Update on the Tree of Birds

| 31 Comments

The tree of birds just got a bit more accurate with a study published last October. We first covered the ever-evolving tree in 2014, when we posted about a study in Science magazine that used phylogenomics and thousands of genes sequenced from 48 bird species to produce what was thought to be the most accurate phylogenetic tree of birds to date (Jarvis et. al., 2014; see their tree here). Since then, a different team of scientists published a new phylogeny of birds that it claims is the most comprehensive (Prum et. al., 2015; see their tree below). So what is the difference between these two trees and how they were constructed, and which is more accurate?

The biggest difference between the methods of the two studies is the amount of data used. In the Jarvis et. al. study, the authors sequenced the whole genomes of 48 bird species and aligned thousands of genes. But Prum et. al. criticize this methodology as too “sparse” of a sampling; instead, they used 198 bird species and two crocodile species. Because sequencing that many whole genomes would be costly and time-consuming, Prum et. al. developed genetic markers that targeted highly conserved “anchor” regions of vertebrate genomes – regions did not change much over many years. Using this technology, the new tree of birds could be developed with only about 400 genetic regions instead of the thousands of genes in the previous study.

If there is a tradeoff between analyzing more genes or more species, is it more accurate to compare fewer genes between more species, or more genes between fewer species? One is not inherently better than the other, but rather, the way in which each is used relative to common issues in constructing a phylogenetic tree determines accuracy of the tree.

One such issue is distinguishing important genetic signals from noise. Genomic data contains a certain amount of “phylogenetic signal,” the informative genes that determine lineage. This signal must be differentiated from non-phylogenetic signal–genes that falsely suggest certain relationships. For example, non-phylogenetic signal can arise because species divergence events that happened close together in time are difficult to distinguish, or when species that diverged from a common ancestor a long time ago independently develop similar traits (called homoplasy). A 2011 article in PLOS Biology analyzed published phylogenetic trees and noted that merely adding more genes did not improve their accuracy because adding genes amplifies all signal (non-phylogenetic and phylogenetic alike).

nature15697-f1.jpg

Additionally, a phylogeny will only be accurate if the orthologous genes–those genes shared between species that were inherited from a common ancestor–are correctly identified. And that depends on the ability of software to distinguish orthologous genes from similar genetic sequences between species that code for genes that are not orthologous but rather are xenologous (transferred via horizontal gene transfer instead of inherited from the common ancestor) or paralogous (resulting from duplication of a gene). (Read more about orthologous, xenologous, and paralogous genes here.)

The model of evolution that researchers choose to use in their analysis can also greatly influence phylogeny accuracy. The PLOS article authors analyzed models and found some have difficulty detecting nucleotide substitutions, resulting in trees that are dominated by non-phylogenetic signal.

While analyzing a larger set of species won’t help when a model of evolution is inadequate or software has issues identifying orthologous genes, it can help with the issue of non-phylogenetic signal. Increasing the number of species in a study generally increases the phylogenetic signal-to-noise ratio, making it easier to detect substitutions that can lead to homoplasy, and also can improve accuracy by breaking up long branches. But the PLOS article states that it is not enough to just add more species; researchers should analyze more species that evolve slowly and comprise outgroups closely related to the group of interest.

Thus, including more species to construct a phylogenetic tree may be beneficial for tree accuracy, but only as long as methods for determining orthologous structures and modeling evolution are sufficient, and the chosen species are appropriate. Because Prum et. al. looked at more species while keeping these important factors in mind, and developed quality genetic markers that analyze enough genetic regions to determine phylogenetic relationships, they argue their tree is the most accurate yet. It is a convincing argument for the moment, but phylogenetic analysis can always be improved with better software and models, and the tree of birds (and the tree of life in general) will be constantly revised in the future as these methods improve.

The latest tree of birds presents a few differences from the Jarvis et. al. tree, some of which Prum et. al. suggest resulted from their larger sample size. One of the most striking differences is in the classification of the major bird groups. Jarvis et. al. propose that the initial divergence of a highly debated branch of birds, called Neoaves, resulted in two main groups: Columbea, containing birds like doves and flamingoes, and Passerea, containing a wide variety of species (parrots, falcons, penguins, and eagles, to name a few). But Prum et. al.’s tree instead splits Neoaves into five groups: Strisores (nightjars, hummingbirds, and frogmouths), Columbaves (cuckoos, pigeons, and sandgrouse), Gruiformes (cranes, coots, and rails), Aequorlitornithes (grebes, flamingoes, and shorebirds), and finally the very diverse Inopinaves (owls, vultures, and parrots). Also, Jarvis et. al. place pigeons, mesites, and sandgrouse in their own branch (Columbea) apart from the rest of Neoaves, while Prum et. al. rejected that for their five-group system. The Prum et. al. classification of Neoaves is likely the most accurate because they included more species that diverged close to speciation events (called nodes), which is especially important when the time between multiple nodes is short.

These findings bring up some new ideas about bird evolution and also support some old ones. For one, the new tree of birds developed by Prum et.al. supports a previous theory that swifts and hummingbirds, neither of which is nocturnal, evolved from a group of birds that had been nocturnal for 10 million years (Jarvis et. al. finds a similar relationship). Also, the new finding of the group consisting of waterbirds and shorebirds (Aequorlithornithes) suggests that the divergence of birds into different environments occurred with some level of restriction, known as evolutionary constraint. But as interesting and exciting as the new tree and its implications for bird evolution are, it is unlikely to be the final word on bird evolution. Other studies have also been published examining parts of the bird tree (like Rocha et. al. on the bird genus containing woodcreepers and Bell et. al. on an extinct group of Cretaceous birds). A new, more accurate complete tree of birds that supports or rejects these theories may be only another year away. Such is the nature of scientific research.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

31 Comments

So not only is the nested hierarchy robustly supported, but now we know exactly how accurate the topology is likely to be and how the degree of confidence can be increased even further in the future. How can anyone possibly doubt that evolution has produced the diverity of birds that we see today after seeing this evidence?

And for the die hard ark fantasy players, I count at least ten baramins, maybe more depending on how much “microevoluton” you are willing to accept.

Sadly, the paywall is high. I do think the Prum et al. approach is superior to the Jarvis et al. approach. With only 48 sequences it’s hard to get good alignments, much less good tree estimates. The Prum et al. tree seems characterized by an inordinate fondness for passerines, especially sub-oscines, but with 198 taxa much can be forgiven. Do I detect that it seems to fit Hackett et al. a little better than Jarvis et al. in cases of conflict?

Oh, good. We’ve conclusively proved that all extant birds are related back to a common ancestor.

Therefore, apparently, they are all just different kinds of birds.

stevaroni said:

Oh, good. We’ve conclusively proved that all extant birds are related back to a common ancestor.

Therefore, apparently, they are all just different kinds of birds.

All of which are descended from the common ancestor… the dove. Oh wait… uh… oops…

Remember that the Biblical word commonly translated “bird” includes bats.

Out of curiousity (and laziness), how close are these to the tree that Sibley and Ahlquist made by DNA hybridization methods in the 1980s, and which they published in a book in 1990?

At the time their methods were very unpopular with avian taxonomists (that is, with the people, not the birds). Sibley oversold their methods by arguing that they were based on the totality of the single-copy DNA, but of course they had some measurement error so they were not as good as a total genome sequence. Maybe more like having a few thousand bases of DNA.

Anyway, how did they do?

Joe Felsenstein said:

Out of curiousity (and laziness), how close are these to the tree that Sibley and Ahlquist made by DNA hybridization methods in the 1980s, and which they published in a book in 1990?

Not very close at all. A few of the more recent nodes are retained (for example, they got charadriiforms almost completely right, and even better if you accept their Fitch trees over their UPGMA trees). But almost all their deep nodes, and all the nodes connecting traditional orders, are garbage.

At the time their methods were very unpopular with avian taxonomists (that is, with the people, not the birds). Sibley oversold their methods by arguing that they were based on the totality of the single-copy DNA, but of course they had some measurement error so they were not as good as a total genome sequence. Maybe more like having a few thousand bases of DNA.

Anyway, how did they do?

In addition to the bit about charadriiforms, they had some notable successes that mostly aren’t displayed on Prum et al.’s tree, being lower-level things, mostly within passerines. For some of those successes, see Harshman J. Reweaving the Tapestry: What can we learn from Sibley and Ahlquist (1990)? Auk 1994; 111:377-388 and Harshman J. Classification and phylogeny of birds. In: Jamieson B.G.M. editor. Reproductive biology and phylogeny of birds. Enfield, NH, Science Publishers, Inc., 2007. p. 1-35.

S and A had four major methodological problems: 1: use of UPGMA almost exclusively (and sometimes just an impression of what UPGMA ought to do if it could be applied given objection 2); 2: an extremely sparse data matrix; 3: attempts to measure distances beyond the range of the method; 4: interpretation of ambiguous data/analyses in accordance with Charles Sibley’s personal prejudices. Given all that, it’s amazing they were as successful as they were.

stevaroni said:

Oh, good. We’ve conclusively proved that all extant birds are related back to a common ancestor.

Therefore, apparently, they are all just different kinds of birds.

No, as used by creationists, “kind” refers to holobaramin, the most inclusive group related by common descent. If all birds are related by common descent, there can be at most one kind of bird. I say “at most” because birds aren’t a kind; they’re only part of a kind, and if you do enough phylogenetic analysis you will find that the only kind is life: universal common descent.

The MODEL of evolution being used , the author says, changes the results. WELL the model OF evolution itself changes the results. This thread once again shows its all about comparing genes (in other matters morphology) and that without any other options for why birds/creatures did change from parent populations. I mean that genetic change is not only from drifting parent-offspring populations. if there were other mechanisms for genetic change it would not show up by mere comparison of genes. A creationist sees original kinds of birds and THEN variety can come from many mechanisms. So comparing and so concluding about common descent of bird groups or all into a original bird is rejectiong, without knowledge, other mechanisms. its a possible/probable waste of time comparing genes of birds for their origins. Its not accurate scientific method to rule out other options for genetic likeness. In fact the thread hinted about traits coming from independent populations and confusing things.

All that is shown here is a evolutionary presumption a comparitive presumption based on common descent. It doesn’t prove common descent but presumes it and then imagines it proves it. Not scientific accuracy here folks at a high level.

Robert Byers said:

Not scientific accuracy here folks at a high level.

Speaking of high levels, what are you smoking today, Booby?

Hey folks, Panda’s Thumb is having server problems. You can see new comments if you “Update”, but they vanish if you refresh the page. Things are broken. The Crew is working the problem.

Well Robert, perhaps you could explain the observed pattern for us. Exactly why is there a nested hierarchy? What processes do you think are responsible for producing this pattern? Exactly why is this pattern consistent between independent data sets? Exactly how many bird baramins are there? How do you know? If you are unable or unwilling to answer these questions, your mindless jibberish will be ignored, as usual;

Not to burst anyone’s balloon, but the tree shown here is a Bayesian tree, all but one of whose nodes are supported at the 100% level. However, a maximum likelihood bootstrap tells a different story: many nodes have low support, including almost the entire backbone of Neoaves. None of the structure among the five main groups survives, and three of the groups (Columbaves, Aequorlitornithes, and Inopinaves) can’t be confirmed either. So this all depends on your confidence in Bayesian confidence measures. I am personally going to treat all the nodes that are not confirmed by likelihood bootstrap as unresolved for the present. To see just what that involves, look at the supplementary info, figure S1.

This means, among other things, that the hoatzin is still the most annoying bird in the world, and we still have no good idea where it ought to go on the tree.

Let me repeat what I think someone ought to do: the taxon sample here is just what is needed, but if you’re going to grab 400kbases, it would be better to take it in bigger junks than 1500 bases; something like 8 50kbase pieces would be much better. That would help deal with questions of lineage sorting and make species tree methods a lot more workable. I don’t know how you would accomplish such a sequence capture, though, or at least not easily or cheaply.

Corrections: put down “chunks” as another word autocorrect doesn’t like. And the taxon sample is just what is needed except for the unwarranted concentration on suboscine passerines; the effort would have been better spent on another grebe, a kagu, another ibis, and a few more caprimulgiforms.

Great article, Emily! In case any avian systematists are reading along, I am looking for a collaborator to validate a logic-based alignment of Prum et al. (2015) and Jarvis et al. (2014) that accounts for name:meaning stability and change. Can be contacted @ https://sols.asu.edu/people/nico-franz

Too bad this thread is dead. It’s my favorite subject. Getting back to the conclusions of the study, if you collapse all the poorly supported nodes on Prum et al.’s maximum likelihood bootstrap, you get an 11-way polytomy at the base of Neoaves, consisting of Strisores, Musophagidae, an unnamed clade of Cuculidae + Otididae, Columbimorphae, Gruiformes, Mirandornithes, Charadriiformes, an unnamed clade of Sunbittern-Kagu-Tropicbirds, Aequornithes, Opisthocomus, and Telluraves. There are a number of cool features of the remaining tree, some new but most confirming past analyses. Oddly, I find the most interesting the confirmation that parids are sylvioids and regulids are muscicapoids, which Prum et al. don’t say much about.

I presume nobody else here is this obsessed with bird phylogeny.

Nico Franz said:

Great article, Emily! In case any avian systematists are reading along, I am looking for a collaborator to validate a logic-based alignment of Prum et al. (2015) and Jarvis et al. (2014) that accounts for name:meaning stability and change. Can be contacted @ https://sols.asu.edu/people/nico-franz

Not sure what that means, but I’m an avian systematist. Please explain.

Thank you, John. Here are two examples of the approach:

DOI: 10.1371/journal.pone.0118247 (weevil example) http://arxiv.org/abs/1412.1025 (primate example)

The general idea is to represent each tree as is, add a third set of tree1-node to tree2-node relationships, then throw this into a logic reasoning tool that finds a consistent alignment (hopefully) and thereby also assesses for any pair of taxonomic labels in trees 1,2 whether their taxonomic meanings are congruent, overlapping, exclusive of each other, etc. The outcome is specifically not “which tree is right?”, but instead “how can we logically represent the name:meaning congruences and incongruences?” Why do this? Again, in my view, see: http://biorxiv.org/content/early/20[…]07/10/022145 I hope this clarifies the intention.

Nico Franz said:

Thank you, John. Here are two examples of the approach:

It’s probably all explained by the links, but what do you mean by “consistent alignment”?

John Harshman said:

Nico Franz said:

Thank you, John. Here are two examples of the approach:

It’s probably all explained by the links, but what do you mean by “consistent alignment”?

Let’s say we have this:

taxonomy 2015 Prum (Psittaciformes Psittacidae) Read: “2015.Psitticidae is a child of 2015.Psittaciformes” (Psittacidae Barnardius) ditto (“2015.Barnardius is a child of…”)

taxonomy 2014 Jarvis (Psittaciformes Psittacidae) Read: “2014.Psitticidae is a child of 2014.Psittaciformes” (Psittacidae Melopsittacus) …

articulation 2015-2014 [2015.Psittaciformes equals 2014.Psittaciformes] [2015.Psittacidae equals 2014.Psittacidae] [2015.Barnardius disjoint 2014.Melopsittacus]

This third articulation (disjoint = exclusive of each other), jointly with the former two, creates a logical inconsistency.

In common language: given the two 2015/2014 trees, and if 2015.Barnadius and 2014.Melopsittacus are the only specified children of the corresponding parents, and given that they are exclusive of each other in terms of taxonomic identity, then it it not logically consistent to assert that the parents are congruent (by virtue of having congruent sets of children).

Simpler example.

1. A includes B 2. B includes C 3. C includes A

Jointly these assertions are logically inconsistent. A consistent alignment has no such logically contradicting relations.

Nico Franz said: Let’s say we have this:

taxonomy 2015 Prum (Psittaciformes Psittacidae) Read: “2015.Psitticidae is a child of 2015.Psittaciformes” (Psittacidae Barnardius) ditto (“2015.Barnardius is a child of…”)

taxonomy 2014 Jarvis (Psittaciformes Psittacidae) Read: “2014.Psitticidae is a child of 2014.Psittaciformes” (Psittacidae Melopsittacus) …

articulation 2015-2014 [2015.Psittaciformes equals 2014.Psittaciformes] [2015.Psittacidae equals 2014.Psittacidae] [2015.Barnardius disjoint 2014.Melopsittacus]

This third articulation (disjoint = exclusive of each other), jointly with the former two, creates a logical inconsistency.

In common language: given the two 2015/2014 trees, and if 2015.Barnadius and 2014.Melopsittacus are the only specified children of the corresponding parents, and given that they are exclusive of each other in terms of taxonomic identity, then it it not logically consistent to assert that the parents are congruent (by virtue of having congruent sets of children).

Simpler example.

1. A includes B 2. B includes C 3. C includes A

Jointly these assertions are logically inconsistent. A consistent alignment has no such logically contradicting relations.

Thanks for the common language. But I still don’t understand what you mean by “alignment”. And it is not clear to me that choosing different exemplars of a taxon makes two trees inconsistent. It means only that we must assume that the two exemplars are both members of that taxon in order to reconcile the trees.

John Harshman said:

Nico Franz said: Let’s say we have this:

taxonomy 2015 Prum (Psittaciformes Psittacidae) Read: “2015.Psitticidae is a child of 2015.Psittaciformes” (Psittacidae Barnardius) ditto (“2015.Barnardius is a child of…”)

taxonomy 2014 Jarvis (Psittaciformes Psittacidae) Read: “2014.Psitticidae is a child of 2014.Psittaciformes” (Psittacidae Melopsittacus) …

articulation 2015-2014 [2015.Psittaciformes equals 2014.Psittaciformes] [2015.Psittacidae equals 2014.Psittacidae] [2015.Barnardius disjoint 2014.Melopsittacus]

This third articulation (disjoint = exclusive of each other), jointly with the former two, creates a logical inconsistency.

In common language: given the two 2015/2014 trees, and if 2015.Barnadius and 2014.Melopsittacus are the only specified children of the corresponding parents, and given that they are exclusive of each other in terms of taxonomic identity, then it it not logically consistent to assert that the parents are congruent (by virtue of having congruent sets of children).

Simpler example.

1. A includes B 2. B includes C 3. C includes A

Jointly these assertions are logically inconsistent. A consistent alignment has no such logically contradicting relations.

Thanks for the common language. But I still don’t understand what you mean by “alignment”. And it is not clear to me that choosing different exemplars of a taxon makes two trees inconsistent. It means only that we must assume that the two exemplars are both members of that taxon in order to reconcile the trees.

In the example above, no other assumptions are made about the parents; hence their respective children “fully define” them. Under that constraint, an inconsistency is obtained. If that constraint is relaxed, for example by representing parent-level synapomorphies in addition to children, then a consistent result becomes possible. In the Prum/Jarvis use case that latter approach seems reasonable because the authors are aiming at resolving higher-level relationships, more so than testing genus-level monophyly (as an example).

I (and others) have published on this “concept taxonomy” approach a good bit by now; see for instance the “alignments” in the current sense in Figs. 3 and 4 here: http://zookeys.pensoft.net/articles.php?id=6001 But perhaps I need not copy/paste all that here, when the hope was (and still is) to recruit a collaborator.

Nico Franz said: In the example above, no other assumptions are made about the parents; hence their respective children “fully define” them. Under that constraint, an inconsistency is obtained. If that constraint is relaxed, for example by representing parent-level synapomorphies in addition to children, then a consistent result becomes possible. In the Prum/Jarvis use case that latter approach seems reasonable because the authors are aiming at resolving higher-level relationships, more so than testing genus-level monophyly (as an example).

I (and others) have published on this “concept taxonomy” approach a good bit by now; see for instance the “alignments” in the current sense in Figs. 3 and 4 here: http://zookeys.pensoft.net/articles.php?id=6001 But perhaps I need not copy/paste all that here, when the hope was (and still is) to recruit a collaborator.

I don’t think I’m the person you’re looking for. I don’t think any useful concept of “Psittacidae” can be derived from the trees of Prum et al. or Jarvis et al. or any reconciliation or alignment (whose meaning I still don’t understand) of both. If that’s even what you’re trying to do.

John Harshman said:

Nico Franz said: In the example above, no other assumptions are made about the parents; hence their respective children “fully define” them. Under that constraint, an inconsistency is obtained. If that constraint is relaxed, for example by representing parent-level synapomorphies in addition to children, then a consistent result becomes possible. In the Prum/Jarvis use case that latter approach seems reasonable because the authors are aiming at resolving higher-level relationships, more so than testing genus-level monophyly (as an example).

I (and others) have published on this “concept taxonomy” approach a good bit by now; see for instance the “alignments” in the current sense in Figs. 3 and 4 here: http://zookeys.pensoft.net/articles.php?id=6001 But perhaps I need not copy/paste all that here, when the hope was (and still is) to recruit a collaborator.

I don’t think I’m the person you’re looking for. I don’t think any useful concept of “Psittacidae” can be derived from the trees of Prum et al. or Jarvis et al. or any reconciliation or alignment (whose meaning I still don’t understand) of both. If that’s even what you’re trying to do.

Thank you for considering, John.

It’s worth noting that Prum et al.’s “Inopinaves” is almost identical to Jarvis et al.’s “Telluraves” or “core landbirds”: a basal tree of raptors (including New World vultures), with the kingfishers+woodpeckers branching off from the owl lineage, and the parrots+perching birds branching off from the falcon lineage. The two analyses differ slightly on the position of this clade’s root, and on whether hoatzins should be included.* But between them, Hackett et al. (2008) in Science, and Per Ericson (2012) in Journal of Biogeography, it seems like we’re really nailing down the evolutionary history of this group.

*Nobody ever agrees on where hoatzins are supposed to go anyway, so that’s not too surprising.

Coupe of notes: “Inopinaves” was in fact as defined as Telluraves + hoatzin. The name Telluraves was introduced by Yuri et al. 2013. A primary reference for Ericsson would be Ericsson et al. 2006.

Ericson P.G.P., Anderson C.L., Britton T., Elzanowski A., Johansson U.S., Källersjö M., Ohlson J.I., Parsons T.J., Zuccon D., Mayr G. Diversification of Neoaves: Integration of molecular sequence data and fossils. Biology Letters 2006; 2:543-547.

Yuri, T., R.T. Kimball, J. Harshman, R.C.K. Bowie, M.J. Braun, J.L. Chojnowski, K.-L. Han, S.J. Hackett, C.J. Huddleston, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and E.L. Braun. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology 2013; 2:419-444.

Well, a few of us are still reading. Now I am told that the server software is fixed, discussion can proceed. In case anyone wonders why the discussion is so hard to follow, it is because the folks now discussing are actual researchers in evolutionary biology.

One thing I get out of the discussion on nomenclature and “alignment” of taxa is that phylogenies are much more interesting than taxonomies. To me, anyway.

John Harshman has given us a depressing summary of current knowledge about the phylogeny of Neoaves. Although it leaves a distressing number of issues unsolved, we can perhaps comfort ourselves with the thought that resolving those uncertainties may not matter very much, at least for our understanding of evolution of genes and characters in birds. If two bifurcations in the tree follow each other closely, and are thus very hard to resolve, maybe that part of the tree topology does not make much of a prediction of how characters will be distributed in modern birds, or what the pattern of similarities will be among present-day gene sequences. It is the other side of the coin: it is precisely when we are having a hard time finding evidence to resolve the pattern of bifurcations that we also suspect that this pattern does not make much of a prediction about present-day biology.

(Puts head down waiting for pointed responses from Anton, Nico, and John).

Joe Felsenstein said: John Harshman has given us a depressing summary of current knowledge about the phylogeny of Neoaves. Although it leaves a distressing number of issues unresolved, we can perhaps comfort ourselves with the thought that resolving those uncertainties may not matter very much, at least for our understanding of evolution of genes and characters in birds. If two bifurcations in the tree follow each other closely, and are thus very hard to resolve, maybe that part of the tree topology does not make much of a prediction of how characters will be distributed in modern birds, or what the pattern of similarities will be among present-day gene sequences.

I hope that summary wasn’t too depressing. This paper is a big advance and resolves much that was not previously clear. It just doesn’t go as far as the tree above would suggest. But you do make a good point that the resolution of short branches doesn’t make much difference for comparative studies as long as the comparative method being used takes their shortness into account.

I still want to know, though, and I’m still thinking there are few if any genuine hard polytomies. Prum et al. isn’t the last word, but I think there eventually will be a last word. Once more, I suggest that a dozen or so long sequences of 10 to 50kb, each capable of resolving short branches and within each of which there should be infrequent recombination, ought to be ideal.

Joe Felsenstein said:

Well, a few of us are still reading. Now I am told that the server software is fixed, discussion can proceed. In case anyone wonders why the discussion is so hard to follow, it is because the folks now discussing are actual researchers in evolutionary biology.

One thing I get out of the discussion on nomenclature and “alignment” of taxa is that phylogenies are much more interesting than taxonomies. To me, anyway.

Thank you, Joe. I am almost an ignoramus on this, but it may be that some humans (and their evolutionarily constrained brains) derive more understanding from a topology, while others just cannot let go of “getting the language as right as possible”. For that latter group, words are our preferred tool with which to reach out to the world and ask it questions that we need answered. I think you are right to say that in some cases we will not be satisfied, because the phenomena that unfolded may not have left enough of a trace to be amenable to scientific language generation. But I’d like to suggest that your stated preference for the phylogeny as a means of gaining understanding, and a complementary preference to also and continuously update classificatory language - both preferences may not be “only purely scientific choices” but may instead also reflect how our perhaps slightly different preferential modes of cognition are evolutionarily constrained. See e.g. http://www.indiana.edu/~abcwest/pmw[…]ain.1998.pdf

Nico Franz: Thanks for the link to Scott Altran’s exhaustive (and exhausting) work. Of course I have not had time to read it carefully, let alone look at the many responses. Altran makes the case (if I understand) that a hierarchical clustering of organisms is built into our conceptual and perceptual) apparatus. I believe that some of the respondents who commented on his paper are skeptical of this.

I wonder how his view squares with the schemes that were attempted immediately before Darwin’s work – for example attempts to find particular geometrical forms such as triangular or pentagonal arrangements. Or the idea that people frequently have that there are linear continua with species grading into each other (Buffon seemed to think that way).

I don’t think that it is obvious that the language we use to describe organisms has to obey the rules of monophyletic taxonomy to be useful to us; why, for example, are we not to use terms like “invertebrate” or “reptile”? But it does seem to me to be wholly defensible to use the phylogeny, rather than any verbal taxonomy, to analyze the distribution of traits across species.

Joe Felsenstein said:

Nico Franz: Thanks for the link to Scott Altran’s exhaustive (and exhausting) work. Of course I have not had time to read it carefully, let alone look at the many responses. Altran makes the case (if I understand) that a hierarchical clustering of organisms is built into our conceptual and perceptual) apparatus. I believe that some of the respondents who commented on his paper are skeptical of this.

I wonder how his view squares with the schemes that were attempted immediately before Darwin’s work – for example attempts to find particular geometrical forms such as triangular or pentagonal arrangements. Or the idea that people frequently have that there are linear continua with species grading into each other (Buffon seemed to think that way).

I don’t think that it is obvious that the language we use to describe organisms has to obey the rules of monophyletic taxonomy to be useful to us; why, for example, are we not to use terms like “invertebrate” or “reptile”? But it does seem to me to be wholly defensible to use the phylogeny, rather than any verbal taxonomy, to analyze the distribution of traits across species.

Thank you, Joe. Yes, it is fair to say that Atran’s inferences stretch quite far. I also agree that if a group shares a number of symplesiomorphies that are fairly “close” to its root, that ought to sustain some reliable phylogenetic (and other) inferences about the group.

I did not mean to say much about tree-based analyses of trait distributions. What I am saying is hopefully as simple as this. We may hypothesize that for any tree that can be inferred, with some limits on precision and reliability that we might learn in due time, there is a taxonomic vocabulary that best fits that tree. And based on that presumption, finding the best tree and adjusting the best vocabulary are how we measure progress and success in our science.

About this Entry

This page contains a single entry by Emily Thompson published on January 4, 2016 10:00 AM.

Luskin: “I am leaving Discovery Institute” was the previous entry in this blog.

Iridescence with wave clouds is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.381

Site Meter