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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A dubious honour...

It seems that my latest paper has been nominated for a dubious honour. That is, I've been singled out as having committed a cardinal sin of systematics: appeals to the reality or significance of paraphyletic groups.

This post was some time ago, and I have not had time to address it. And, I'll mostly not address it in detail here as it is not terribly worth it. Mostly, it is a kind of juvenile stunt, rather than a serious academic undertaking. However, since the authors Williams & Ebach (with whom I actually agree about much, even with respect to fossils), have ascribed to me ideas I do not actually subscribe to: namely a belief in paraphyletic groups, I'll post a little response here. In fact the point of Brazeau (2009) is to demonstrate that a group that is commonly appealed to in the literature, the "Acanthodii" is, in fact, a non-real group.

Most of Williams & Ebach's gripe with my paper is derived from either a BBC report or a non-specialist, non-technical, non-peer-reviewed interview piece in Nature. I have never used the term "missing link" in my article, nor did I use it in discussions with journalists. In fact, I try as much as possible to disabuse journalists of such popular misconceptions.

No, what is most surprising are the factual errors about my work that Williams and Ebach have made:

What any systemtist should do - re-classify the osteichthyans and chondrichthyans in light of this new evidence. Brazeau is naive to suggest that this discovery will "...not overturn a general consensus about gnathostome interrelationships" If Ptomacanthus is more closely related to chondrichthyans then bang goes the acanthodians. They need to be reclassified along with the chondrichthyans.

This contains several patently wrong statements. The monophyly of the Chondrichthyes and Osteichthyes remains after my analysis, as did their status as each other's extant sister group (which my analysis could hardly have contradicted apart from finding if their respective monophyly is not challenged). That general consensus is not changed by my result, so there is no need to re-classify either osteichthyans or chondrichthyans.

The acanthodians do not all get re-classified with chondrichthyans because, as my results showed, some "acanthodians" are members of the osteichthyan stem. So, we have to reclassify some as chondrichthyans and some as osteichthyans. Something I entirely agree with. Figure 3 of my paper clearly shows where I have placed Ptomacanthus in the group Chondrichthyes and a bunch of other "acanthodians" under Osteichthyes and highlighted in bright colours so that you could see that this is what I already did!

Figure caption: a, Strict consensus trees of the 2,904 shortest trees from the global analysis (left; treelength: 318 steps; consistency index: 0.44; retention index: 0.76; rescaled consistency index: 0.34) and the 30 most parsimonious trees from the endocranial data set (right; treelength: 83 steps; consistency index: 0.64; retention index: 0.85; rescaled consistency index: 0.54). b, Bothriolepis. c, Buchanosteus. d, Tetanopsyrus. e, Ptomacanthus. f, Cladodoides. g, Acanthodes. h, Mimia. Vertical arrow shows position of palatoquadrate-braincase articulation that corresponds to the basipterygoid articulation shown in Fig. 2. Double digits indicate percentage bootstrap support; single digits show Bremer decay indices (when greater than 1). Illustrations are modified from refs 5 and 18 (also see Supplementary Information).

Continuing, Williams & Ebach write:

But rather than saying the obvious, Brazeau descends into evolutionary explanation "... populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes". No it does not reveal anything other than that Ptomacanthus is a chondrichthyan and that acanthodians are paraphyletic!

I did state the obvious. It's in the figure. Look at it. I did not "descend into evolutionary explanation". The nested series of monophyletic groups that imply acanthodian paraphyly actually do provide sequences of character acquisition along the chondrichthyan and osteichthyan stem segments. As Williams & Ebach know well, each monophyletic group is supported by synapomorphies, and those nested groups synapomorphies are simply synonymous with what we call 'sequences of character acquisition'. This is how we make sense of fossils (or any other newly discovered taxon) and the implications fossils have, if any, on further hypotheses of synapomorphy (homology). If it's not the sequences of nested homologies that define monophyletic groups (the groups that matter) then what does? I'm perplexed as to why Williams & Ebach, of all people, would challenge this, since this seems to be their own view. I thought we had accepted and moved beyond disputing the idea that "evolution", when talking about fossils and the unrepeatable past, was only reducible to our best systematic hypotheses. In the quoted statement, that is all it is to me. It seems, perhaps, I wasn't careful enough and Williams & Ebach saw what they wanted to see in it. If so, then I'll take responsibility for my error, but note that my critics are playing fast and loose ascribing ideas to me which I have not explicitly stated.

Finally, they raise the following gripe:

"The study also suggests that some acanthodians are ancestors to all modern jawed vertebrates" (BBC Online, 19 January 2009).
This is false and misleading - the study shows quite the opposite.

Mostly, Williams & Ebach are just being pedantic and annoying, but this is infuriating bullshit. Those are not my words!

My words in the BBC article were:

"This figures in nicely with the emerging idea that acanthodians don't form a group of fishes that are all closely related to each other. Some of these fossils are primitive sharks while others are primitive bony fishes."

Even in the BBC article I state clearly that some are chondrichthyans (though I used the term "sharks" as a shorthand) and others are osteichthyans.

I believe my primary sin in that paper is to refer to terminal taxa as "basal". As I will cover here in another post, this is a problematic use of the term "basal", and one that is infectiously used amongst people who apply systematic methods. Maybe that could net me a Pewter Leprechaun, but if you nominate me on that basis you have to nominate just about anybody who talks about trees these days.

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Nice fossil, shame about the name...

Poor Darwinius, getting all this attention that it can never possibly live up to. Thankfully, a number of blogs out there are offering good summaries and the straight dope on the significance of the fossil. Just to add another fly in the ointment, I must sadly report that the name may become a problem due to it's being published in an online-only journal.

According to the International Code of Zoological Nomenclature:

Article 8.6 Works produced after 1999 by a method that does not employ printing on paper. For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself.

I see no evidence in the original paper that this condition has been met. Thus, under the rules of the ICZN, the name Darwinius may not be considered considered "published".
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The origin of whales and "missing links"

The remains of a very basal member of the whale lineage was described this week in Nature. Carl Zimmer's got the gist of it, and you can see pics at Pharyngula. In short, this new fossil material suggests that an aquatic mode of life evolved in the whale lineage at some considerably earlier stage than their predatory mode. The finding is interesting because it illuminates some of the earliest stages in whale evolution.

But at times like this, the term "missing link" likes to fly around in the popular media (but certainly not in Carl Zimmer's writing!). "Missing link" has a certain seductive quality in that it's a familiar concept and can be used to easily grab the interest of lay readership. But therein lies the problem: this does nothing to dispel the misleading notions carried with the term "missing link", and instead only perpetuates them.

As others have pointed out, I'm sure, evolution is not viewed as a chain or a ladder, and concepts that apply such linearity are definitely misleading. However, one could defend the term by nothing that, often times, a fossil might alter the grouping we make and thus "link" one group to another group -- something we didn't know before. But even if that is the case (and it rarely is), no single fossil holds a privileged place in illuminating the tree of life. We understand the importance of a fossil, such as Indohyus, because of what it shares in common (or doesn't share in common) with other fossil forms and other living taxa as well.

Indeed, these forms to which we often apply the label "missing link" do demonstrate structures and charicter combinations that are in some sense intermediate between groups as we recognise them, but that is somewhat misleading as well. For instance, Tiktaalik is widely regarded as a "fish-tetrapod intermediate". In a sense this is true, but it implies the reality of fish as distinct from tetrapods and that one animal somehow bridges this otherwise un-crossable boundary between types. Instead, we understand tetrapods as nested within the bony fishes, with the lobe-finned fishes sharing a special common grouping with them. Among these lobe-finned fishes exists a range of forms that are either more or less like tetrapods than others.

It is within this comparative context that transitions are understood. Sequences of character change are built up be recognizing the common features shared among groups in a hierarchy. It is thus a branching picture, rather than a straight chain with some missing links. The so-called "missing links" get portrayed as somehow essential to the whole story, the last piece of evidence required to prove some otherwise incomplete notion. In reality what they do is quite often to fit neatly into a picture that we already understand very well and serve instead to make the details much clearer.

In the case of Indohyus, it adds important new information in understanding the origin of whales, both from a phylogenetic perspective, but mostly from a functional and ecological perspective. It's not so much a "missing link" no longer missing, as a piece of the puzzle that helps us decide between competing solutions.
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Science as a process: placoderm muscles revisited

You might recall the discovery of fossil placoderms with preserved muscle tissue from earlier this year. I posted on it here, but noted that there was a problem with the analysis, but I didn't say exactly what. This week, the journal Biology Letters published a comment on this paper by a colleague and myself, along with the response from the authors of the original paper.

It's tempting to write a counter rebuttal here, but I'll just let you read the papers if you have access to them. The point is, this is how science works: we depend on other workers being willing and able to criticise our work when they think there is reason to do so. Because of this, science maintains its credibility and its integrity. A case example for your edification. Enjoy.
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Where the fossils are

Today I had a rare opportunity to see something that gets most palaentologists excited. First, a little introduction. If you're not very familiar with finding fossils, you'll first need to know that fossils are found in sedimentary rock: the type of rock that is formed by deposited sediments (ie. sand, mud, or chemical precipitates). However, as any palaeontologist or amateur fossil collector will recount, you can search through vast amounts of sedimentary rock without ever finding a fossil. One can sift through tons of rock in some places and not find a single scrap of bone, or shell, or leaf of plant. On the other hand, there are places where one cannot take two steps without walking on fossils.

Fossil preservation can be a very selective thing. Some environments are more conducive to finding fossils than others. This week, I am in Wales where I had the oppotunity to visit some Early Devonian fossil sites (about 410 million years old) that are worked by a local amateur palaeontologist. At one of his sites, I pointed out some geological structure that explains the high quality of the material collected there, and the promise for more fossils. If you're out looking for fossils, this is where you want to look.

Take a look at the image below. It shows a sequence of sedimentary rock layers and shows a classic type of structure known as a channel form. Notice the two different rock types. The upper rock is a coarse material, with heavy bedding. It's base is tapered to the left forming what's normally called a "lense" or a "lenticular bed". Below it is a noticably different-textured rock. It's heavily cracked and broken up. It is mudstone.



Here's the same image with some guides.



In the mudstone below the massively bedded (typically coarse-grained, but not greatly in this case) is where the fossils are. This is one of the best types of sequences for finding fossils and, in large part, is where articulated fossil animals are to be found. It should be no surprise then, that this friend of mine has actually recovered quite a few articulated fossils from there. He became quite excited when I remarked that this is the ideal type of sedimentary sequence in which to find articulated fossils. So, let's hope, some exciting discoveries will come from this site.

Why do fossils preserve so well in these sequences? What are they? These deposits form in a river channel, and the image below shows quite nicely the lenticular shape of the channel.



What you can see is that there is deposition of sediments in one direction that partly causes the channel to migrate (concomitant erosion of the opposite bank is the other cause). In such settings, bodies of animals are buried very rapidly. Moreover, they are quite prone to flooding and the rapid deposition of sediments (that is often why the bedding above is massive, as it was filled in rapidly, rather than in progressive layering).

This is where the fossils are.
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