara.bc.ca/biology/mario/Biol1215notes/biol1215chap32.html Chapter 32]: Introduction to Animal Evolution - explains the characteristics in the divergence of the main metazoan divisions

[http://www.cals.ncsu.edu/course/zo402/taxa.html Suggested Phylogenetic Classification of Invertebrate Animals]

Fungi

Bmeyers3535 — Sat, 19 Aug 2006 02:16:26 GMT

Bmeyers3535: initial load of the fungi entry

Archaea
|--Eubacteria
`--Eukarya
|--Chlorobionta
`--+--Fungi
| |--Chytridomycota
| `--+--+--Zygomycota
| | `--Trichomycota
| `--+--Basidiomycota
| | |--Ustilaginomycetes
| | `--Hymenomycetes
| `--Ascomycota
| |--Saccharomycotina
| `--Pezizomycotina
`--Metazoa
|--Deuterostomata
`--Protostomata

== Lists ==

=== A. Glossary of terms and abbreviations. ===
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

=== B. Taxon Index: alphabetical list of taxa. ===
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

==== C. References: literature citations by author. ===
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

== What are the Fungi? ==

The Fungi are the great saprophytes, the master recyclers. They are the black rot, the dry rot, and the white rot, the colorful fate of last week's lasagna left too long in the 'fridge, and the great, grey walls of stinking mould that can destroy whole buildings. But, they are also the baker's yeast and the brewer's yeast. They are the difference between grape juice and Chateauneuf du Pape. They are the portobellos and the morels and the cloud ears and the truffles. In fact, the French could not be half so obnoxious about their cuisine were it not for the Fungi. But, then again, perhaps they could [1].

We leave that conundrum for another day. The first order of business ought to be the matter of definition. How do we define this group? We have found no hint that anyone is using a workable phylogenetic definition of the Fungi. A phylogenetic definition, for those who have somehow managed to escape our interminable, high-pitched whining on the subject, is a definition based on some explicit hypothesis about a group's relative position in phylospace. For example, Dinosauria is defined as the last common ancestor of Triceratops and birds and all descendants of that ancestor. This may be conveniently abbreviated: "Triceratops + birds". Such a definition is quite different from a definition based on some arbitrary set of characteristics which approximate an implicit, unstated, and therefore untestable notion of what a dinosaur "ought" to look like. That second type of definition is referred to as an "apomorphy-based" definition. It is properly viewed with the same derisive contempt with which M. Auguste Escoffier (at right) would regard the use of corn starch to thicken a demi-glace [3].

Phylogenetic definition of FungiWere we in a position to impose a phylogenetic definition on the Fungi, our leading candidate would be the stem group "toadstools > toads" (all organisms more closely related to Basidiomycota than to Tetrapoda [2]). That definition presupposes a close relationship between Metazoa and Fungi. However, such an assumption shouldn't slow us up much. The Metazoa-Fungi connection now seems quite secure. This definition would, however, require us to gather the Microsporidia into the brotherhood of the Fungi. Microsporidia could be Fungi under many definition of the taxon, but they are certainly closer to Fungi than to toads. Such a definition would also dispense with meaningless arguments about the inclusion of the Chytridiomycota within Fungi.

To our discredit, the foregoing discussion may serve as a useful study in the use of the English conditional mode for advanced students of the language, but it ignores the realities of fungal phylogeny. That reality is illustrated in the following examples.

Fungus, sensu Madigan et al. (2003)The "fungi contain cell walls and produce spores." Madigan et al. (2003). So ferns are Fungi?

The Tree of Life will not venture even this far. It contents itself with a list of common names: "The organisms of the fungal lineage include mushrooms, rusts, smuts, puffballs, truffles, morels, molds, and yeasts, as well as many less well-known organisms." In other words, the fungi are defined by listing a number of vague, vernacular terms with a completely indefinite catch-all category at the end.

"What is Fungi? Fungi are a group of organisms and micro-organisms that are classified within their own kingdom, the fungal kingdom, as they are neither plant nor animal. Fungi draw their nutrition from decaying organic matter, living plants and even animals. They do not photosynthesize as they totally lack the green pigment chlorophyll, present in green plants. Many play an important role in the natural cycle as decomposers and return nutrients to the soil, they are not all destructive." WHAT IS FUNGI? But this description would apply equally as well to most bacteria.

Chytrids"These nonmotile eukaryotes lack flagella and develop from spores." Dr. Fungus- Fungi, Fungus, Fungal. But see the image.

We could beat this drum for quite a long time. The point is that, of the hundreds of references and sites on the web which purport to discuss the Fungi, not one of the many we have reviewed supplies a reasonable definition. Some sources are very useful in listing numerous characteristics of Fungi. But, the more characters listed, the more Fungi (in any phylogenetic sense) they exclude. A substantial majority of sources simply dodge the issue.

Ultimately, we are left in the untenable position of admitting that there is no definition in general use for the word "fungus." Happily, this yawning gap at the threshold of mycology seems to bother mycologists even less than it bothers the Fungi themselves. Thus, in a manner sanctioned by the universal practice of man and mushroom alike, we will pointedly ignore the yawning abyss at our feet, and move on to other matters.

== Characteristics of the Fungi ==

We never eat bread cookies
For cookies have yeast,
And one little bite
Turns a man to a beast
O, can you imagine
A sadder disgrace
Than a man in the gutter
With crumbs on his face?

-- Song of the Salvation Army (trad.)

So, what about all those characteristics mentioned in the last section? The following is a list of the most commonly cited characters shared by most Fungi:

* The Fungi are eukayotes, which may exist in nature as either single and multi-celled organisms, or in both at different points in the the life cycle.
* Fungi are avascular -- no specialized respiratory, digestive or transport systems beyond the hyphae themselves.
* Most fungi grow as tubular filaments called hyphae. A connected mass of hyphae is a mycelium.
* Fungi have a vegetative body called a thallus, composed of hyphae.
* The walls of hyphae are often reinforced with chitin, a polymer of N-acetylglucosamine.
* Fungal cell membranes contain ergosterol, rather than cholesterol.
* The Fungi have a unique biosynthetic pathway for lysine.
* Fungi produce a unique form of tubulin in connection with nuclear division.
* Fungi have small nuclei with very little repetitive DNA
* Mitosis occcurs without dissolution of the nuclear membrane.
* Fungi are never autotrophs. No fungus has chlorophyll or chloroplasts.
* Fungi are usually found either as opportunistic saprophytes (living on dead organic matter) or in some parasitic or symbiotic relationship with plants or other autotroph.
* Fungi digest food outside their bodies: they release enzymes into the surrounding environment (exoenzymes), breaking down organic matter into a form the fungus can absorb
* food reserves stores as glycogen (like animals), not starch (like plants).
* Fungi reproduce by means of spores, budding, or fragmentation.
* Spores may be either sexual or aesexual.
* Spores may be used as a dormant, resting phase, like bacterial spores

In short, Fungi are a rather odd, and distinctly different, part of the tree of life.

== Diversity of the Fungi ==

The following is our usual diversity table, which somewhat overemphasizes the basal Fungi. Recent work suggests that fungal diversity may be undersampled even at the highest taxonomic levels. Specifically, a taxonomic survey of alpine fungal communities which flourished under snow cover suggests that there may be 1-2 high-level fungal taxa between Basidiomycota and Ascomycota. Schadt et al. (2003).
Fungi

=== Chytridomycota ===

Blastocladiella The chytridomycotes, or "chytrids," are usually aquatic, either marine or freshwater. Presumably this is the original domain of the chytrids, and of all Fungi, but chytrids are also found in terrestrial communities almost as soon as there were terrestrial communities to be found in. So, for example, several different groups of chytrids are known from the Early Devonian Rhynie Chert. The implication is that they had begun to radiate even before the Devonian. They are a remarkably diverse lot, as one might expect from a basal radiation of the Fungi, and there is some possibility that the Chytridomycota may be paraphyletic, i.e. that all Fungi are descended from chytrids.

The chytrids are mostly single-celled forms, traditionally classified as protists. In fact, some sources still classify them with the Chromista, even though, so far as we can tell, chytrids have no light-sensitive pigments at all. What chytrids do have is a single- celled zoospore with an anterior flagellum, which is distinctly odd for a fungus. In fact, chytrids are the only large taxon of Fungi which produces a zoospore of any kind.

However, there's no real doubt about their position any more. For example Borneman & Hartin (2000) showed that rDNA primers from all of four basic fungal phyla (Trichomycota was not included) permit amplification of rDNA in the other fungal groups, including Chytridomycota, but don't amplify anything else. This strongly suggests that that rDNA from all four groups was very similar and that all are closely related.

That same conclusion can be reached for any number of other reasons. Chytrids have an absorptive mode of nutrition, like other Fungi. Chytrids have cell walls composed of chitin. Chytrids form hyphae. They share, with the other Fungi, key enzymes and metabolic pathways that are not found in other fungus-like protozoans (slime molds and water molds), in addition to oddities of molecular structure. Alkemar & Nygard (2003). The chytrids are surely the most basal Fungi, but Fungi they are.

This group is sometimes referred to as Zygomycota, with Zygomycetes and Trichomycetes treated as included taxa.

=== Zygomycota ===

RhizopusZygomycotes, like chytrids, are known from the Rhynie Chert, although, in this case, the identification is more tentative. What are actually seen are fungal hyphae which appear to pierce other cells, a characteristic of many zygomycotes. Definitive zygomycotes are found in Carboniferous exposures. A more familiar present-day example of a zygomycote is Rhizopus, the black bread mold.

The Zygomycota are named for their characteristic teleomorph, which is referred to as a zygosporangium. The images at the glossary entry for gametangium are of Phycomyces and Rhizopus, both zygomycotes. They illustrate how the zygosporangium is formed from the head-on meeting of two hyphae whose ends have specialized as gametangia. The contents of the gametangia are mixed in the zygosporangium, which develops between them. The haploid nuclei from the gametangia then fuse. The zygosporangium develops a hard, thick chitin shell, which is frequently ornamented and may bear spines or other appendages. The remains of the gametangia protrude from the sides and are referred to as suspensors. The zygosporangium also serves as a resting phase, which will develop when conditions are favorable.

Zygomycotes also reproduce asexually. The haploid spores develop in a bulbous mitosporangium at the tips of specialized vertical hyphae referred to as sporangiophores.

=== Trichomycota ===

From time to time we find a web resource that is so comprehensive well-organized that there is no point in providing a summary here. That is the case with the Trichomycota. We happily defer to The Trichomycetes: Fungal Associates of Arthropods. The authors' own summary of their work is Chapter 1 of the treatise. Trichomycotes are obligate commensals (sometimes parasites) of insects and are thought to have developed with neopteran insects in the Mississippian.

=== Basidiomycota ===

mushroomsThe basidiomycotes are the rusts, smuts, gilled mushrooms, puffballs, stinkhorns, and club, shelf or coral fungi. They are one of the two major divisions of Fungi, the other being the Ascomycota. Definitive Basidiomycote fossils are known from the Late Devonian, although there has been a recent report of a possible Early Devonian lichen incorporating a probable basidiomycote fungus.

The Basidiomycota is such a large and diverse group, that the living members have little in common. The basidiomycote life cycle has a four unique properties which are probably synapomorphies, but which are no longer shared by all members of the group:

(1) The taxon is named for the basidium where sexual spores are produced.

(2) The life cycle generally includes a persistent dikaryon, frequntly large (e.g., a mushroom) in which each cell in the thallus contains two haploid nuclei, typically as the resulting of a mating event

(3) Clamp connections (explained at the glossary entry) are unique to Basidiomycota and are used to maintain the dikaryon state during hyphal division.

(4) Many basidiomycotes can launch spores into the air in a process referred to as ballistospory.

The basidiospores bear a single haploid nucleus. They germinate into hyphae with a single nucleus in each compartment, a monokaryon. A mating event results from end-to-end fusion of hyphae, as in Zygomycota, or fusion of a hypha with an oidium, a specialized mating spore. Then the resulting dikaryon divides through clamp connections so that the dikaryon state is maintained. Many basidiomycotes remain in the dikaryon state indefinitely. Under appropriate conditions, the dikaryon will produce fruiting bodies. Some of these hyphae produce basidia, such as the cells lining the "gills" under the cap of gilled mushrooms. Ultimately, the two haploid nuclei in each basidium fuse (karyogamy) to form a diploid nucleus. This then undergoes meiosis to produce four haploid nuclei whch migrate into the basidiospores and are dispersed into the environment.

=== Ascomycota ===

AscomycotaThe Ascomycota are the largest and most diverse group of Fungi. They include the yeasts, most of the fungal elements of lichen, and such famous Fungi as Saccharomyces, Aspergillus, Candida and Neurospora, as well as morels, truffles and similar delicacies. The current understanding is that supposed pre-Devonian (even Proterozoic!) lichens are probably artifacts, making the earliest known ascomycote of Carboniferous age.

The Ascomycota are united by the presence of asci (see glossary entry). Like Basidiomycota, ascomycotes remain indefinitely in the dikaryon state, with the fungal filaments (hyphae) partitioned into cells each containing two haploid nuclei -- one from each parent. Also as in basidiomycotes, nuclear fusion (karyogamy) occurs only in connection with the formation of sexual spores. At that time the newly diploid nucleus undergoes one (sometimes more) round of mitosis, followed by meiosis, to yield eight (or a multiple of eight) haploid nuclei. The nuclei are then partitioned by internal membranes into individual ascospores. The Ascomycota also share with Basidiomycota the use of conidia for the development of asexual spores.

Another unique character (but not present in all ascomycotes) is the presence of Woronin bodies on each side of the septa separating the hyphal segments. The septae are pierced by pores which allow most cytoplasmic constituents (but not nuclei) to travel freely between hyphae. However, if an adjoining hypha is ruptured, the Woronin bodies block the pore to prevent loss of cytoplasm into the ruptured compartment.

For more information, see Ascomycota.

Chlorobionta

Bmeyers3535 — Sat, 19 Aug 2006 01:42:40 GMT

Admin: /* Embryophyta */

== Chlorobionta (Green Plants) ==

<table border=1>
<tr><td>
LIFE (=Archaea?)
|--Eubacteria
`--Eukarya
|--+--Rhodophyta
| `--CHLOROBIONTA
| |--Chlorophyta
| `--Charophyta
| |--(various green algae)
| `--Embryophyta
| |--Bryophyta
| `--Rhyniophyta
| |--Lycophytina
| `--Euphyllophytina
| |--Moniliformopses
| `--Spermatophytata
| |--trimerophytes
| `--Spermatopsida
`--+--Fungi
`--Metazoa
|--Deuterostomata
`--Protostomata
</td><td>
Lists
Glossary
Taxa
References
"The Wearing of the Green"
Evolution of Land Plants
Green Algae
Plants Conquer the Land
The Devonian Period
The Carboniferous Period
The Diversity of Plants
Chlorobionta (Prasinophyta)
Chlorophyta
Charophyta
Embryophyta
Bryophyta
Rhyniophyta
Lycophytina
Euphyllophytina
Moniliformopses
Spermatophytata
Links
</td></tr></table>

== Lists ==

A. Glossary of terms and abbreviations.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

B. Taxon Index: alphabetical list of taxa.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

C. References: literature citations by author.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

== "The Wearing of the Green" ==

Beginning in the [[Archean]] era, Cyanobacteria evolved photosynthesis, which enabled them to use sunlight to draw carbon dioxide from the atmosphere and convert it to oxygen, water and glucose (a simple carbohydrate). These could be considered the first simple "plants" Plants therefore might be seen as any organism that is able to use sunlight, carbon dioxide, and water, to manufacture its own food, that is, as a special class of autotroph. However, that's far too broad. It would include all kinds of things like diatoms, chromists, and photosynthetic bacteria which have nothing to do with plants in a phylogenetic sense. They are, to be sure, all within the subject matter of a General Botany class. All of these groups share some essential biochemistry. However, what they don't share is a common ancestor to the exclusion of all other organisms. This similarity arises from (a) convergent evolution and (b) the exchange of plastids.

The description above also fails because it is only partially correct, even as a general description. Plants not only breathe out (respire) oxygen, but parts of their tissues also respire carbon dioxide, just as animals (heterotrophs) do. These processes provide the plant with energy for growing and maintaining its life support systems, and go on at all times. During the sunlit day, more carbon dioxide is consumed than is released in respiration, but at night photosynthesis ceases and the plant respires only carbon dioxide, returning a portion of its carbon to the atmosphere.

One better approach to defining "plants" is the "Chlorobionta" hypothesis, as used on the Tree of Life site:

There are two major lineages of green plants. One consists of most of what have been classically considered "green algae" -- mostly microscopic freshwater forms and large seaweeds. The other lineage contains several groups of "green algae" that are more closely related to land plants. Because these two lineages are monophyletic, they have been placed in a single monophyletic group called green plants, or, in technical parlance, the subkingdom Chlorobionta ...

This suffers only from being vague. Is there anything else in the box besides green algae and land plants? The ToL authors don't suggest any other content. Alternatively, this Gelidium coulteri might be an attempt to suggest a crown group: "the last common ancestor of Chlorophyceae and evergreens and all of its descendants," or something like that. That sounds like a workable definition, but that can't be right, since they include the prasinophytes among the Plants. Some, but not all, prasinophytes would be excluded from the plants by a crown group definition. We think what the ToL authors actually had in mind is an even better choice: the stem group "green algae > red algae." This includes all of the prasinophytes, all other green algae and all plants, as those terms are normally used, but not much of anything else.

Why do we care about definitions? The price of admission to doing good science taking an explicit position, so that others can prove you wrong. A vague definition, such as ToL's original formulation, is not good science. Unless we know precisely what they mean by "plant" we can't really make testable statements about what are or are not plants, nor about what characteristics plants have or do not have, nor about whence they might have derived their characteristics. Without really crisp definitions, these issues quickly get bogged down in semantics and arm-waving. Arguably that is exactly what happened to the whole business of taxonomy for the better part of a century.

Of course, definitions can never be "wrong," in a logical sense. However, they can be useless, if they fail to draw lines within our area of Quercus alba interest. A vague definition is always useless because it draws no line at all. Phylogenetic definitions have revived the whole business of evolutionary systematics because they are quite precise and refer to historical events (e.g., the evolution of red and green algae from a common ancestor), rather than to some man-made list of (sometimes fuzzy) characteristics. However, this precision also comes at a price. A phylogenetic definition is built around a phylogenetic hypothesis. Unlike a definition, a hypothesis can be wrong. If so, any definition based on that hypothesis usually must be abandoned, and a lot of good work may go down the tubes.

Suppose for example, that we interested in the evolution of birds. Our hypothesis is that birds are the sister group of dinosaurs, and that some "dinobird" was their last common ancestor. We thus define birds as Struthio (ostrich) > Struthiomimus (a theropod dinosaur which looked like an ostrich) and dinosaurs as Struthiomimus > Struthio. Sadly, after years of frustrating labor sorting out the characteristics of the supposed dinobird ancestor, we realize that birds are dinosaurs. Oops. Our definition of "bird" turns out to include embarrassingly unbirdlike things like therizinosaurs, while our definition of "dinosaur" includes only tyrannosaurids and ornithomimosaurs. How to explain this little faux pas to those notoriously humorless folk whose grants supported our research the last three years? Again, that is simply the price of doing good science.

For that reason, we should be careful, as well as explicit, in framing the definition and articulating the underlying hypothesis. Here, the hypothesis is that red algae, in a colloquial sense, are closely related to green plants, in an equally colloquial sense. This then allows us to define both rigorously in terms of that relationship. Strictly speaking, we should do so in terms of particular anchor taxa, just in case either group turns out to be polyphyletic (which is possible). By all means, then, let's do so. On the red algae side, we'll pick Gelidium coulteri, a randomly chosen species of a well-known and very successful genus of red algae. On the green plant side, let's use an angiosperm, a highly derived group, and Quercus albus, because (as any citizen of the state of Connecticut will know) it symbolizes the willingness to take risks to vindicate historical truth. Based on our phylogenetic hypothesis, our working definitions are Chlorobionta (plants) = Q. alba > G. coulteri, and Rhodophyta (red algae) = G. coulteri > Q. alba.

Was that so hard? Of course not. But then, unlike ToL, we are not subject to the temptations to waffle which come with peer review and the caprice of granting agencies. Lest we be misunderstood, we support both peer review and post hoc review by grantors as excellent things for science; but they are not unmixed blessings. The inducements to please everyone may become irresistable. Now, unlike ToL, the purpose of Palaeos is only to amuse those who write it. However, if we can, occasionally, counterweight the temptation for others to hide behind intentionally vague and inconsistent pronouncements made in the service of their own comfort, perhaps it may serve another purpose as well.

== [[Evolution of Paleozoic Land Plants]] ==
(''See article for details'')

== [[Devonian Plant Evolution|The Devonian Period]] ==
(''See article for details'')

== The Diversity of Plants ==

(''See article for details'')

== [[Embryophyta]] ==

(''See article for details'')

== Links ==

[http://www.ucmp.berkeley.edu/plants/plantae.html Introduction to the Plantae - The green kingdom]

[http://www.ucmp.berkeley.edu/IB181/HpageIB181.html Integrative Biology 181/181L - Paleobotany]

[http://www.science.siu.edu/landplants/ Land Plants On-line - covers recent plants only, links to images etc]

[http://www.uni-wuerzburg.de/mineralogie/tapho/tapho1.html International Plant Taphonomy Meeting] - The purpose of the International Plant Taphonomy Meetings is to stimulate scientific research and to promote contacts among scientists engaged in the study of plant taphonomy including living and fossil plants of all geological periods.

[http://www.science.smith.edu/biology/bio240/xsmith/BotLinks.htm Botany]

=== Web Sites by Subject ===

Excellent annotated list of links to Botany and related subjects - note, some of these links are no longer current.

[http://taggart.glg.msu.edu/bot335/botclass.htm A BASIC BIOLOGICAL CLASSIFICATION OF PLANT-LIKE ORGANISMS]

[http://www.uni-muenster.de/GeoPalaeontologie/Palaeo/Palbot/ewald.html#1 A History of Palaeozoic Forests] - Hans Kerp - very informative - originally published in German.  Deals with forests of the Devonian, Carboniferous, and Permian periods.

[http://www.xs4all.nl/~steurh/home.html Hans' Paleobotany Pages] - info on the earliest land plants and on the lycopod Lepidodendron

[http://taggart.glg.msu.edu/isb200/carbfor.htm Carboniferous Forests] Ralph E. Taggart - good non-technical intro, covers main groups of Carboniferous plants, also brief mention of insects, amphibians, and reptiles'

[http://www.abdn.ac.uk/rhynie/ The Biota of Early Terrestrial Ecosystems: The Rhynie Chert] - includes useful information on Early Devonian plants from this location

[http://scitec.uwichill.edu.bb/bcs/bl14apl/conq.htm The First Land Plants] - The Conquest of the Land - gives a good introduction to basic concepts regarding the transition of plants from water to land

[http://www.ortobotanico.unina.it/Museopaleo/paleo_eng.doc Orto Botanico] - somewhat technical but not too difficult coverage of plants and paleobotany. Includes glossary.

[http://www.ucmp.berkeley.edu/IB181/HpageIB181.html Integrative Biology 181/181L] - Paleobotany - at UC Berkeley - includes material on Paleozoic plants.  A bit technical but if you stick at it you will learn a lot.

Sponges

Bmeyers3535 — Sat, 19 Aug 2006 01:19:03 GMT

Bmeyers3535: first load of the sponge entry

== Phylum Porifera ==
(Latest Vendian to Recent)

The most primitive form of multicellular animal life, it is thought that sponges evolved independently of metazoan animal life. In many respects they are little more than colonial choanoflagellate protozoa. Over 5000 recent species are known, and many more fossil species. All are benthic, sessile, suspension-feeders which inhabited a wide variety of exclusively marine environments, from the early Cambrian to the present day.

Sponges make their skeleton out of both organic fibers (primarily a material called spongin (the stuff of an natural bath sponges), secreted by spongocyte cells and inorganic spicules (calcium carbonate or opalline silica needle-like structures secreted by sclerocyte cells).

The major fossil record of these animals consists of the resistant spicules. After death, spicules are scattered across the sea floor and may be found as disarticulated microfossils.

== Classification ==

There are four main classes:

Class Calcarea
Class Demospongiae
Class Sclerospongiae
Class Hexactinellida

Two fossil groups are often included - the Stromatoporoidea and the Archaeocyatha. The former are most likely Porifera (possibly Sclerospongiae or Demospongiae), while the precise relationships of the latter remain controversial.

== Organization of the Poriferan Body Plan ==

The basic body form of sponges consists of numerous small incurrent canals called ostia (sing. ostium) and one or more large excurrent opening called oscula (sing. osculum). Organization of chambers and channels varies however from simple to quite complex

<table border=1>
<tr><td>asconoid structure image</td>
<td>syconoid structure image</td>
<td>leuconoid image</td></tr>
<tr><td>asconoid</td><td>syconoid</td><td>leuconoid</td></tr>
</table>

Levels of Porifera organization, from simplest (left) to most complex (right

== Phylogeny ==

<===o PORIFERA
| ?--o Archaeocyatha
|--o Demospongiae [Demospongea]
| |--o Homoscleromorpha
| |-- Tetractinomorpha
| `-- Ceractinomorpha
|--o Sclerospongiae
| |?-o Stromatoporoida
| |--o Ceratoporellida
| `--o Merliida
|-- Calcarea
`-- Hexactinellida

== References and Links ==

Parker, Sybil P. (ed.), 1982: [http://www.amazon.com/exec/obidos/ASIN/0070790310/kheper-20 Synopsis and Classification of Living Organisms] New York: McGraw-Hill Book Co., 2 vols.

[http://www.amazon.com/exec/obidos/ASIN/0030266688/kheper-20 Invertebrate Zoology] by Edward E. Ruppert, Robert D. Barnes

[http://www.ucmp.berkeley.edu/porifera/porifera.html Introduction to the Porifera]

[http://animaldiversity.ummz.umich.edu/porifera.html Phylum Porifera]

[http://www.interchange.ubc.ca/csmecher/ Curt Smecher Home Page] - a lot of excellent info on Sponges, including a comprehensive systematic review with description of each taxon.

[http://users.skynet.be/dhs/fossiles/pori.htm Les porifères] - a Belgian page on fossil sponges

[http://paleo.cortland.edu/tutorial/Protista/porifera.htm Porifera] - short intro to recent and fossil groups

[http://tolweb.org/tree/eukaryotes/animals/porifera/porifera.html Porifera - Sponges] - when last checked, had references and links but no essay. Classification down to subclass only

Eukarya

Bmeyers3535 — Sat, 19 Aug 2006 00:54:52 GMT

Bmeyers3535:

Eukarya

<table border=0>
<tr><td>
Archaea
|--Eubacteria
`--Eukarya
|--Metamonada
`--+--Discicristata
`--+--Rhizaria
`--+--+--+--Alveolata
| | `--Chromista
| `--Plantae
`--+--Fungi
`--Metazoa
|--Deuterostomata
`--Protostomata
</td><td>
Eukarya
General Introduction
Lists
-Glossary
-Taxa
-References
Organization
</td></tr>
</table>

== General Introduction ==

Organisms in which the genetic material is contained within a nuclear membrane are known as Eukaryotes, the name means "true kernel". This domain includes all multicellular forms of life: Plants, Fungi, and Animals. However, in this section, we will deal only with the group classically called "Protista," single-celled Eukarya. In fact, the line is a bit vague. By convention, slime molds are treated as "protists" while sponges and Cnidaria (or at least most of them, as we will see) are treated as Metazoa. Similar uncertainty marks the borderlands of the plants and fungi.

Unlike prokaryotes, (the Archaea and Eubacteria) the Eukarya have a more compartmentalized cellular structure. These structures have sometimes been very different from the compartments of the average plant or animal cell. However, all eukaryotes confine the bulk of their genetic material in a well-defined nucleus surrounded by a membrane. The eukaryote cell also usually includes organelles such as mitochondria, which combine carbohydrates and fatty acids with oxygen to generate energy, and/or chloroplasts, which carry out photosynthesis, gathering energy from sunlight and storing it in the form of carbohydrates. According to the standard explanation, these particular organelles evolved through a symbiotic association of specialized prokaryotic organisms, each providing a different function and gradually evolving into organelles within a single eukaryotic cell. Almost all eukaryotes also possess -- in varying degrees -- a complex cytoskeleton of microfibrils and microtubules which maintain the integrity of the cellular compartments and organelles, as well as a number of different types of internal membrane-bound structures with specialized functions.

With eukaryotes also came sexual reproduction, which opened up tremendous variability within a species through the shuffling of genes parents, as opposed to simple binary fission. This in turn changed the fundamental nature of evolution and genetic transmission. (For discussion of an alternate paradigm possibly applicable to early prokaryotes, see A Different Kind of Evolution.).

Both prokaryotes and eukaryotes evolved in environments in which oxygen was scarce or absent. However, the diversification of eukaryotes seem to be linked to the rise in atmospheric oxygen during the Middle Proterozoic era. Perhaps it was at this time that many eukaryotes acquired mitochondria and chloroplasts, or perhaps the compartmentalized cell design of the eukaryotes was simply well suited to aerobic metabolism. The nature of the linkage remains a matter of speculation, and many eukaryotic forms retain an essentially anaerobic metabolism.

For the first two thirds or so of their history, eukaryotes remained unicellular. It was probably only in the Vendian Era that macroscopic multicellular life appeared. But that is another part of the story altogether. This section concerns the single-celled Eukarya, most of which have no fossil record.

Lists

<table border=1><tr><td>
A. Glossary of terms and abbreviations.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

B. Taxon Index: alphabetical list of taxa.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

C. References: literature citations by author.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
</td></tr></table>

== Organization ==

Our original concept was to adopt a phylogenetic organization, similar to our approach to the Vertebrates. Unfortunately, the study of the basal Eukarya ("Protistology"), is at some distance yet from the kind of phylogenetic certainty that prevails among the vertebrates. Nevertheless, after 18 months of experimentation, we're now convinced that our current "best-guess cladogram" is fairly stable. So, with considerable trepidation, we're trotting out this tree for testing. In simplified, form, it proceeds as follows:

EUKARYA
|--Metamonada
`--+--Discicristata
`--+--Rhizaria
`--"Metabiotiformes"
|--+--Chromalveolata
| | |--Alveolata
| | `--Chromista
| `--Plantae
| |--Rhodophyta
| `--CHLOROBIONTA
`--+--Amoebozoa
`--Opisthokonta
|--FUNGI
`--METAZOA

The derivation of this arrangement is discussed at Top Level Cladograms.

The clade uniting plants and animals doesn't seem to have a name, so we have given it one, "Metabiotiformes," for convenience. Until more of the high-level taxa are filled in, your best bet will probably be to consult the alphabetical index of taxa.

Eubacteria

Bmeyers3535 — Fri, 18 Aug 2006 18:38:39 GMT

Bmeyers3535: starting eubacteria

This is the Domain of the Germs. The Eubacteria, in their hundreds of trillions, are the reasons you weren't allowed to pick up the candy you dropped on the floor or eat that egg salad that looked so good a week ago. They are behind every torture you have ever suffered at the hands of the dentist, and they are the root cause of childhood afflictions from antiseptics to acne. They have a lot to answer for. Then again, they're probably not too happy with us, either. Its hard to tell, since bacteria don't go in much for light conversation or email rants. They grow, or they don't, just as they have for the last three or four billion years, and without making much fuss about it. Bacterial psychology is thus a rather limited field. But such simplicity has its advantages. We are never tempted to paint human thoughts and emotions onto a 4 � long pill-shaped blob of protoplasm. We can safely view the bacterium for what it is, a small biochemical machine, without having to steer the usual narrow passage between the twin perils of anthropomorphism and reductionism.

However, to say that the Eubacteria are biochemical machines is not to belittle them. Consider Gomphosphaeria K�tzing 1836, the somewhat larger than average, but otherwise undistinguished, phytoplanktonic cyanobacterium [1] on the right. If we allowed a single cell of Gomphosphaeria to grow and divide under optimum conditions for only about 4.5 days we would be up to our armpits in Gomphosphaeria over the entire surface of the Earth [2]. Even man's most perfect machines, for example the 1976 Toyota Corolla, couldn't come close to matching this kind of performance.

This page will be devoted to considering the basic structural and functional units of the Eubacteria as biological machines. More specific matters, as well as considerations of ecology, phylogeny and evolution will be taken up in connection with more the specific groups to which these matters pertain. Eubacteria structuresSo, how are these machines put together? Some of the basic parts are shown in the figure on the left. Look at it carefully, because we have a good bit to cover, starting from outside.

This survey also takes us into some rather dense discussion of cell biology, a little biochemistry, and even a smidgen of thermodynamics. In fact, this page will serve, for the present, as a very condensed introduction to cell biology for the entire site. If you don't want to hear about that stuff, you probably shouldn't be reading about bacteria -- or single-celled organisms of any kind.

Geometry and mechanics dictate that the first structures we encounter in any cell -- and most multicellular organisms, for that matter -- are structures dealing with movement, sensation, and interaction with the world outside. In our model eubacterium, these include a flagellum and a system of pili.

The bacterial flagellum looks a bit like the eukaryotic organelle of the same name, but it is an entirely different structure. The "tail" portion has no microtubules and consists more or less of an extended filament of a single protein, flagellin. The tail is anchored on what amounts to a rotor. The rotor extends through the outer layers of the cell into the cytoplasm. The system actually works something like a propeller, with the rotor forcing the flagellum to turn in a spiral. The motive force is supplied by sodium or hydrogen ions flowing down a concentration gradient from the outside.

This ion gradient system is the same basic mechanism which is used in a number of other well-known systems, for example in some of the "light reactions" of photosynthesis. It is worth knowing reasonably well. The usual currency of energy in the cell is adenosine triphosphate (ATP). When the cell has ATP to spare, it uses ATP to pump certain ions (here, sodium) out of the cell. Since the sodium concentration is higher outside the cell, the pumps have to pump against the gradient using the energy of ATP. This makes the entire cell a sort of storage battery. To use that stored energy, the cell merely allows some of that sodium to flow back in by means of specialized sodium channels. These channels span the cell membrane and cell wall. When the sodium channel proteins are activated by signals inside the cell and come in contact with a sodium ion outside the cell, they change shape, allowing the ion into the cell and, at the same time, performing some useful work, such as turning the "rotor" of a flagellum [3]. The key concept is that the ion channel system takes small bits of energy (ATP molecules) which are all the same and are dispersed throughout the cell, and ultimately concentrates the energy for use at a time and place controlled by specific "signal" molecules that open specific ion channels linked to specific mechanical tasks -- a very elegant system!

E. coli attached to phage by pilusThe bacterial pili are the bug's equivalent of hands, both as tactile, sensory structures and as tools for grabbing onto and manipulating things at a distance. Our diagram is a bit misleading, since the pili can be quite long. See image (~20,000X) at right from Le rev�tement cellulaire des cellules procaryotes. As this image shows, the pilus can serve as a guide for the formation of a cytoplasmic bridge, as for the exchange of DNA. This is a rare, but important event with profound implications for bacterial evolution. Bacteria are not terribly fastidious about who they exchange DNA with. Thus genes can be acquired from unrelated bacteria, and even from non-bacteria. For example, DNA is being exchanged between Escherrichia and a virus in the image. For this reason, "lateral inheritance" of genes from unrelated organisms is quite frequently observed in bacteria.

Pili perform a great many functions, and consequently are structurally quite diverse. Typically the backbone of the pilus is made up of a long chain protein or polysaccharide (sugar chain) with some type of functionally specific arrangement at the tip. One function of considerable clinical interest is cell - to - cell recognition. The complex array of carbohydrates in and on the pili are the method by which bacteria recognize other cells, and are recognized by them. So, for example, one strain of a germ may be harmless to us while another, differing only in a few sites, may be a deadly pathogen if it recognizes our cells as food, or has surface features which our cells do not recognize as dangerous. Shorter pili, usually referred to as fimbriae, are a structurally distinct group of extrusions which operate mostly in bacterial attachment to substrate or to other cells.

The next structure we may encounter is the bacterial capsule. The composition, nature, and even existence of the capsule are highly variable, even within a species. It may be composed of polysaccharide or protein, may be tightly or loosely bound, or it may not be found at all. The capsule may be best thought of as an extremely dense layer of short pili. It functions in cell attachment, resistance to desiccation, and as a defense to being swallowed (phagocytosed) by other cells. Streptococcus pneumoniae is a case in point. The R strain of Streptococcus has no capsule and will not cause disease. It is readily engulfed by human cells. The bacterium is then encased within the membranes of a "vacuole" (a membrane-bound bubble inside the cell) and digested by lysozymes within the vacuole. The S strain has a capsule which prevents digestion. It uses the normally lethal environment of the phagocytic vacuole to grow, replicate and prepare to devour the cell from inside.

Within the capsule is the relatively rigid cell wall [4]. The fundamental scaffolding of the cell wall is peptidoglycan. See, generally, The Cell Wall. Peptidoglycan is an absolutely bizarre material. As this is not a biochemical essay, we will have to skip over much of the good stuff.

The first element of peptidoglycan is a chain of repeating sugar molecules (a slightly modified glucose, N-acetylglucosamine). This part of the structure is precisely the same as chitin, the material which makes up the exoskeleton of insects and, in more or less modified form, in almost all arthropods. Significantly, it is also found in the radular "teeth" of molluscs, the setae (bristles) and jaws of annelid worms, and the cell walls of Fungi. So, this is exceedingly ancient stuff, possibly predating the split between bacteria and metazoans.

However, in the Eubacteria, every second sugar residue is linked at the 3-position with an amino acid, threonine, which in turn leads on to a strange and unique chain of amino acids (i.e., a peptide chain). The ordinary amino acids which make up all proteins are asymmetrical. That is, they can occur in left-handed (L) or right -handed (D) forms (racemers). All higher organisms use only the L-racemers. In fact, even bacteria use only L racemers for ordinary proteins. But they also use certain D-racemers in peptidoglycan. Does this suggest that the bacterial cell wall is older than the standard machinery of protein synthesis and harks back to a time when life wasn't so picky about which racemers it used? It could mean this. Certainly some scientists have thought so. But, since there are no similar structures in the Archaea or the Eukaryota, the more likely explanation is that this is a specialized feature of Eubacteria.

Perhaps, instead, these weird amino acids evolved as an ancient defense against attack by protein-digesting enzymes (proteases) which are efficient only in cutting ordinary peptide bonds. Notice the sequence of amino acids here: L-D-L-D. The region around the peptide bond [5] between amino acids will be neither left-handed nor right-handed, but a mixture likely to "confuse" proteases which are adapted to digest ordinary proteins. This kind of attack is most like to occur when a bacterium has been engulfed by a eukaryotic cell. So, the moral of this story may be that Eubacteria are not primitive forms at all, but specialized organisms which have been co-evolving with the eukaryotes for a very long time.

Bacterial cell walls contain a number of other typical components. However all of these are somewhat variable between different groups of bacteria; and we will defer discussion of these components for now. Briefly, the usual cell wall materials include teichoic acids, polysaccharides of various types, proteins and various derived lipids (fats). Teichoic acids may be of particular evolutionary interest, because they have elements of all of the major types of biomolecules. However, teichoic acids are found only in certain bacteria, and are not encountered outside the Eubacteria.

Gram positive cell envelopeMoving inward from the cell wall, we encounter the plasma membrane. The bacterial cell membrane is, like virtually every other cell membrane, internal or external, based on a phospholipid bilayer. This basic structure of the membrane and wall together is shown in the figure on the left. To see why it forms a bilayer, we need only refer to the structure of a phospholipid. A phospholipid looks something like this:

The "head" of the molecule contains a phosphate group, glycerol, and the carboxyl groups from two long-chain fatty acids. The details need not concern us, but it is important to recognize that these are all polar groups, groups that bind water tightly. That is, the head is hydrophilic. The long chain of carbons on the two "tails" of the molecule has no polar groups and so cannot bind water. These chains are hydrophobic. We might say that they are like oil in water. However, they are not simply like oil in water. That long featureless run of carbons is chemically identical to oil. With this kind of dual nature, the hydrophilic part will face the water and the hydrophobic part will exclude water. The most natural way to accomplish both tendencies is to form a bilayer, as shown in the image. See the footnote for a bit more detail [6].

The bacterial plasma membrane is a bit simpler than the plasma membrane of most eukaryotes. Eukaryotic cells have, in addition to phospholipids, cholesterol and other big, flat, mostly non-polar molecules which tend to stabilize the membrane and make it stiffer. Bacteria don't have cholesterol. Eukaryotes also frequently have a good many elaborate lipoproteins (proteins with fats attached) and glycoproteins (proteins with sugars attached). These derivitized proteins do many of the same jobs which are performed by the cell wall and capsule in bacteria. Eukaryotes also have an extensive internal membrane system including the Golgi apparatus, endoplasmic reticula, vesicles, mitochondria, and a nuclear membrane. The Eubacteria have none of these. Some bacteria have small folds in the plasma membrane, in which some specialized functions may occur -- notably the ATP-driven active transport of ions discussed above, as well as photosynthesis in the blue-green algae. However, there are no cytoplasmic membranes.

The cytoplasm itself is thus a rather uniform solution without a lot of structure. It does contain cytoplasmic inclusions of various kinds for storage of various critical metabolites. These include metachromatic granules of phosphate, glycogen (a polymer of glucose), grains of starch and salts, and poly(3-hydroxyalkanoate), the bacterial equivalent of fat.

In addition, the cytoplasm may contain plasmids. These are small, circular pieces of DNA derived from bacterial viruses (bacteriophages), other bacteria, or perhaps even other organisms. The genes carried on the plasmid may simply be dead weight, which continues to reproduce with the bacterium only because it happens to contain a working site for DNA polymerase. Thus, when this enzyme is active in the cell preparing the bacterial DNA for cell division, it tends to make a copy of the plasmid as well, even though the plasmid serves no biological function. On the other hand, plasmids can be of great practical importance, to humans as well as the bacterial host. Antibiotic-resistant disease bacteria often carry the extra genes which confer resistance on plasmids acquired from some completely different species. Plasmids may also contain other virulence factors, genes which code for proteins which can turn a harmless symbiotic species into a lethal disease vector.

As a starting point for comparison, let's briefly discuss DNA and what it does in metazoans -- you, for example. We won't worry about the structure of DNA for now. Its enough to know that DNA is a polymer made of billions of nucleotides. Each nucleotide contains one of 4 bases. The sequence of bases is precisely the same in each cell of your body (with some exceptions for special cells), even though you have about 6 billion DNA nucleotides in each cell. Mitochondria and chloroplasts [7] have a bit of their own DNA. All of the rest is contained in a membrane - bound nucleus. This nuclear DNA is encased in chromatin, i.e., a regular coat of basic structural proteins (histones). The sequence of bases on the DNA is critical because it specifies a code for making proteins, as we'll discuss in a minute. However, eukaryotic DNA also contains very large stretches of DNA which serve other purposes: binding sites for regulatory proteins, recognition sequences for ligases, and many other functions, some unknown.

In the typical eukaryotic cell, RNA polymerases use DNA as a template to make long strands of RNA -- a very similar polymer which has almost the same nucleotide/base structure. The process of making RNA from DNA is called transcription. The transcribed RNAs are spliced, recombined and "edited" in various steps in the nucleus, before being transported to the cytoplasm as mature messenger RNA (mRNA). In the cytoplasm, typically on the surface of an internal membrane system (the endoplasmic reticulum), the mRNA associates with ribosomes. Ribosomes are complex structures of protein and two molecules of ribosomal RNA, or rRNA. Ribosomes, and the rRNA molecules in them, are extremely conservative. The ribosomes of all eukaryotes are very similar. Because rRNA changes very slowly, rRNA is a good tool for looking at evolutionary relationships over huge lengths of time.

The ribosomes attach to the mRNA and use the sequences of RNA bases to make proteins according to the "genetic code." Proteins are polymers of amino acids. There are 20 amino acids commonly found in all organisms, and the sequence of amino acids determines what the protein is. Each run of three nucleotides on mRNA (each codon) specifies a particular amino acid. Since there are 4x4x4 = 64 possible codons, the code is redundant. That is, more than one codon sequence may specify a particular amino acid. This code is almost unbelievably conservative. Every living thing uses essentially the same code, with only a few, minor variations. See Table of Standard Genetic Code. This process of assembling proteins from the genetic code in mRNA is called translation. Translation is performed by the ribosomes using another type of RNA, transfer RNA or tRNA. There are 61 different tRNAs. Three codons are termination codons which signal the end of a coding sequence. Naturally, these have no tRNA. Each tRNA molecule has an anticodon at one end that binds to a specific mRNA codon. At the other end of the tRNA is the corresponding amino acid. The ribosomes move along the mRNA molecule, matching up the codons with tRNA anticodons, popping off the amino acid from the tRNA's far end, and adding the amino acid to the growing protein chain.

The bacterial chromosome is a single, circular molecule of DNA, vastly larger than any naturally occurring plasmid, but much smaller than almost all eukaryotic chromosomes. Bacterial DNA contains relatively few regulatory sites, by comparison with eukaryotic DNA, and has no extensive non-coding regions. Bacteria have no chromatin and, as mentioned above, there is no nucleus. The DNA is simply suspended in the cytoplasm. The Eubacteria use the same genetic code as metazoans. However, the bacterial ribosome, and ribosomal RNA, is considerably different. This may reflect a sharp functional difference. Bacterial DNA is not "edited" and transported. The ribosomes attach to the RNA even as it is being synthesized, so that transcription and translation are simultaneous and closely coupled.

This more or less concludes our whirlwind tour of cell biology and the bacterial cell. It is conventional to have lots of pictures and diagrams of transcription and translation. We have deliberately chosen to depart from this tradition in the interests of getting these painful necessities over quickly and without visual distraction. For good or evil, we will have plenty of opportunities for graphics later.

ATW030228.

[1] Phytoplankton is an ecological term referring to any photosynthetic microorganism normally found in water, including forms (like Gomphosphaeria) that are often found attached to some substrate. The Cyanobacteria are the large group of very basal photosynthetic Eubacteria traditionally called "blue-green algae" because they use phycocyanin (a bluish pigment), as well as chlorophyll a (a green pigment), for photosynthesis of carbohydrates.

[2] Try it. Assume each cell is a cylinder 4 � long, with a radius of 1 � (1 � = 10-6 m). Further assume a generation time of 1 hour and that the radius of the earth is 6.35 X 106 m. You can assume what you like about armpit height. It doesn't make much difference to the result.

[3] DO NOT get the idea that the bacterial cell has a net electrical charge. It doesn't. For every sodium (Na+) the cell pumps out, it must let some other positive charge in, typically potassium (K+). This "battery" works by entropy, not enthalpy. I'll try to explain in a few sentences as follows. The pore cells are symmetrical. They grab onto any sodium -- inside or outside the cell -- change shape, then release the sodium and return to their original shape. There is no net gain or loss of potential chemical or electrical energy (or enthalpy). However, if there is much more sodium outside than inside, the net effect is that the transport works only one way, and can therefore perform useful work. How can this be? We seem to be getting work energy from nowhere!

In thermodynamics, at constant temperature, ΔG = ΔH - TΔS. ΔG is the change in free energy, energy that performs work. Doing work means that ΔG decreases. ΔH is the change in enthalpy, or (roughly) potential energy, including the energy stored in chemical bonds. If we break bonds, the ΔH decreases. T is the temperature measured from Absolute Zero, and ΔS is the change in entropy or the amount of disorder in the system. So, we can get useful work out of a system by reducing enthalpy (i.e. breaking bonds or discharging an electrical potential) or by increasing entropy (increasing the amount of disorder). By breaking down a concentration gradient, we increase entropy. The bacterial cell breaks down high-energy ATP molecules to create a sodium gradient, and so uses enthalpic potential energy to reduced entropy. Then it recovers its investment by letting the sodium back in, so increasing entropy, and converting that change in entropy to free energy used to turn the rotor.

[4] If you're familiar with plant cell walls, try to forget what you know. This is a completely different, and only distantly related, structure.

[5] The peptide bond is the -CONH- part that links two amino acids.

[6] Actually, the water excludes the long carbon chains, rather than the reverse. This turns out to be another entropy effect. In a bilayer, the non-polar lipid tails are do not interact with water and are free to be very disordered with respect to each other. The polar water molecules, like tiny temporary magnets, form temporary, shifting structures with their nearest neighbors. However, if a lipid molecule is forced into water solution, the water molecules still have no way to interact with the nonpolar tail. Instead, the water molecules form a sort of cage around the lipid, interacting with each other and creating a structure which has a good deal of long-range order. Worse, each water molecule near the tail has fewer neighbors, reducing the randomness of the interactions. Thus entropy strongly favors the bilayer. Even though it looks more ordered, the entropy of the entire system, including the water, is much higher when the long chains are only in contact with each other.

[7] Don't worry about what these are in detail either, if you aren't familiar with these organelles. Mitochondria are small, convoluted membranous structures in the cell which perform oxidative metabolism. That is, they use oxygen to break down sugars and related nutrients into water and carbon dioxide, using the energy released to create ATP for future use as en energy resource. Chloroplasts are layered membranous structures that perform photosynthesis. That is, they use energy from sunlight to build up sugars from carbon dioxide and water, releasing oxygen in the process. In essence, mitochondria and chloroplasts are opposites.

Deiphon

Admin — Fri, 18 Aug 2006 18:34:52 GMT

Admin:

<div style="float:right;">
<table border="1" cellspacing="0" cellpadding="2">
<tr><th bgcolor="#CCCCCC">'''Arthropoda'''</th></tr>
<tr><td>
*[[Domain]]: [[Eukarya]]
*[[Kingdom]]: [[Animalia]]
*[[Phylum]]: [[Arthropoda]]
*[[Subphylum]]: [[Chelicerata]]
*[[Infraphylum]]: [[Trilobitomorpha]] ?
*[[Class]]: '''[[Trilobita]]'''
</td></tr>
<tr><td>
'''Order:'''
*[[Phacopida]] † <br />
</td></tr>
<tr><td>
'''Family'''
*[[Cheiruridae]] [[extinction|†]] <br />
</td></tr>
<tr><td>
'''Genus'''
*''Deiphon'' † <br />
</td></tr>
<tr><td>
'''Species'''
*D. forbesi † (type species)<br />
*D. barrandei † <br />
*D. fleur † <br />
*D. salmoni † <br />
*D. americanus † <br />
*D. dikella † <br />
*D. brabrooki † <br />
*D. grovesi † <br />
*D. pisum † <br />
</td></tr>
<tr><td>
Fossil_range:
[[Silurian]]
</td></tr>
</table>
</div>

'''''Deiphon''''' was a distinctive genus of [[phacopid]] [[trilobites]] found in Western and Central Europe, and in Central and Eastern United States. The type [[species,]] ''D. forbesi'', from Bohemia, in what is now the Czech Republic, was discovered and described by the French paleontologist, [[Joachim Barrande]] in 1850.

The species of ''Deiphon'' were highly modified for a [[pelagic]] existence. The [[glabellum]] was inflated, and globular-shaped, and covered in small wart-like bumps. If it was filled with fat, or oil, the glabellum would have helped to have made the creature positively buoyant. The cheeks of the [[cephalon]] formed a pair of long, curved spines, and the segments of the [[pleural lobes]] were separated and elongated to form rib-like struts. These modifications, along with the [[pygidium]] forming a "V," give these trilobites a sort of cartoon "fish-skeleton" appearance. However, the spherical glabellum and the curved, rib cage-like pleural lobes would have been hindrances for hydrodynamic streamlining, so it is presumed that ''Deiphon'' species were not fast swimmers. Instead, ''Deiphon'' may have fed on phytoplankton, or small, slow-moving zooplankton, living at a slow, easy going pace compared to its streamlined, torpedo-like cousin ''[[Crotalocephalus]]''.

==Links==

Reconstruction of ''D. forbesi'' [http://www.deviantart.com/deviation/33737908/]

Reconstruction of ''D. forbesi'' in comparison to ''Eurypterus remipedes'' [http://www.deviantart.com/deviation/36974185/]

[[Category:Prehistoric invertebrates]]
[[Category:Trilobita]]

Archaea

Bmeyers3535 — Fri, 18 Aug 2006 18:31:04 GMT

Bmeyers3535: an outside reference for later

Three Domains

Admin — Fri, 18 Aug 2006 18:15:06 GMT

Bmeyers3535:

The Three Domains of Life include the Archaea, including the halophiles, methanogens, and thermophiles, the Eubacteria, including gram-positive and gram-negative bacteria, and cyanobacteria, and the Eukarota, including protists, plants, animals, and fungi.

Modern genetic research over the last decade or so has revealed that anaerobic bacteria found in harsh oxygen-free conditions are genetically and metabolically completely different to other, oxygen-breathing organisms. These bacteria, called Archaeobacteria, or simply [[Archaea]], are actually "living fossils" that have survived since the planet's very early ages, before the Earth's atmosphere even had free oxygen. DNA and RNA analysis has shown that instead of five kingdoms there are actually three "Domains", [[Archaea]], [[Bacteria]], and [[Eukarya]] (Eukaryota). This last group refers to organisms whose genetic material is contained in a special membrane as the nucleus, and includes all higher organims from protists to humans. Rather than just four kingdoms it would seem to include over a dozens. So much so that the term "Kingdom" has become (in this usage) meaningless. So we have:

<table border=1 cellspacing=3>
<tr>
<td>two kingdoms</td>
<td>five kingdoms</td>
<td COLSPAN="2">three domains and who knows how many "kingdoms"</td>
</tr>
<tr>
<td>Animalia</td>
<td>Animalia</td>
<td ROWSPAN="11">Eukarya</td>
<td>Animalia</td>
</tr>
<tr>
<td ROWSPAN="2">Plantae</td>
<td>Fungi</td>
<td>Fungi</td>
</tr>
<tr>
<td>Plantae</td>
<td>Plantae</td>
</tr>
<tr>
<td ROWSPAN="8">either Protozoa (=Animal) or Algae (=Plant)</td>
<td ROWSPAN="8">Protoctista</td>
<td>Alveolata</td>
</tr>
<tr>
<td>Stramenopiles</td>
</tr>
<tr>
<td>etc...</td>
</tr>
<tr>
<td>Sporozoa</td>
</tr>
<tr>
<td>Mycetozoa</td>
</tr>
<tr>
<td>Euglenozoa</td>
</tr>
<tr>
<td>etc...</td>
</tr>
<tr>
<td>Archezoa</td>
</tr>
<tr>
<td ROWSPAN="2">Plant (bacteria and blue-green algae)</td>
<td ROWSPAN="2">Monera</td>
<td>Eubacteria</td>
<td>(kingdoms not specified)</td>
</tr>
<tr>
<td>Archaea</td>
<td>Euryarchaeota
<br>Korarchaeota
<br>Crenarchaeota</td>
</tr>
</table>

Thus the diversity of life is seen to be far more complex than was envisaged, and familiar organisms like animals and plants are just a tiny proportion of all of the many different forms.

The following diagram illustrates the relationship between the Three Domains, and the various subbranches of each.

[[Image:Fig01 16.JPG]]

== External References ==

[http://www.ucmp.berkeley.edu/alllife/threedomains.html UCMP The Biosphere: Life on Earth - Three Domains of Life]

[http://tolweb.org/tree?group=Life_on_Earth&contgroup= The Tree of Life Project]

[http://home.manhattan.edu/~frances.cardillo/plants/intro/whitt.html The Whittaker System - useful diagram]

[http://www.il-st-acad-sci.org/kingdoms.html Illinois State Academy of ScienceThe Kingdoms Project The Kingdoms Project at the ISAS]

[http://web1.manhattan.edu/fcardill/plants/intro/kingdoms.html Survey of the Plant Kingdoms - actually an excellent brief intro to the development of Kingdoms in biology]

[http://www.nearctica.com/nathist/phylog.htm Natural History - General - Phylogeny]

[http://www.wri.org/biodiv/f01-key.html Relative Number of Described Species in Major Taxa]

Hadean

Bmeyers3535 — Fri, 18 Aug 2006 12:55:10 GMT

Bmeyers:

[[Time]] > [[Hadean]]

== The Hadean Eon ==

The Hadean Eon of Precambrian Time: 4500 to 3800 million years ago

The name Hadean was coined by geologist Preston Cloud for the pre-Isuan sequence whose record may not be preserved on Earth but is better known from Moon rocks. Consequently, the time sequence and stratigraphy of the Hadean are largely based on lunar events. For example the [[Nectarian Era]] is defined by reference to the formation of the Nectaris Basin (southwestern Nearside). The Hadean has no place in the ICS system followed in the rest of Palaeos. The ICS lumps everything earlier than 3600 Mya into the [[Eoarchean]] Era of the [[Archean]] Eon.

During Hadean time, the Earth and Solar System formed by coagulation and gravitational contraction from a large cloud of gas and dust around the sun, called an accretion disc. The sun formed the nucleus, shrinking in on itself by gravitational compaction until it reached a stage where it ignited with nuclear fusion and give off light and heat. The surrounding particles within this cloud coalesced into planetisimals which then aggregated to form microplanets (rather like modern asteroids). The energy of the collisions between the larger microplanets, as well as interior radioactive and gravitational heating, generated a huge amount of heat, and the Earth and other planets would have been initially molten. The Earth and Moon formed rather late in this process, from a collision between two large bodies -- a mars-sized planetoid and a slightly larger body.

During this period the heavier molten iron sank to the down to become the core, while the lighter rock rose to the surface. The lightest of all became the crust as a sort of "scum" on the surface. There was also an outgassing of volatile molecules such as water, methane, ammonia, hydrogen, nitrogen, and carbon dioxide. An initial steam atmosphere formed of water from comets and hydrated minerals. Rain fell to form a proto-ocean 4.3 to 4.4 billion years ago. All terrestrial planets had a similar process in their early histories.

Once most of the planetisimals were gone the planetary bombardment stopped, and a stable rocky crust was able to formed on the Earth. This is the age of the oldest rocks on earth and also of moon rocks. Atmospheric water condensed into oceans and proto-life formed in the soup of primordial organic molecules, either in the early oceans or in clay or rocks within the crust itself. These stages are considered in detail below.

Image: Nectaris Basin from Lunar Orbiter Imagery.

=== The Geological Time-Scale of the Hadean ===

<table border=1>
<tr><th>Eon</th><th>Stage(Era)</th><th>when began<br>myrs ago</th><th>duration<br>myrs</th></tr>
<tr><th rowspan=4>Hadean</th><td>Early Imbrian</td><td>3,850</td><td>50</td></tr>
<tr><td>[[Nectarian]]</td><td>3,950</td><td>100</td></tr>
<tr><td>Basin-Groups 1-9</td><td>4,150</td><td>200</td></tr>
<tr><td>Cryptic</td><td>4560</td><td>410</td></tr>
</table>

=== The Dynamics of the Hadean[2] ===

The Hadean or Pregeologic Eon is the time period during which the Earth was transformed from a gaseous cloud into a solid body. In terms of "Year of the Earth," it begins on January 1 and ends about 26 February. The process of solidification is poorly known, however, and the Hadean may have lasted as long as one billion years.

Earth cross-sectionThis is the period during which the Earth's crust [1] was formed. This crust melted and reformed numerous times, because it was continuously broken up by gigantic magma currents that erupted from the depths of the planet, tore the thin crust, and then cooled off on the surface before sinking again into the heart of the Earth.

The details of this slow, destructive process are still uncertain. However, it is thought that the heavy elements, like iron, tended to sink towards the center of the Earth because of their higher density, while the lighter components, particularly the silicates, formed an incandescent ocean of melted rock on the surface. Approximately 500 million years after the birth of the Earth, this incandescent landscape began to cool off. When the temperature fell under 1000� C., the regions of lower temperatures consolidated, become more stable, and initiated the assembly of the future crust.

=== Development of the Earth's Crust ===

In principle therefore the Earth was a sphere of melted rock, churned by convective movements between the hot inner layers, while the outer, surface regions were in contact with the cold of surrounding space. The dissipation of heat to space began the cooling of our planet. In the magma ocean blocks began to appear, formed from high melting point minerals. These red hot, but solid slabs were similar (although on a very different scale) to the thin edges of crust that we see forming on the surface of flowing lava. The result is what sees in the imaginative reconstruction to the right. Note that, in those times, the Moon, still burning, was only 16,000 km from the Earth (compared to 384,000 km today), and for that reason occupied a big part of the sky. Truly a nightmare landscape!

But those first fragments of crust must also have been very unstable, easily resorbed by the liquid mass of magma and sucked into the depths. Only, with the further cooling of the planet, might those fragments become numerous and large enough to form a first, thin, solid cover -- that is to say, a true primitive crust. This primordial crust might have developed as a warm expanse of rocks (some hundreds of degrees Celsius), interrupted by numerous large breaks, from which enormous quantities of magma continued to erupt. At this early point in the history of the Solar System, meteoric bombardment was intense, and it would have continually opened new holes in the crust, immediately filled by magma. The scars left by this intense meteoric bombardment, which continued for at least 700 or 800 million years, have been almost totally erased on the Earth by subsequent reworking of the crust. However, the resulting impact craters and lava flows are perfectly preserved on the Moon and on many other bodies in the Solar System whose geological evolution ended long ago.

=== The Primordial Atmosphere ===

As a result of the high temperatures at the center of the Earth, and due to volcanic activity, the crust emitted halogen gasses, ammonia, hydrogen, carbon dioxide, methane, water vapor, and other gasses. In the following 100 million years, these gasses accumulated to form the primordial atmosphere. This atmosphere was quite similar to the atmosphere of Titan, one of the larger moons of Saturn. The primordial atmosphere is believed to have reached a pressure of 250 atmospheres and would have been extremely toxic to life as we now know it.

Little by little our planet assumed a more familiar look, with a dense gaseous cloud zone we could call an atmosphere, a liquid zone with oceans, lakes and rivers, or hydrosphere, and a solid zone, or lithosphere with the first outlines of what would one day become continents. Then, under the lithosphere, the mantle and the core differentiated (see below).

=== Outgassing ===

The process of cooling and consolidation of the Earth's surface was accompanied, as still occurs in volcanoes, by strong outgassing of new atmosphere, formed essentially from methane (CH4), hydrogen (H2), nitrogen (N2) and water vapor, with smaller amounts of noble gases and carbon dioxide. Most of the hydrogen, the lightest component, escaped into space as also happens today. The other gases and vapors accumulated, including water vapor. The water did not condense at this point, because the temperatures of the crust was still very high. From a petrographic point of view, the primitive crust was similar to basalt, a dark volcanic rock, with less than 53 % SiO2 by weight. This basalt was formed from the material of the mantle, but had a rather different composition. The more ancient blocks found on the Moon, approximately 4.6 billion years old, are in fact just basalts with a high aluminum content. But the composition of the crust must have differed even more from that of the mantle. Disrupted by highly energetic convective movements, the thin lithospheric covering would have been fragmented into numerous small plates in continuous mutual movement, separated and deformed by bands of intense vulcanism. The remelting of part of the crust, analogous to subduction, gradually produced magmas richer in silicates. Thus, around the basalts appeared andesites: fine granular volcanic rocks, whose name derives from the Andes, where several volcanoes are known to form rocks of this type.

=== Formation of the oceans ===

At the same time, another important series of events began to unfold that led to the formation of sedimentary rocks through the processes of erosion, drift, and accumulation. These processes began to occur as soon as the surface cooled enough to allow the water cycle to establish itself In fact, the primitive Earth long remained covered in darkness, wrapped in dense burning clouds into which continuously poured water vapor from volcanic emissions. When temperatures finally cooled sufficiently, the clouds began to melt into rain, and the primordial atmosphere produced storms of unimaginable proportions, under which the Earth groaned and flowed. At first, falling on incandescent rock, the rain evaporated, but the evaporation gradually cooled the crust until the water could accumulate in the depressed regions of the Earth's surface, forming the first oceans. On the primordial continents, the first river networks were created, and they transported detritus torn from elevated regions and then deposited on the bottom of the primordial seas. The metamorphism and remelting of the products of the erosion ultimately produced magmas and lava increasingly rich in silicates, and therefore of different composition from the mantle and the primitive crust.

=== The Birth of granites ===

From all these processes, such as the remelting of part of the basaltic primitive crust, accompanied by metamorphism and melting of large quantities of sediments, there gradually formed magmas similar in composition to granites, and therefore able to "float" on basalt.

Fragment by fragment, formed in the beginning from island chains similar to modern-day volcanic island arcs, the continental crust was born, and so the external land cover of the planet. This new type of crust had a unique feature of fundamental importance: its low density kept it riding on the surface. Thus it was able to undergo intense transformations, such as mechanical deformation (tectonics) or metamorphism, but remain always in proximity to the surface. While the primitive basaltic crust has probably been permanently lost, geologists have found some traces of those first outlines of continental crust. In 1983, in western Australia, were found the most ancient rocks known to date. These rocks are dated to about 4.2 billion years. Remarkably, they are sandstones. This means that they were derived from the erosion of other rocks, still more ancient!

[1] The Crust: The more external part of the crust, or Lithosphere constitutes the superficial covering of the Earth. Two kinds of crust are easily distinguished by composition, thickness and consistency: continental crust and oceanic crust. Continental crust has a thickness that, in mountainous regions chains may reach 40 kilometers. It is composed mainly of metamorphic rock and igneous blocks enriched in potassium, uranium, thorium and silicon. This forms the diffuse granitic bedrock of 45% of the land surface of the Earth. The oceanic crust has a more modest thickness, on the order of 5-6 kilometers, and is made up of basaltic blocks composed of silicates enriched in aluminum, iron and manganese. It is continuously renewed along mid-ocean ridges.

[2] From Era Precambriana by Prof. Franco Maria Boschetto, translated from the Italian by ATW040312.

Life

Bmeyers3535 — Fri, 18 Aug 2006 12:39:00 GMT

Bmeyers3535:

__FORCETOC__
==The Meaning of Life ==

But natheless, whil I have tyme and space,<br>
Er that I ferther in this tale pace, <br>
Me thynketh it acordaunt to resoun <br>
To telle yow al the condicioun <br>
Of ech of hem, so as it semed me, <br>
And whiche they weren, and of what degree, <br>
And eek in what array that they were inne ... <br>

Chaucer, Canterbury Tales: Prologue.

This section is the heart of Palaeos. We have to begin this section somewhere, and so this is also the Beginning of Life. If time permits, we will one day add sections on the definition of "life" and the ways it may have begun. However, that kind of systematic treatment is not exactly what this site is all about (see, infra, the Purpose of Life). So instead, we'll get right to business.

Broadly speaking, we will follow the "[[Three Domains]]" model of evolution, at least for organizational purposes. In this model, the earliest and most basic life forms are the [[Archaea]]: relatively simple, mostly chemautotrophic single-celled organisms. Today, these organisms are still often found as "extremeophiles," living in harsh, toxic environments using a remarkable diversity of metabolic tricks and adaptations to survive under apparently impossible conditions.

From the Archaea developed two, quite different groups, the [[Eubacteria]] and the [[Eukarya]]. The Eubacteria are also single-celled organisms, but with complex cell walls, involving peculiar biochemicals which allow us to conclude, with moderate confidence, that they are a natural group. They include the organisms we normally think of as bacteria and also the blue-green algae. The Eukarya include all organisms made up of cells with nuclei. That is, their DNA is walled off in a separate compartment of the cell. Again, this feature is striking enough that we can be reasonably sure that the Eukarya all derived from a single common ancestor, probably within Archaea. Eukaryotes may be single-celled organisms (such as Amoeba or Paramecium), multi-celled organisms (such as oak trees or humans), or at some intermediate stage of organization (like [[sponges]] or slime molds).

From the Eukarya evolved three sorts of multi-celled organisms: plants ([[Chlorobionta]]), [[Fungi]], and Animals ([[Metazoa]]). Animals were originally radially symmetrical, like a simple [[jellyfish]], or lacked any symmetry, like [[sponges]]. However, at some point, six or seven hundred million years ago, some animals (Bilateria) evolved strict bilateral symmetry. This sounds trivial, but it was a very significant breakthrough. Most importantly, it allowed segmentation of body sections, so that different segments of the body could specialize for different functions. This required the evolution of an entirely different type of genetic regulation because genes had to operate differently depending on which segment they might be in. This is substantially more complicated than sponge or jellyfish-style development.

From the basic bilaterian plan, two developmental styles evolved. This gets a bit further into developmental biology than we wish to go at the moment. It is sufficient to note that these are the deuterostomes (echinoderms and chordates) and the protostomes (almost everything else). The chordates include the vertebrates, which includes us. Because we are vertebrates, this group has always had a special place, and we refer to all non-vertebrate metazoans as "invertebrates." We will retain this bit of phylogenetic chauvinism in Palaeos for some organizational purposes, until we hear objections from any brachiopods or priapulid worms who might have occasion to offer their comments.

Finally, its important to remember that this site, like life, was not planned. It grew and evolved. It began and, one day, we will become bored and it will die. It may be useful, but it has no overriding mission other than the fun of creating it. So, if you need something thoroughly vetted and organized, try the [http://tolweb.org/tree/phylogeny.html Shrub of Life Homepage]. Palaeos is ... different.

== The Facts of Life ==

[[Cladograms]], or "trees of life," are appropriate phylogenetic schemes for metazoans (multi-celled eukaryotes) but sometimes misleading in other organisms. Nonetheless, we have to have some kind of roadmap, and cladograms at least have the virtue of being testable. The following map is roughly equivalent to a three-color map of the world with just some the major continents sketched in.

LIFE (= [[Archaea]]?)
|--[[Eubacteria]]
`--[[Eukarya]]
|--[[Chlorobionta]] (green plants)
`--+--[[Fungi]]
`--[[Metazoa]] (animals)
|--[[Deuterostomata]]
| |--[[Echinodermata]]
| `--[[Vertebrata]]
`--[[Protostomata]]
|--[[Mollusca]]
`--[[Arthropoda]]

At this level there are many uncertainties. Are the Fungi more closely related to animals (Metazoa) than to plants? Quite likely. Are eukaryotes really descended from the Archaea, or do they derive from Eubacteria, or from some fusion of the two? Anybody's guess at this point. We look forward to changing our minds at frequent intervals.

== The Purpose of Life ==

Frankly, we're less worried about being wrong than about missing the show completely. The discussions on this site are of quite variable quality, format, accuracy, and style. We're not worried by that, either. As this site has developed, we've learned that the paleo web is dominated by two groups: educators and academic scientists. The educators tend to want everything boiled down to colorful, but tasteless and insubstantial uniformity. The academic scientists tend to be paralyzed by detail. We aim to steer a middle course, avoiding neither the difficult and technical problems, nor the uncertainty inherent in saying anything meaningful about deep time. Truthfully, we scarcely steer at all, but proceed from subject to subject in the manner of a bumper car ride or a destruction derby. We have no overriding mission to educate or provide definitive guidance. Rather, our's is a more self-indulgent attempt to explore the world and to pick up rocks just to see what's under them.

Then again, maybe that is the purpose of life.

Eurotamandua

Admin — Fri, 18 Aug 2006 03:45:23 GMT

Admin:

<div style="float:right;">
<table border="1" cellspacing="0" cellpadding="2">
<tr><th bgcolor="#CCCCCC">'''[[Mammalia]]'''</th></tr>
<tr><td>
*[[Domain]]: [[Eukarya]]
*[[Kingdom]]: [[Animalia]]
*[[Phylum]]: [[Chordata]]
*[[Subphylum]]: [[Vertebrata]]
*[[Infraphylum]]: [[Gnathostomata]]
*[[Class]]: '''[[Mammalia]]'''
</td></tr>
<tr><td>
'''Order:'''
*[[Pholidota]] <br />
</td></tr>
<tr><td>
'''Family:'''
*[[Manidae]]
</td></tr>
<tr><td>
'''Genus:'''
*'''''Eurotamandua'''''[[extinction|†]]
</td></tr>
<tr><td>
Fossil_range:
[[Eocene]]
</td></tr>
</table>
</div>

'''''Eurotamandua''''' ('[[Europe]]an tamandua') is an extinct genus of [[pangolin]]. It was about 90 cm (3 ft) long. When it was first discovered, it was originally thought to be an [[anteater]], as it did not have the characteristic fused-hair scales of other pangolins.

''Eurotamandua'' was one of the first members of the family, but aside from its lack of scales, it already bore all typical characteristics: long [[claw]]s, a long [[tail]], a strongly elongated snout and most likely the same long, sticky [[tongue]]. Presumably it also fed on [[ant]]s and [[termite]]s. ''Eurotamandua'' got its name because it strongly resembled modern arboreal anteaters of the genus ''[[Tamandua]]''.

While ''Eurotamandua'' is the most primitive known pangolin, it is not the ancestor of modern pangolins, as the [[Eocene]] pangolin, ''[[Eomanis]]'' is its contemporary. It is presumed that ''Eomanis'' and ''Eurotamandua'' diverged from a common ancestor either during the late [[Paleocene]], or the early [[Eocene]].

== Links ==
Photo of fossil [http://www.uvm.edu/~jdecher/Eurotamandua.JPG]

[[Category:Prehistoric mammals]]
[[Category:Pangolins]]
[[Category:Eocene mammals]]
[[Category:Eocene extinctions]]

Eomanis

Admin — Fri, 18 Aug 2006 03:44:48 GMT

Admin:

<div style="float:right;">
<table border="1" cellspacing="0" cellpadding="2">
<tr><th bgcolor="#CCCCCC">'''[[Mammalia]]'''</th></tr>
<tr><td>
*[[Domain]]: [[Eukarya]]
*[[Kingdom]]: [[Animalia]]
*[[Phylum]]: [[Chordata]]
*[[Subphylum]]: [[Vertebrata]]
*[[Infraphylum]]: [[Gnathostomata]]
*[[Class]]: '''[[Mammalia]]'''
</td></tr>
<tr><td>
'''Order:'''
*[[Pholidota]] <br />
</td></tr>
<tr><td>
'''Family:'''
*[[Manidae]]
</td></tr>
<tr><td>
'''Genus:'''
*'''''Eomanis'''''[[extinction|†]]
</td></tr>
<tr><td>
Fossil_range:
Middle [[Eocene]]
</td></tr>
</table>
</div>
'''''Eomanis''''' is the earliest known true [[pangolin]] from the Middle [[Eocene]] [[Europe]]. [[Fossil]]s collected from the [[Messel Pit]], [[Germany]], indicate that this 50 cm long [[animal]] was rather similar to the extant pangolins. However, unlike modern pangolins, its tail and legs did not bear scales. According to the stomach contents of the excellently preserved Messel specimens, ''Eomanis’'' [[diet (nutrition)|diet]] consisted of both [[insect]]s and [[plant]]s. Its contemporary was the scale-less, [[anteater]]-like ''[[Eurotamandua]]''.

== References ==
* {{cite book | author=Cox, Barry; Savage, R.J.G.; Gardiner, Brian; Dixon, Dougal | year=1988 | title=Macmillan Illustrated Encyclopedia of Dinosaurs and Prehistoric Animals | chapter=Insectivores and creodonts | editor= | others= | pages=213 | publisher=Macmillan London Limited | id=ISBN 0-333-48699-4 | url= | authorlink= }}

[[Category:Pangolins]]
[[Category:Prehistoric mammals]]
[[Category:Eocene mammals]]

Megacerops

Admin — Fri, 18 Aug 2006 03:24:47 GMT

Admin:

Brontotheriidae

Admin — Fri, 18 Aug 2006 03:15:38 GMT

Admin:

<div style="float:right;">
<table border="1" cellspacing="0" cellpadding="2">
<tr><th bgcolor="#CCCCCC">'''Mammalia'''</th></tr>
<tr><td>
*[[Domain]]: [[Eukarya]]
*[[Kingdom]]: [[Animalia]]
*[[Phylum]]: [[Chordata]]
*[[Subphylum]]: [[Vertebrata]]
*[[Infraphylum]]: [[Gnathostomata]]
*[[Class]]: '''[[Mammalia]]'''
</td></tr>
<tr><td>
'''Order:'''
*[[Perissodactyla]] <br />
</td></tr>
<tr><td>
'''Family'''
*[[Brontotheriidae]] [[extinction|†]]<br />
</td></tr>
<tr><td>
Fossil_range:
[[Eocene]]
</td></tr>
</table>
</div>

'''Brontotheriidae''', also called '''Titanotheriidae''', was a [[family]] of [[extinct]] [[mammal]]s belonging to the order [[Perissodactyla]], the order that includes [[horse]]s, [[Rhinoceros|rhino]]s, and [[tapir]]s. Although '''brontotheres''' were probably most closely related to horses, they bore a strong, yet superficial resemblence to [[rhinoceros]]es, with which they are often confused, even though the brontotheres were not true rhinos. They lived around 58-30 million years ago, from the early to late [[Eocene]]. In their time, the brontotheres were highly successful, radiating out from their origins within North America into Asia, then Europe, before they became extinct at the end of the Eocene period.

Brontotheres retained four toes on their front feet and three toes on their hind feet. Their teeth are adapted to shearing (cutting) relatively nonabrasive vegetation. Their [[molars]] have a characteristic W-shaped [[ectoloph]] (outer shearing blade). The earliest brontotheres, such as ''[[Eotitanops]]'', were rather small, no more than a meter in height, and were hornless. Later brontotheres evolved massive body sizes, although some small species, such as ''[[Nanotitanops]]'' did persist through the Eocene. Some genera, such as ''[[Dolichorhinus]]'', [[Evolution|evolved]] highly elongate skulls. Later brontotheres were massive in size, up to 2.5 m in height, and had evolved bizarre hornlike appendages. For instance the [[North America]]n brontothere ''[[Megacerops]]'' evolved large [[sexual dimorphism|sexually dimorphic]] paired horns above their noses. The sexually dimorphic horns suggest that brontotheres were highly gregarious (social) and males may have performed some sort of head clashing behavior in competition for mates. However, unlike rhinos, the horns of brontotheres are composed of bone, the [[frontal bone]] and [[nasal bone]], and were placed side-to-side rather than front-to-back.

==Classification of Brontotheres==

Two classification systems for the Brontotheriidae are presented below. The first contains 43 genera and 8 subfamilies and although it is based on a recent publication (McKenna and Bell, 1997), it summaries research that was conducted before 1920 and is badly outdated. The second classification is based on very recent research (Mihlbachler et al., 2004a, 2004b; Mihlbachler, 2005). It indicates that many of the previous subfamily names are invalid. Also several recently discovered brontotheres are included in the newer classification. Note that although ''[[Lambdotherium]]'' and ''[[Xenicohippus]]'' were previously included in the Brontotheriidae, they are no longer considered to be members of this family. ''Lambdotherium'', though excluded, may be the closest known relative to brontotheres. ''Xenicohippus'' is now thought to be an early member of the horse family, [[Equidae]].

Old Classification (summarized by McKenna and Bell, 1997):

*'''Family Brontotheriidae'''
**''[[Pakotitanops]]'' ''[[incertae sedis]]'', from [[Pakistan]]
**''[[Nanotitanops]]'' ''[[incertae sedis]]'', from [[Asia]]
***Subfamily Lambdotheriinae
****''[[Lambdotherium]]'', from North America
****''[[Xenicohippus]]'', from North America
***Subfamily Palaeosyopinae
****''[[Palaeosyops]]'' (including ''Eotitanops''), from North America, 0.5 m tall
****''[[Mulkrajanops]]'', from [[Pakistan]], 1.25 m tall
***Subfamily Dolichorhininae
****''[[Metarhinus]]'', from North America, 1 m tall
****''[[Sphenocoelus]]'', from North America, 1.25 m tall
****''[[Mesatirhinus]]'', from North America, 1 m tall
***Subfamily Brontotheriinae
****''[[Duchesneodus]]'', from North America
****''[[Brontotherium]]'', from North America
****''[[Megacerops]]'', from North America, 2.5 m tall
***Subfamily Embolotheriinae
****''[[Titanodectes]]'', from Asia
****''[[Embolotherium]]'', from [[Mongolia]], 2.5 m tall
****''[[Protembolotherium]]'', from Outer Mongolia, 2 m tall
***Subfamily Brontopinae
****''[[Brachydiastematherium]]'', from [[Eastern Europe]], 2 m tall
****''[[Pachytitan]]'', from Inner Mongolia, 2 m tall
****''[[Dianotitan]]'', from China, 2 m tall
****''[[Gnathotitan]]'', from Inner Mongolia, 2.5 m tall
****''[[Microtitan]]'', from Inner Mongolia, 0.75 m tall
****''[[Epimanteoceras]]'', from Inner Mongolia, 2 m tall
****''[[Protitan]]'', from Inner Mongolia, 2 m tall
****''[[Rhinotitan]]'', from Inner Mongolia, 2.5 m tall
****''[[Metatitan]]'', from Mongolia, 1.5 m tall
****''[[Protitanotherium]]'', from North America, 2 m tall
****''[[Parabrontops]]'', from Mongolia, 2 m tall
****''[[Oreinotherium]]'', from North America
****''[[Brontops]]'', from North America
****''[[Protitanops]]'', from North America, 2 m tall
****''[[Pygmaetitan]]'', from China, 0.5 m tall
***Subfamily Telmatheriinae
****''[[Acrotitan]]'', from Inner Mongolia, 0.3 m tall
****''[[Desmatotitan]]'', from Inner Mongolia, 1.25 m tall
****''[[Arctotitan]]'', from China
****''[[Hyotitan]]'', from Inner Mongolia, 2.2 m tall
****''[[Sthenodectes]]'', from North America, 1.25 m tall
****''[[Telmatherium]]'' (including ''Metatelmatherium''), from North America and Inner Mongolia, 1.5 m tall
****''[[Sivatitanops]]'', from Asia and Europe
***Subfamily Menodontinae
****''[[Diplacodon]]'', from North America, 2 m tall
****''[[Eotitanotherium]]'', from North America
****''[[Notiotitanops]]'', from North America, 2 m tall
****''[[Menodus]]'', from Europe and North America
****''[[Ateleodon]]'', from North America

New classification (Mihlbachler et al., 2004a, 2004b; Mihlbachler, 2005):

*'''Family Brontotheriidae'''
**''[[Pakotitanops]]'' ''[[incertae sedis]]'', from [[Pakistan]]
**''[[Mulkrajanops]]'' ''[[incertae sedis]]'', from [[Pakistan]], 1.25 m tall
**''[[Eotitanops]]'', from North America, 0.5 m tall
**''[[Palaeosyops]]'', from North America, 1 m tall
**Subfamily Brontotheriinae
***''[[Bunobrontops]]'', from [[Asia]]
***''[[Mesatirhinus]]'', from North America, 1 m tall
***''[[Dolichorhinus]]'', from North America, 1.25 m tall
***''[[Sphenocoelus]]'', from North America, 1.25 m tall
***''[[Desmatotitan]]'', from Inner Mongolia, 1.25 m tall
***''[[Fossendorhinus]]'', from North America
***''[[Metarhinus]]'', from North America, 1 m tall
***''[[Microtitan]]'', from Inner Mongolia, 0.75 m tall
***''[[Sthenodectes]]'', from North America, 1.25 m tall
***''[[Telmatherium]]'', from North America, 1.25 m tall
***''[[Metatelmatherium]]'', from North America and Inner Mongolia, 1.25 m tall
***''[[Epimanteoceras]]'', from Inner Mongolia, 2 m tall
***''[[Hyotitan]]'' ''[[incertae sedis]]'', from Inner Mongolia, 2.2 m tall
***''[[Nanotitanops]]'' ''[[incertae sedis]]'', from [[Asia]]
***''[[Pygmaetitan]]'' ''[[incertae sedis]]'', from China, 0.5 m tall
***''[[Acrotitan]]'' ''[[incertae sedis]]'', from Inner Mongolia, 0.3 m tall
***''[[Arctotitan]]'' ''[[incertae sedis]]'', from China
***''[[Qufutitan]]'' ''[[incertae sedis]]'', from China
***Tribe Brontotheriini
****''[[Protitan]]'', from Inner Mongolia, 2 m tall
****''[[Protitanotherium]]'', from North America, 2 m tall
****''[[Rhinotitan]]'', from Inner Mongolia, 2.5 m tall
****''[[Diplacodon]]'' (including ''Eotitanotherium''), from North America, 2 m tall
****''[[Pachytitan]]'', from Inner Mongolia, 2 m tall
****''[[Brachydiastematherium]]'', from [[Eastern Europe]], 2 m tall
****''[[Sivatitanops]]'', from Asia and Europe
****Subtribe Embolotheriina
*****''[[Gnathotitan]]'', from Inner Mongolia, 2.5 m tall
*****''[[Aktautitan]]'', from Kazakstan, 2.5 m tall
*****''[[Metatitan]]'', from Mongolia, 1.5 m tall
*****''[[Nasamplus]]'', from Inner Mongolia
*****''[[Protembolotherium]]'', from Outer Mongolia, 2 m tall
*****''[[Embolotherium]]'' (including ''Titanodectes''), from [[Mongolia]], 2.5 m tall
****Subfamily Brontotheriina
*****''[[Parabrontops]]'', from Mongolia, 2 m tall
*****''[[Protitanops]]'', from North America, 2 m tall
*****''[[Notiotitanops]]'', from North America, 2 m tall
*****''[[Dianotitan]]'', from China, 2 m tall
*****''[[Duchesneodus]]'', from North America
*****''[[Megacerops]]'' (including ''Menodus'', ''Brontotherium'', ''Brontops'', ''Menops'', ''Ateleodon'', and ''Oreinotherium''), from North America, 2.5 m tall

==References==

*McKenna, M. C, and S. K. Bell. 1997. Classification of Mammals Above the Species Level. Columbia University Press, New York, 631 pp.

*Mihlbachler, M.C. 2004. Phylogenetic Systematics of the Brontotheriidae (Mammalia, Perissodactyla). Ph.D. Dissertation, Columbia University. 757 pp.

*Mihlbachler, M.C. , S.G. Lucas, and R.J, Emry. 2004a. The holotype specimen of Menodus giganteus, and the “insoluble” problem of Chadronian brontothere taxonomy. In S.G. Lucas, K. Zeigler, and P. E. Kondrashov (eds.), Paleogene Mammals. Bulletin of the New Mexico Museum of Natural History 26: 129-136.

*Mihlbachler, M.C., S.G. Lucas, R.J. Emry, and B. Bayshashov. 2004b. A new brontothere (Brontotheriidae, Perissodactla, Mammalia) from the Eocene of the Ily Basin of Kazakstan and a phylogeny of Asian "horned" brontotheres. American Museum Novitates 3439: 1-43.

[[Category:Brontotheres]]
[[Category:Eocene mammals]]

Brontops

Admin — Fri, 18 Aug 2006 03:14:18 GMT

Admin:

Brontotherium

Admin — Fri, 18 Aug 2006 03:12:03 GMT

Admin:

Mene rhombea

Admin — Fri, 18 Aug 2006 03:08:25 GMT

Admin:

'''''Mene rhombea''''' was a perciform fish found in the Tethys Ocean during the Eocene. As suggested by their fossils' small, upturned mouths, M. rhombea was a planktivore. Their fossils from the laggerstat Monte Bolca are greatly valued.

==Links==

Weigert-Fossil [http://www.weigert-fossil.de/html/coralf29.html]
Reconstruction of ''M. rhombea'' [http://www.deviantart.com/deviation/33325675/]

Mass extinction

Admin — Fri, 18 Aug 2006 02:52:44 GMT

Admin:

'''Mass extinction''' refers to the abrupt disappearance of a significant number of life forms in a relatively short time period. The surviving life forms then rapidly evolve to fill in the newly available [[niches]]. This leads to rapid [[speciation]]. Mass extinction is usually taken to be the result of a globally significant event, such as the impact of a large meteorite; the onset of an ice age; or a massive volcanic explosion. Classic examples in geologic history include the [[Permian]] - [[Triassic]] or [[PT-Boundary]] event in which some 90% of species became extinct and the [[Cretaceous]] - [[Tertiary]] or [[KT-Boundary]] event in which some 75% of species disappeared.

The current impact of [[humankind]] upon the [[biosphere]] is sometimes considered to rank alongside these examples. See: <i>The Sixth Extinction : Patterns of Life and the Future of Humankind</i> by Richard Leakey ( ISBN 0385468091 ).

More recent work on the topic (Bambach et al, 2004) suggests that differences in rate between extinction and origination of species may explain some events previously thought to be mass extinctions. The Ashgillian, Djhulfian, and Maastrichtian extinctions retain their characterization as mass extinctions in this perspective but the late Frasnian and Norian extinctions may now be considered as different. These stages show a dramatic decrease in origination rate below the mean while extinction rate remains constant. Other unknown processes appear to be at work supressing the rise of new species during the Frasnian and Norian stages. This process gives an appearance of extinction rate increasing when in fact it is a decrease of species originations that is responsible for the observed decline in biodiversity during these stages.

Mass extinctions are a key part of the [[Punctuated Equilibrium]] hypothesis of [[Stephen Jay Gould]] and [[Niles Eldredge]]. See: <i>Time Frames: The Evolution of Punctuated Equilibria</i> ( ISBN 0691024359 )

==References==
# Bambach, R., Knoll, A., Wang, S. 2004. Origination, extinction, and mass depletions of marine diversity. <i>Paleobiology</i> v30 p522-542

[[Category:Biogeography]]

Extinction

Admin — Fri, 18 Aug 2006 02:52:03 GMT

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'''Extinction''' is the technical term for what happens to a [[species]] when none of its members are living. It wasn't so very long ago that prominent [[Creationists]] declared it wasn't possible for any species to go extinct, because that would indicate that God had messed up somehow when He created the universe. [[Georges Cuvier]] first showed otherwise, demonstrating that [[mammoths]] are a now-extinct species of elephant, and that several other fossil species correspond to no living ones.

While extinction is usually the result of a species' chronic failure to reproduce, it should be noted that a species may also be reduced to a population of zero when, due to gradual accumulation of mutations over time, the species' current offspring can no longer be recognized as belonging to the ancestral species.

Extinction can also occur due to abiotic factors, e.g., extraterrestrial causation, volcanism, etc.

See [[Mass extinction]]

Necromanis

Admin — Fri, 18 Aug 2006 02:50:39 GMT

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<div style="float:right;">
<table border="1" cellspacing="0" cellpadding="2">
<tr><th bgcolor="#CCCCCC">'''[[Mammalia]]'''</th></tr>
<tr><td>
*[[Domain]]: [[Eukarya]]
*[[Kingdom]]: [[Animalia]]
*[[Phylum]]: [[Chordata]]
*[[Subphylum]]: [[Vertebrata]]
*[[Infraphylum]]: [[Gnathostomata]]
*[[Class]]: '''[[Mammalia]]'''
</td></tr>
<tr><td>
'''Order:'''
*[[Pholidota]] <br />
</td></tr>
<tr><td>
'''Family:'''
*[[Manidae]]
</td></tr>
<tr><td>
'''Genus:'''
*'''''Necromanis'''''[[extinction|†]]
</td></tr>
<tr><td>
'''Species:'''
*'''''N. franconica''''' (type species)†<br />
*'''''N. quercyi'''''†<br />
*'''''N. edwardsi'''''†<br />
<tr><td>
Fossil_range:
[[Miocene]]
</td></tr>
</table>
</div>

'''''Necromanis''''' is an [[extinct]] [[genus]] of [[pangolin]]s from the [[Miocene]] of France. ''Necromanis'' is descended from the [[Eocene]] pangolins of genus ''[[Eomanis]]''.

From what can be derived from the fossil specimens, the species of ''Necromanis'' were, for the most part, identical to modern ''Manis'' pangolins in anatomy, diet, and behavior.

There are at least three [[species]] recognized.

== Links ==

Reconstruction of ''N. fraconica'' [http://www.deviantart.com/deviation/37240730/]

[[Category:Prehistoric mammals]]
[[Category:Pangolins]]

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128.6.51.12 — Tue, 04 Apr 2006 22:50:39 GMT

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Admin — Sun, 26 Feb 2006 14:56:21 GMT

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128.6.51.12 — Mon, 09 Jan 2006 16:48:03 GMT

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http://tn1-3.deviantart.com/fs10/150/i/2006/135/6/a/Mene_rhombea_by_avancna.jpg