The end of phylogenetic controversies

By Razib Khan | October 7, 2012 11:10 pm

I put up kind of a ridiculous title. But I do hope that at some point in the near future we’ll have some of the same flavor of debates on the macroevolutionary time scale that we have on the human microevolutionary time scale. There’ll be a surfeit of sequence at nearly every node of interest on the tree of life, and computational power galore devoted to analyzing variation and reconstructing any phylogeny we can conceive of. To be fair, one could argue we aren’t there even with human phylogenetics either. But it is rather strange we’re debating the origin of mammals and the nature of the lineage’s phylogenetic tree at this time. This is the kind of thing that I hope a more robust and assertive molecular phylogenetics can resolve (and paleontology as well, but I’m not up on the latest in computational analysis of morphological characters).

In any case, here’s a cool manuscript up at arXiv, A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements:

Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Divergence time estimation based upon 14 fossil calibrations reveals that crown teleosts appeared ~270 Ma at the end of the Permian and that elopomorphs, osteoglossomorphs, ostarioclupeomorphs, and euteleosts diverged from one another by 205 Ma during the Triassic. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.

H.T. Haldane’s Sieve.

MORE ABOUT: phylogenetics
  • Mike Keesey (@tmkeesey)

    If I had nickel for every time someone said “mammal” when they meant “placental”….

    (The root of Mammalia is pretty solidly understood, at least in terms of extant taxa. There is a little trouble figuring out whether some fossil taxa are part of the crown group or not.)

    Placental mammals and neoavian birds seem to have diversified very rapidly somewhere around the Cretaceous-Paleogene event — that’s why the branching order is hard to nail down.

  • Mike Keesey

    So the divergence of Telesotei is linked to the Permian-Triassic extinction? Leads to me to formulate a hypothesis: when a crown group’s internal branching order is difficult to pin down (Placentalia, Neoaves, Teleostei), it probably diversified rapidly in conjunction with a major extinction event.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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