The Extant Phylogenetic Bracket

This is a topic I have been long meaning to cover on the musings as it is a pretty core part of modern palaeontology but exactly the kind of thing that never makes it from the research papers into newspapers of documentaries and thus I suspect many will not have even heard of it as a concept, let alone its application. As ever, this will be a reduced and simplified version so for those who do know better, please forgive the glossing over of details, but essentially the EPB runs as follows – if you have an unknown characteristic in an extinct species, but there are living relatives of that animal that phyologenetically are both more basal and more derived, then you can fairly safely conclude (with caveats, inevitably) that this was also a feature of your extinct organism.

To put this into practical perspective with an archosaurian example, crocodiles are related to dinosaurs but a phylogentically basal to them, and birds derived from dinosaurs and are thus more derived than them. However, while the non-avian dinosaurs are extinct, both crocs and birds are still alive today. Thus characteristics shared by birds and crocs were likely shared by dinosaurs. For example, even without the extensive evidence for dinosaur nests, if we had never found any eggs it would still have been quite a safe assumption that dinosaurs laid eggs since both crocodiles and birds do.

This as a concept obviously has enormous benefits as we can use it to try and reconstruct missing data from direct observation of living animals. We don’t have dinosaur muscles to work from (although muscle scars on bones give us a good idea) but with guidance from the EPB we can be much more confident in our restorations. Furthermore we can also use it to prune out bad ideas (or at least challenge them) if you want to argue that all dinosaurs had no lungs (to take an extreme example!) without any physical evidence it should be pretty obvious that since both birds and crocs have this (and yes, quite a few other things too), it’s going to be a very odd to assert that they are missing in dinosaurs.

There are of course problems with the method and I’ll elaborate on just a couple since in day-to-day archosaur work these are not huge issues normally (i.e. for the average person reading a dinosaur story, they don’t have much impact but are worth watching out for). First off there are obviously huge gaps of time and morphology going on between say the most basal theropods and living birds.

Similarly, one is also effectively trying to use these animals to reconstruct the condition of characteristics in dinosaurs, yet we know some things have changed which make these animals unsuitable. All living crocodiles are rather sprawling in posture, but not all of the extinct ones were and it’s unclear exactly what posture was adopted by animals around the time that crocs separated from the lineage that would become dinosaurs. As such just using them freely as a proxy is not always a good idea. In a similar vein, there are some things for which the EPB is wholly unsuited. For example if you want to (as I do) try and reconstruct the predatory behaviour of theropods the EPB is not a great way to go, modern crocs are largely specialised ambush or aquatic predators and most birds are not predatory (and those that are largely hunt in the air and the few that do not are rather derived and are certainly not basal taxa), so given the huge specialisations of these animals to their respective hunting methods it’s unlikely their behavioural adaptations can tell us much about an Allosaurus trying to take down a sauropod.

There are also times where the EPB is not so much problematic, as just not very helpful. Endothermy (or warm bloodedness to be less technical and less accurate) is an obvious example. Birds are endotherms, crocs are not – so how do you interpret dinosaurs? Were they endotherms or not, or only some and if so, which? Are the basal ones more likely to be ectotherms since they are closer to crocs and derived ones endotherms since they are closer to birds? Or were even basal birds ectotherms? And what about the orniothischians, they separated out from the saurischian (and ultimately bird) lineage over 50 million years before Archaeopteryx appeared so are they the same or different? Of a different note but equally an issue are things like pterosaurs – if these are indeed archosaurs then the EPB for them would be crocodiles and birds, though if they are actually more basal archosauromorphs then the EPB would be lizards and crocs – a very different consideration.

That in essence is the EPB, we can use living relatives to help reconstruct the missing in fossil data. These are inferences, not absolutes and you need to combine these suggestions with other information (is there a muscle scar present for where you think one should be, is that gait possible given the trackways we see, has this already changed in crocs making this inference problematic etc.) to come to a conclusion. It can be incredibly powerful and has been very influential in vertebrate palaeontology by providing a firm and reasoned foundation for making inferences about extinct animals based on real, observable evidence (living creatures).

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20 Responses to “The Extant Phylogenetic Bracket”


  1. 1 Brian 06/12/2009 at 7:44 pm

    I find your ‘ratites are the living birds most closely related to dinosaurs and gharials the living crocodilians closest to dinosaurs’ rather odd. Isn’t any living bird or crocodilian just as closely related to, say, *Triceratops* or *Herrerasaurus* as the next?

    • 2 David Hone 06/12/2009 at 7:59 pm

      Well no not really. At least not in a phylogenetic sense, though yes in a temporal sense. In other words, yes, the lineage thatled to Deinonychus say separated from birds in about the Middle Jurassic and thus all living birds are around 130 million years ‘away’ from that bird-dromaeosaur split. However, phylogenetically there are numerous lineages of birds (raptors, passerines, galliforms etc.) that have branched off from the ‘main’ bird lineage at various times. Some of these happened before others (obviously, the birds didn’t diversify into a whole bunch of very disparate things simulataneously).

      Of course soem (many even) went extinct and others survived to the presetn day. Of those that *did* make it, the ratites where the the earliest to branch off (i.e. are phylogenetically and by extent temporally the most basal). Thus, although they have had a good few million (perhaps tens of millions, I’d have to check) of years separating them from the dinosaurs, we would expect them to have undergone fewer changes in their biology in that time and thus be closer to the dinosaurs that other bird groups.

      In essence we are making the best of a bad job – of course there’s a huge gap between all modern birds and the dinosaurs, but less of one for ratites than others and thus they should be our preferred choice.

  2. 3 Mickey Mortimer 07/12/2009 at 1:47 pm

    Er, I don’t think that’s quite right. It’s not like ratites stopped evolving when Paleognathae split from Neognathae after all. The only reason we think of paleognaths as the basal group is because there are less of them than neognaths. There should have been about as many generations (and thus chance for mutations) from the first avian to an ostrich as there is from that avian to a sparrow. While sparrows modified their palatal complex, enlarged their hallux, etc., ostriches lost two of their toes, fused their pubic symphysis, etc.. I don’t think there’s any rule that says the first taxon to branch from a clade resembles the clade’s ancestor more than any other _contemporaneous_ member of that clade. Other obvious examples are a frog and iguana, a marsupial mole and a shrew, an ankylosaur and a pachycephalosaur, etc.. As paleontologists, we probably overlook this easily because we’re used to thinking of basal taxa that _lived earlier_ than derived taxa, so did indeed accumulate less mutations.

    • 4 David Hone 07/12/2009 at 2:21 pm

      “It’s not like ratites stopped evolving when Paleognathae split from Neognathae after all”

      Well that’s not quite what I said. Still, if you look at the phylogenetics of the situation, it much be largely true. Yes, both sparrows and ostriches have had equal times to deviate from the point at which their respective lineages split from the stem avian one, but cladistics puts the ratites (OK, yes perhaps better paleognaths, depeingon quite who you believe) them basal to say passerines *because* they have more characters in common with earlier clades than do passerines. Though yes, there is a difference between ratites in general and extant ratites. But even then, most modern bird phylogeneis are based almost entirely on non-skeletal characteristics and the palaeognathus still come out as being basal which implies that more than just the characteristcs of ancient, extinct, basal ratities are closer to the ancestral state and that extant ones have retained many of these characters.

      “I don’t think there’s any rule that says the first taxon to branch from a clade resembles the clade’s ancestor more than any other _contemporaneous_ member of that clade.”

      Or I, but it still seems to be employed that way.

  3. 5 Mickey Mortimer 08/12/2009 at 5:06 am

    That’s an illusion of the size of each clade. We have the habit of arranging cladograms with the smallest subclade of each clade branching off on the left, giving the illusion of a “spine of progress” that leads to the largest group (an exception is when a cladogram contains humans in one of its branches, so we think of that group as being most derived). Imagine you have a molecular or morphological phylogeny with equal amounts of paleognaths and neognaths. You’d get a cladogram with two equal-sized bushes emerging from the avian common ancestor. There would be no way to say which group is basal. Sure, paleognaths branch off before passerines in that tree, but neognaths branch off before struthioniforms.

    A nice example are the modern monotremes. Because they’re such a small group, they appear to be basal in any mammal cladogram. But really, platypi and echidnas are very modified compared to opossums, shrews, tenrecs, tree shrews, etc.. We only think of them as basal because they lack characters (viviparity, etc.) the large (and human-containing) mammal clade has. We could just as easily say eutherians are the basal ones, since we lack poison spurs, etc..

    • 6 David Hone 08/12/2009 at 9:18 am

      That’s not quite true though, since we have to consider both the phylogenetic hypothesis at hand and the temporal information. Sure, you could say that tyrannosaurs are no more basal than are birds since tyrannosaurs are the sister-taxon to all the more derived coelurosaurs etc. but then tyrannosaurs *did* diverge from the stem before the dromaeosaurs or birds or passerines etc. And we think this is true because they appear earlier in the fossil record and the basal members have characters that are more in common with what we understand the ancestral states to look like / more basal / earlier taxa to the tyrannosaurs that with later coleurosaurs / birds etc.

  4. 7 Mickey Mortimer 08/12/2009 at 10:57 am

    Yes, tyrannosauroids branched off before avialans, but Tyrannosauroidea and Avialae are not equal clades. Avialae is only a small part of the (Passer<-Tyrannosaurus) clade that contains most coelurosaurs. You could turn it all around by instead using only a small part of Tyrannosauroidea for your comparison. For instance,

    "but then maniraptoriforms *did* diverge from the stem before the tyrannosaurines or albertosaurines etc. And we think this is true because they appear earlier in the fossil record and the basal members have characters that are more in common with what we understand the ancestral states to look like / more basal / earlier taxa to the maniraptoriforms that with later tyrannosaurines etc."

    It's the same issue as when comparing paleognaths to passerines. You can turn it all around by comparing struthionids to neognaths instead. To tie it back to the original topic, for reconstructing the ancestral avian condition you'd be just as well choosing a basal neognath like Gallinuloides as you would a basal paleognath like Lithornis. And both are worse than an ostrich or a sparrow. And for the ancestral coelurosaurian condition, Dilong and Ornitholestes are both about equally good choices, both much better than Tyrannosaurus or Ichthyornis. But I don't think there's an objective way to say whether the ostrich or sparrow, or Tyrannosaurus or Ichthyornis, is more similar to the common ancestor for each pair.

    • 8 David Hone 08/12/2009 at 1:42 pm

      Just as a warning to readers struggling through this (and Mickey and Mike) this is getting deep and complex and I really don’t want to dig into the depths of it too much. Also I got these last two comments together and actually wrote this reply after the one below to Mike’s comments, though with my answer here in mind so it should all make sense if you read it together but will likely be a mess if each is read in isolation. Furthermore, discussions of tree topologies and tracings of characters etc. are perhaps *the* classic situation of when you need to be in a pub with a pint in hand and more importantly some paper and pens with which to scribble down trees. Discussions can rapidly go past people when each of you has a different tree in your head or different transformations on branches / at nodes and everyone gets frustrated that they can’t ‘see’ your tree (and I’m worried that I’m trying myself up in knots with several concurrent and overlapping points being made by different people). So! bearing all that in mind….

      I think part of the problem here is that we are seeing clades / branches in different ways. Yes of course brahces can be rotated around nodes such that at one level tyrannosaurs are equivalent to all other theropods (inc. birds) but at another level they are not showing far less morphological diversity (inevitably) and so while I take your point that Dilong would be better than Tyrannosaurus I think you could say that, derived though it is, the latter would be be a better choice than say a sparrow (though of course here we have moved from extant into extinct brackets or even combinations of the two – i.e this is a more general point about clade / positional interpretation and character evolution than the EPB).

      As I mention above (though also see below – man this is getting complex) while using a number of birds is not bad as such, I still think that there is a case for preferring paleognaths becuase of their position. Yes they are perhaps better thought of as sister-taxa to everhyting else rather than just ‘basal’, but the fact that thy do branch of from everything else and this position is recovered in analyses is because of their character states not because of it.

      The question then becomes (I hope) perhaps less of pf phylogenetic position (since we agree on where they go!) but whether or not that position (sister taxon to everything else) means they likely have more in common with ancestral forms that do other birds. I think so, (hence my position), though while I’m of course prepared to be wrong, if noting else, hopefully this has simplified the argument. I think so, since aside from that point, I think that actually the three of us are largely saying the same thing albeit in different ways.

      Right, I’m off for a lie down in a dark room to recover from all that.

  5. 9 Mike Keesey 08/12/2009 at 11:20 am

    I have to agree with Brian and Mickey here on the statement about gharials and ratites — that’s just an artifact of the fact that they are in less speciose clades.

    There’s also a problem in this statement: “crocodiles are related to dinosaurs but a phylogen[e]tically basal to them”. Crocodylia and Dinosauria are disjoint clades — one’s not basal to the other. (If anything, Crocodylia originated later than Dinosauria, if I’m not mistaken.) I think what you’re trying to say is better summed up this way: “Birds are living dinosaurs, and crocodylians are the closest living relatives of dinosaurs (including birds).”

    “Basal” is a term that gets abused a lot. It’s supposed to mean “toward the base” or “of the base”, not “outside the group most people are interested in”. Ostriches are not phylogentically closer to the base (i.e., the avian concestor) than sparrows are.

    • 10 David Hone 08/12/2009 at 1:20 pm

      Yes, in the strict sense Crocodilia is a late originating clade (rather than say the bigger Crocodyliformes etc.) but please remember that while I do strive for accuracy on here I am mostly trying to write for non-experts (though oddly enough it seems that almost my entire audience consists of experts) and a little trimming or twisting of specifics can help make things easier (thus I try to avoid talking about Dinosauria, vs Dinosauriformes vs Dinosauromorpha etc. etc.).

      I do also agree that one can (and indeed often should) use a range of extant taxa since yes, there obvious has been a great deal of change even in extant ratites perhaps compared to other clades and indeed this is widely adopted. However, I’d also say that it’s true that most people (from what I have read) have focused on using ratites / paleognaths as their primary source (though admittedly without justification, I think this is the case fort the reasons outlines above).

      And yes, following on from a discussion on another thread about the use of ‘basal’, I agree it is complex, but I would not necessarily say misused. As noted above (and this is not a discussion I want to get dragged into as it falls well outside of my interests and the scope for this blog, though I’d be interested to see some work on this) I think it’s a question of *how* you look at trees and while of course branches are freely rotate-able I think there is also a pattern of states and states and temporal issues that also count.

      • 11 Mike Keesey 09/12/2009 at 8:31 am

        I don’t think using “basal” in this way helps clear things up for the layman, though. For one thing, most laymen have never heard of that term. For another, as we’ve pointed out, it’s misleading to use it in this way. Compare my rewrite of the sentence above — which version is easier for laymen to grasp?

      • 12 David Hone 09/12/2009 at 8:50 am

        Well yes, few people do know the term, though of course I have covered things like that on here before. Though yes, as I said, I agree it needs cleaning up and I should be more careful about it.

  6. 13 David Marjanović 09/12/2009 at 9:48 pm

    I can’t see anything getting deep or complex here. It is not defensible to use only palaeognaths or only gharials; what must be used is the MRCA of Neornithes and the MRCA of Crocodylia, in other words, representatives of both Palaeo- and Neognathae, and of both *Gavialis gangeticus* and Brevirostres, because both sister-groups evolve on their own, and because there’s no way to predict which of them has undergone fewer changes in the character one happens to be interested in at the moment.

    “Basal” is a purely subjective term. It means “least closely related to the clade I’m interested in at the moment”, and therefore means completely different things on different trees, even when that means differently expanded trees that are compatible with each other! Let’s see if I can write trees here…

    –+–
    `–

    –+–
    ..`–

    • 14 David Hone 10/12/2009 at 9:11 am

      “what must be used is the MRCA of Neornithes and the MRCA of Crocodylia, in other words, representatives of both Palaeo- and Neognathae, and of both *Gavialis gangeticus* and Brevirostres,”

      Yes, sorry that is correct. My bad. I’ll adjust the text accordingly and this makes most of the rest of the debate above moot. It seems to be a combination of the two though in a sense in that I was arguing for ‘only palaeoganths’ and the others ‘any bird’. I agree the combination is correct.

  7. 15 David Marjanović 09/12/2009 at 9:57 pm

    In this tree, the mammals are the basalmost extant amniotes:

    ––+––Mammalia
    ….`––+––Testudines
    ……..`––+––Lepidosauria
    …………`––+––Aves
    …………….`––Crocodylia

    In this one, however, the sauropsids are:

    ––+––Sauropsida
    ….`––+––Monotremata
    ……..`––+––Placentalia
    …………`––+––Didelphidae
    …………….`––+––Australidelphia
    ………………..`––Caenolestidae

    Note that these trees don’t contradict each other.

    One more:

    ––+––Neognathae
    ….`––+––Struthio
    ……..`––+––Casuaridae
    …………|––Rheidae
    …………|––Dinornithidae
    …………|––*Apteryx*
    …………`–Tinamidae

    See? The neognaths are the basalmost extant birds, if I display the tree this way. They’re only one internode away from the base, while the tinamous are at least three internodes away.

  8. 16 David Marjanović 09/12/2009 at 9:58 pm

    Test:

    --+--
      `--
  9. 17 David Marjanović 09/12/2009 at 10:02 pm

    So the <pre> tag works, and I wouldn’t have needed the dots!

    Anyway: the take-home message is “never forget that ladderizing cladograms is an aesthetic convention and nothing else”.

    That in essence is the EPB, we can use living relatives to help reconstruct the missing in fossil data. These are inferences, not absolutes and you need to combine these suggestions with other information (is there a muscle scar present for where you think one should be, is that gait possible given the trackways we see, has this already changed in crocs making this inference problematic etc.) to come to a conclusion.

    Indeed. The EPB is an argument from parsimony; such arguments can still be falsified. Parsimony can only be used to discriminate between hypotheses that are equally compatible with the evidence.


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