Thursday, April 05, 2012

Streamlining the site

This site doesn't get updated at all anymore, but there are still a reasonable number of visitors. I'm streamlining the site to focus more on the science-related posts, regardless of whether or not I still believe the things I said back in 2005 or whatever.

Shorter off-the-cuff posts will be removed. I'll try to pare it down to just the longer posts with some sort of substance.

EDIT: This will be a slow process as Blogger seems to lack facilities for doing this efficiently.

NOTE: 31/10/2012: Streamlining continues...

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Wednesday, February 10, 2010

Rotting the tree of life

There are good papers, great papers, and those clever little papers that make you say "I wish I'd thought of that!". Before I get to that, a little preamble:

Taphonomy is the branch of research that is interested in describing what happens to an organism between dying and ending up as a fossil (or even why it won't end up as a fossil). A lot can happen to an organism in that period of time, as the earth is a dynamic spheroid. The older a fossil, the more possible disturbances it can experience. Taphonomy can tell us a lot about the environment an organism was deposited in and it can provide important controls on the inferences we make about the environment we think a fossil organism once lived in. But taphonomy is also an important consideration in considering what an organism is. That is, the 'life' of a fossil after death, might have a profound impact on how we place that fossil in the tree of life.

Enter the experiments of Rob Sansom and colleague's experiments on lamprey larvae and the title organism of this blog, reported in this week's issue of Nature. Sansom et al. wanted to examine what happens to 'primitive' vertebrates that lack hard, mineralized tissues, the type of tissues that normally fossilize. I say "normally", because there are some 'abnormal' cases in which soft-bodied creatures with no bones, teeth, or hard cuticles actually form as fossils. Some such fossils have played an important role in understanding the timing and early origin of vertebrate animals.

For instance, this species known as Yunnanozoon (Chen et al. 1999) from the Cambrian of China. It represents one of the earliest known vertebrates or vertebrate-like forms.

Yunnanozoon is remarkably well preserved, but other Cambrian chordates can be even more incomplete. The problem with such fossils is that they're difficult to interpret because they're squished, and they're made of soft parts. We have no idea how much they might have decayed, apart from the fact that they seem to be an exception to the rule that soft parts don't fossilize. This usually implies some sort of exceptional conditions favouring preservation, but doesn't necessarily rule out decay or other types of disruption.

Sansom et al. let larval lamprey and lancelets rot in buckets of sea water and recorded the progress of the decay over the period of several months.

The impressive and startling results of watching fish decay are below the fold:

As the animals rotted away, Sansom et al. recorded details of their anatomy. Not just general features, but the types of characters that would be used to score an organism for a phylogenetic analysis. These include classically important features, like the gill filaments, cartilages of the gill arches, the type of heart, the shape of the body muscles, the dorsal rod known as a notochord, and so on. These are characters that have normally played a significant role in establishing the relationships of vertebrates and their nearest non-vertebrate relatives, such as the lancelet.

What this figure shows is the length of time each character survived as the animal rotted. What's striking is that the characters that lasted longer all tend to be characters that we consider phylogenetically more primitive. Characters such as a notochord and segmented axial musculature are all considered to be primitive features shared by the last common ancestor of lancelets and lamprey. On the other hand, features such as eyes, or a chambered heart are more derived features found in modern vertebrates.

This figure shows nicely how the decay features plot out in phylogenetic history. If you go back to figure above, there is a graph showing the relationship between phylogenetic rank and decay stage.

What we see is that the level of decay would lead one to think that the taxon was signicantly more distantly related to the vertebrates, much like the early chordates we find in the Cambrian.

Not only do these results provide a caution against how we interpret soft-bodied Cambrian chordates, but it illustrates a framework for studying the phylogenetic effects of decay. As decay is studied across a wider phylogenetic scope, the more we can determine about the generality of these types of patterns. That will have a profound effect on how we study and interpret the exceptional cases of soft-tissue preservation in fossils.

Chen, Y.-J., Huang, D.-Y., and Li, C.-W. 1999. An early Cambrian craniate-like chordate. Nature 402:518-522 link

Sansom, R.S., Gabbott, S.E., and Purnell. M.A.2010. Non-random decay of chordate characters causes bias in fossil interpretation. Nature 463:797-800 link

Briggs, D.E.G. 2010. Palaeontology: Decay distorts ancestry. Nature 463:741-743 link

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Thursday, January 07, 2010

Early tetrapod footprints from Poland: what changes and what doesn't.

A few years ago, I wrote a post about prediction in the historical sciences. This post came in anticipation of the publication of Tiktaalik roseae, a remarkably well-preserved fossil of an aquatic animal very closely related to the first tetrapods. I offered this figure to illustrate the position of a gap in the fossil record as a predicate for how/where we might look for fossils that would fit within those 'gaps' in phylogeny.

Yesterday, this picture got a lot more complicated. With the publication of tetrapod footprints some 18 million years in advance of this gap by Nied┼║wiedzki et al., the nice congruence between the node order of the tree and stratigraphy no longer appears so nice.

Here's a picture of the trackways (click for the full view):

[More below the fold]

This news has already broken, and I'm usually the last person to blog about it these days. Naturally, Ed Young has a good take on it. As noted by Jenny Clack in Ed's piece, the individual footprints are more convincing than the trackways in terms of their identity. Here's one from the supplementary information file (which is free to access).

[Picture deleted: I made a mistake, reading too fast and posted an image of Triassic temnospondyl footprints! A better image is this digital surface rendering from the main paper posted below]

But how "bad" is the record now that we know this? Well, bear in mind that lungfishes and tetrapods are considered (at least by the phylogenies in question) to be sister groups. That is, they split from their last common ancestor at exactly the same time. The earliest 'true' lungfishes (i.e. lungfishes with toothplates, and upper jaws fused to the braincase, etc.) are Emsian in age, roughly the same age as these new footprints. Recognizable close relatives of lungfishes, such as Diabolepis, Youngolepis and Powichthys, however, are considerably older. Do, we can set a minimum age for the origin of the tetrapod stem lineage down in very earliest part of the Devonian even if we do not have the fossils.

So, not surprisingly, the record is pretty bad. It's certainly 'gappy'. But we should not be too surprised that tetrapods emerged long before the time when we find their first actual fossils.

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Wednesday, January 06, 2010

MAJOR news about early tetrapods today.

Okay, I've exaggerated by putting MAJOR in all-caps, but here it is:

Tetrapod trackways from the early Middle Devonian period of Poland

The fossil record of the earliest tetrapods (vertebrates with limbs rather than paired fins) consists of body fossils and trackways. The earliest body fossils of tetrapods date to the Late Devonian period (late Frasnian stage) and are preceded by transitional elpistostegids such as Panderichthys and Tiktaalik that still have paired fins. Claims of tetrapod trackways predating these body fossils have remained controversial with regard to both age and the identity of the track makers. Here we present well-preserved and securely dated tetrapod tracks from Polish marine tidal flat sediments of early Middle Devonian (Eifelian stage) age that are approximately 18 million years older than the earliest tetrapod body fossils and 10 million years earlier than the oldest elpistostegids. They force a radical reassessment of the timing, ecology and environmental setting of the fish–tetrapod transition, as well as the completeness of the body fossil record.

I'll update with a detailed explanation soon.
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Thursday, October 22, 2009

What's been going on? Some academic musings.

So, what's been happening in the past few days (weeks?) since I last posted? Well, autumn is setting in here, so it's not like I'm spending a lot of time outside right now. I've been focused pretty much on a few things: writing a manuscript, updating a dataset, writing a job application, and learning some programming skills.

One of the nice things about being a postdoc is the flexibility of your time. It is an important period in the life of a researcher where you not only apply those skills you already learned towards being productive, but you have the opportunity to learn new ones. I'm picking up where I left off early in my postgraduate education, learning new tools and tricks for the software environment R. This really is an indispensable tool for biologists, or anyone who applies statistics. I would hope that in the near future, R will become an integral part of undergraduate biology curricula. It combines the ability to analyze data with a programming environment.

As much fun as being a postdoc is, I really want a permanent job—a good one, with lots of interaction with enthusiastic and creative students. Being a postdoc can be limiting, too. There are lots of small cash funds for Ph.D. research projects from various scientific societies, institutions, or funding agencies. I've had a lot of success with these as a Ph.D. student, and I really think they are important in helping students b. On the other hand, faculty tend to operating grants: a fund that supports their research throughout the year or several years. Somewhere in the middle is the postdoc, who has to rely either on his host's grant (allusions to parasitism here may or may not be intended), or the very few small (and therefore competitive) external sources. Thankfully, my current project can make use of a lot of published data, as well as data existing within our collections at this museum. However, I certainly feel the need to grow and develop something much larger and sustained.
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Friday, October 02, 2009

On the use of the stem group concept.

The notion of a 'stem group' is indespensible for a palaeontologist. Much used and abused, it is simply not possible to talk about the relationships of fossils to modern life without the use of the crown and stem group concepts. The crown group is a clade which is delimited by its living (extant) members. The stem group comprises those fossils which are closer to the crown group than to any other extant clade, but do not fall within the crown group. As a result, the stem group is paraphyletic, and thus not really a group at all. It is perhaps more useful to talk about a 'stem assemblage' than a 'stem group'.

While at this year's SVP (and at previous meetings), I was struck by some of the terminological abuses of the term 'stem group'. In various instances, it was used either to refer to the nearest sister taxa of an extinct clade, or it appealed to essentialist nomenclature. I comment further on these below the fold.

'Stem groups' of extinct clades:
When a clade is extinct is has neither a crown nor a stem. If we did not distinguish between extant and extinct clades when applying the crown group concept, then crown groups could be arbitrarily small and stem groups arbitrarily deep. Because nodes in a cladogram are rotatable, we could use any taxon (fossil or living) to be a stem taxon.

We already have a set of terms for this: sister group relationships. This is also what the crown group concept conveys. However, it's purpose is to convey the relationship of fossils to a particular living group. When we talk about fossil or extant clades, we can talk about the nearest sister taxa. When talking about fossils in relation to an extant clade, only then do we apply the crown group concept.

Arbitrarily deep stem groups
One abstract title at this year's meeting struck me, because it referred to the fossil Morganucodon as the earliest stem-mammal. This taxon is almost certainly a stem-mammal. Is it the earliest? Take a look at this figure (from Angielczyk, 2009) (you may have to click on it to see the full image):

Notice the placement of the node "Mammalia". It's a full two internodes displaced from the node that subtends the extant mammalian branches: monotremes, marsupials, and placentals. You'll also notice that the Triassic fossil Morganucodon is the nearest fossil sister group of the three extant mammal lineages. In other words, it's the nearest sister taxon (in this tree) of the mammalian crown group (which, strangely, is unnamed!).

This is a peculiar trait among palaeontologists: give the standard crown group name (i.e Mammalia, Aves, etc.) to some arbitrary node within the group's stem. For instance, Aves (birds) is often considered to be the clade delimited by the last common ancestor of all extant birds + Archaeopteryx.

What you should also notice in the diagram above is that the root node of this tree is called "Synapsida". This means it entire run of taxa in this tree from the Synapsida node up to (but not including) the unnamed mammalian crown group nodes are part of the mammalian stem assemblage. Yes, Dimetrodon is a stem mammal, as well as Morganucodon. This means that a host of Permian (and potentially earlier) forms are also stem mammals, leaving Morganucodon appearing fairly late in the game.

The utility of the stem/crown group concept comes in placing fossils in relation to living groups. When we do this, fossils can be used to build up knowledge of the sequence of acquisition of homologies where living forms provide no clues. Fossils can, in turn, help test hypotheses of homology by providing unexpected combinations of characters, as well as precluding or 'predicting' certain character combinations. It is important that these concepts are applied in the correct fashion, or else they (and fossils) will lose their meaning.

Angielczyk, K. 2009. Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution. Evolution: Education & Outreach 2:257–271.

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Wednesday, September 16, 2009

That snake with a leg...?

There's been a report of a snake with a legs and toes in the media recently. The blogosphere has some interesting comments on it, too. Most notably, there is skepticism. Take a look at our snake in question here:

In a comment on Pharyngula, Jerry Coyne notes:
I suspect that this snake ingested a lizard, and that the lizard's limb simply burst through the side of the snake. I may be wrong, and I hope so, because this is great evidence for evolution.

Some graphic images below the fold illustrate why this is not unreasonable speculation.

Snakes sometimes consider their prey choices poorly. Here's a snake with legs and two tails:

(Hat tip to Febble)

Oops! I sort of skipped the first comment at Pharyngula. This commenter noted first that it was probably something the snake ate. Moreover, they note a fact I forgot to mention in my haste: the limb is quite far from where we'd expect the hindlimb to be, if one were to show up. It would be much closer to the tail, not at mid-length of the body. It should be at approximately the same level as the cloaca. There's the unlikely case that it's an atavistic forelimb however, which would raise the issue of where a snake's neck begins or ends.
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Rampant paraphyly on Wikipedia

I've just been having a look at some of the Wikipedia pages about certain bony fish groups, particularly Sarcopterygii and Rhipidistia. These need some serious fixing. There's a lot of stuff out there about 'ancestral groups'. That is to say, describing a group as the ancestor of another group.

"Tetrapods — four legged[sic] vertebrates were the terapodomorphs'[sic] descendants."

"Rhipidistia is now understood to be an ancestr for the whole of Tetrapoda."

The notion that a group is 'ancestral' is a bit misleading, especially if we accept that groups (i.e. clades) are actually the descendents of a single common ancestor. That's not really the problem, though.

Let's look at each of the quotations below the fold.

The first one claims that tetrapods descended from tetrapodomorphs. The actual meaning of 'Tetrapodomorpha' is the tetrapod total group (Ahlberg, 1991). By definition, this group includes all tetrapods, and any and all fossil taxa that are more closely related to tetrapods than to any other extant group (in this case, probably lungfishes: the Dipnomorpha). Tetrapods are a subset of Tetrapodomorpha, not descendents of them.

The second quotation is similar. Ahlberg (1991) also re-defined 'Rhipidistia' cladistically as the Dipnomorpha + Tetrapodomorpha. In this sense, Rhipidistia is monophyletic. However, the Rhipidistia was a pre-cladistic grouping meant to encompass porolepiforms and 'osteolepiforms'. Porolepiforms (probably a real clade) and the 'osteolepiforms' (not a real clade) represent an assemblage of lobe-finned fishes that would look quite similar to an 'untrained observer'. This similarity is mostly just shared primitiveness. That is, it does not unite them to the exclusion of other taxa (namely lungfishes in the case of porolepiforms; and tetrapods in teh case of 'osteolepiforms').

Figure 1. Some 'rhipidistian fishes'. Top: Holoptychius. Bottom: Eusthenopteron along with an illustration of its pelvic and pectoral fin endoskeletons.

What is significant about 'rhipidistians' in the classical sense (i.e. before Ahlberg's 1991 paper) is that they lack synapomorphies or homologies. They have to be defined on the basis of a set of characters and character absences, implicit and explicit, that is hand picked to exclude other groups. They are 'fishes', meaning they have fins (not digits) with lepidotricia, bony dermal rays. But these are also found in the early tetrapods Ichthyostega and Acanthostega. However, these latter taxa lack an intracranial joint, a division of the front part of the braincase from the back part that contains the ear capsules. Coelacanths also have this division, but they are not rhipidistians. However, coelacanths lack the dermal skull bone characters, such as a maxilla, that are found in 'rhipdidistians' such as Eustheonopteron and Holoptychius showing in Figure 1., above.

As you can see, it quickly becomes obvious how the defining characters are arbitrary, in some sense. They are picked to justify a group of taxa that share some overall similarity. It does not reflect an attempt to discover the hierarchical relationships among characters. This latter process is the discovery of homology: the characters that unite monophyletic groups. It is in this way that real evolutionary relationships are discovered; not through the nomination of "ancestral groups".

Ahlberg, P.E. 1991. A re-examination of sarcopterygian interrelationships, with special reference to the Porolepiformes. Zoological Journal of the Linnean Society 103: 241-287.

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Brief update

This week, I've been working on my presentation for this year's Society of Vertebrate Paleontology meeting in Bristol. The conference is next week and I've got my own talk, plus contributions to another talk and a poster. Unfortunately, I can't post details of my talk until after the meeting, because the abstract is embargoed. This year looks somewhat promising. There was a record number of abstract submissions, so a lot of the papers that focused on strict descriptive alpha taxonomy did not make the cut. I'm quite happy with that, to be honest. I don't really need to travel a long way to see talks on descriptions of new animals when, in a few months, I can read and use the paper. I'm a bit more interested in seeing progress on sorting out the relationships of problematic taxa, and maybe learning about novel uses for fossils. There's some promising stuff this year.

Spent part of last week on holiday in Prague. One of the great things about living in Europe is the short distance to all these great places.

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