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The geological time scale – eons, eras, periods and epochs.

The geological time scale has always fascinated, I think in part, because the duration of human history is such a minuscule fraction of the some 4 and half billion year history of the Earth, or indeed the history of life itself. The figure at the left illustrates this somewhat. It shows the geological time scale with different temporal divisions at increasingly finer scales from eons on the left through to epochs on the extreme right. The dates are approximate as there is some discussion over these. The Hadean is often not considered a formal eon nor is the division between the Archean and Hadean particularly precise. The Quaternary is divided up into Pleistocene and Holocene, the latter of which began approximately 12,000 years ago and is comprised of the thin rectangle above the Pleistocene in the temporal sequence of Epochs to the right of this figure. PH = Phanerozoic. CE = Cenozoic. This figure was modified from Gradstein et al. (2004) and from information contained on the British Geological Survey web site (click on the image to see a larger version).

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Giant feathered dinosaurs!!

But first an aside or two …

The last decade has borne witness to discovery of a spectacular array of feathered dinosaur fossils that have added to our understanding of origins and possible function of feathers, but have also generated some interesting questions about avian and dinosaur evolution.

It has been noted for a long time that birds are probably related in some way to dinosaurs. For example, in the 19th Century many, including luminaries like Thomas Henry Huxley, noted that the morphology of birds mirrored that of some dinosaurs.1  Dinosaurs are a monophyletic assemblage  (i.e. descended from a single common ancestor) that originated sometime in the Triassic, probably about 230 million years before present. Bird origins are suggested to be in the Triassic some time before the famous reptile-bird mosaic species, Archaeopteryx lithographica lived (approx. 150 million years before present). What was most beguiling about the best preserved Archaeopteryx fossils was the feathers, including the flight feathers with a narrow leading edge and wider trailing edge that implied flying ability. The point is that many consider Archaeopteryx to be the first bird with all avian diversity descended from it (a bit of an overstatement to be sure as this could be a side branch to the main avian lineage). Feathers, then, were a unifying attribute of birds, in the parlance of cladistics a synapomorphy or shared derived feature.

This view became less tenable with some spectacular discoveries from fossil beds in China in the 1990s, notably from the Yixian Formation in Liaoning in northeastern China, beginning with a small carnivorous dinosaur, Sinosauropteryx.

Many of these creatures appeared to be reasonably small (e.g. Sinosauropteryx was about a metre long). However in April 2012 Chinese researchers (Xu et al. 2012. A gigantic feathered dinosaur from the Lower Cretaceous of China. Nature 484, 92–95) revealed the largest feathered dinosaur ever, a relative of the fearsome Tyrannosaurus rex. Yutyrannus huali, while not as large as some of its cousins, attained lengths of some 9 metres and weights of over 1000 kg. Important to the discussion here it had long filamentous feathers.

What are the ramifications of such finds? Well certainly it challenges our conceptions of feather function and evolution. But perhaps more relevant to some of the major themes of this course, is that contemporaneous with the “avian” descendents of Archaeopteryx or something akin to it in the lower Cretaceous, were feathered dinosaurs. So it would seem that feathers are not synapomorphies of birds sensu stricto and that feathers are a feature shared with other dinosaur lineages.

Footnote:

1. While birds continue to enjoy the status of vertebrate Class, the reality is that they are indeed allied with dinosaurs and thus should be subsumed within the Class Reptilia (or more radically we should break apart this traditional category all together).

Woese is me.

When I took my introductory zoology class (Zoo 102) at the University of Guelph, back in the day, the diversity of Earth was represented by five Kingdoms: Monera (bacteria), Protista, Fungi, Plantae and Animalia. Below these were the familiar Phylum, Order, Family, Genus, and Species. The five kingdom system was actually a relatively recent development firest proposed by Robert Whittaker in 1969 (Whittaker, R.H. 1969. New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms. Science 163: 150–160 – a gently-modified version of the figure showing his 5-kingdom proposition is shown to the left) and indeed we seem to have progressed from a simple two kingdom system (plant and animal) to this five kingdom system from the time of Aristotle. These classifications reflected our knowledge of anatomy, physiology, and natural history of organisms.

Woese three domain phylogeny.

The advent of molecular techniques and particularly DNA sequencing revolutionized our ability to infer genealogical relationships among living species. In 1977 Carl Woese and George Fox published a paper that proposed a radically different tree of life with three major divisions that were to be called domains, and a division of the bacteria into the Archaebacteria (now Archaea) and Eubacteria (now often simply Bacteria): Woese, C.R. and G.E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences USA 74: 5088–5090. Their tree was based on 16S rDNA sequence, and really was one of the pioneering efforts leading the deluge of molecular phylogenies that we see today.

The first phylogenies

Although graphical representations of the evolutionary tree of life reflecting descent with modification as envisioned by Darwin and Wallace  necessarily postdate the development of evolutionary theory, the representation of nature in tree, network or some other hierarchical form is considerably older.

Drawing of the Great Chain of Being from Didacus Valades, Rhetorica Christiana (1579)

For example, order imparted by an omnipotent Christian deity was viewed as a hierarchy that encompassed all inanimate and living beings in the universe. Many drawings and paintings  of this so-called chain of being were made, including the wonderfully detailed one to the left by the Franciscan missionary Didacus Valades. Note that there are variations in the hierarchy although invariably there is a progression from mineral through plants and animals, to humans, angels and the supreme being at the top. Note too that this in no way represents a genealogy as we would think of it but is simply an artist’s rendering the universe created by a Christian god. By the late 18th Century the notion of the chain of being had fallen out of favour and we begin to see the emergence of trees and networks representing relationships among organisms (see Mark Ragan’s excellent and detailed article on this: Ragan. 2009. Trees and networks before and after Darwin. Biology Direct 4:43 doi:10.1186/1745-6150-4-43). Certainly in the late 1700s and early 1800s we see (or read about) elements of geneaological graphical representations in the work of such famous naturalists as Buffon (1707 – 1788) or Peter Simon Pallas (1741 – 1811).

Tree from Charles Darwin’s 1837 Notebook B.

Darwin is often credited with having provided us with the first true evolutionary tree. For example, in his 1837 Notebook B we see the diagram with explanation shown to the left here. The text associated with this figure reads:

“I think … case must be that one generation should have as many living as now. To do this and to have as many species in same genus (as is) requires extinction. Thus between A + B the immense gap of relation. C + B the finest gradation. B+D rather greater distinction. Thus genera would be formed. Bearing relation” (on the subsequent page) “to ancient types with several extinct forms.”

Lamarck’s tree (“tableau”) from Philosophie Zoologique published in 1809.

Some biologists demur and think that this is an oversight and slight to earlier thinkers. For example, Lamarck did indeed use the visual tree metaphor in his important book, Philosophie Zoologique (1809). However, its important to note that this diagram did not reflect a belief in the descent from a single common ancestor and thus some notion of all species have come from a single common ancestor. Rather, Lamarck’s tree summarizes his assertion that there are multiple independent origins of distinct trajectories that progress through different forms over time. Note that this tree is inverted from the tradition representations of trees.

Edward Hitchcock Paleontological Chart. Elementary Geology (1840)

American geologist Edward Hitchcock (1793-1864) included a fold-out chart in all but the last editions of his book Elementary Geology that shows multiple lineages of organisms. Hitchcock was a contemporary of Darwin but rejected evolution (and wrote an article “refuting” natural selection and atheistic evolution). Indeed Hitchcock asserted that God was the cause of organic change and that species weere created throughout the history of the world.

Haeckel’s tree of life published in Generelle Morphologie der Organismen (1866) with the three branches Plantae, Protista, Animalia.

One of the most famous trees ever published is by the renowned German zoologist, embryologist and philosopher, Ernst Haeckel. Haeckel was a fervent advocate of evolution and Darwinism but made huge contributions in his own right, even coining the term phylogeny! This early tree, published in Generelle Morphologie der Organismen’ (1866), seven short years after Darwin’s The Origin, shows three groups, plants, animals and protists, and a clear pattern of descent and ramifying lineages from common ancestors.

Haeckel published another tree (in 1874) that is one of my favourite figures in the history of publication in evolution (below). It once again has a quite literal tree underlying Haeckel’s representation of the genealogy of life. It also has humans at the pinnacle of the tree, because it was then (and often erroneously also today) thought that humans were the zenith of evolution.

Tree from Haeckel’s Anthropogenie oder Entwicklungsgeschichte des Menschen published in 1874.

Welcome!

Welcome to the 2012 of our Speciation & Macroevolution (BIOL440) Blog. I will (try to) use this to answer questions where I think that all class members might benefit or to post things that I find in my intellectual peregrinations.