The most ambitious arthropod phylogeny yet

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The top-tier journal Nature doesn’t often deal in purely phylogenetic research. So when such a study graces their pages we know it’s big stuff.

Yesterday, Nature published a 62 gene, 75 species analysis of the evolutionary history of the arthropods. Arthropods, as readers of this blog likely know, are animals with a chitinous exoskeleton and jointed legs. They include the insects, arachnids, crustaceans, centipedes, and others. This is a staggeringly diverse group, and one found just about everywhere on the planet. Most animals are arthropods.

This study has been in the works for many years. Jerry Regier’s lab at the University of Maryland has been diligently developing protocols for extracting single-copy nuclear DNA from across the arthropods, and the work has paid off handsomely. They have created the largest and most relevant data set yet assembled for addressing the hard questions in arthropod evolution. This is exciting! Today is like Christmas for arthropod systematists.

There’s a lot to digest here, but below are my first impressions:

  • Yes, insects really are crustaceans. This result emerged in every single analysis and upholds earlier molecular findings that the hexapods (insects, collembolans, diplurans) are just a single lineage of crustaceans that left the ocean for a more terrestrial lifestyle.
  • The sister-group to hexapods is a surprise: the remipedes Xenocarida. Wow. I’ll let Carl Zimmer explain why this is cool. Note, though, that this relationship was only found in the nucleotide data. Analyses using amino acid sequences were less convincing, so I’d still treat this result with some caution.
  • Within hexapods, at least, the morphologists are vindicated. Earlier molecular studies from mitochondrial DNA and ribosomal DNA had found some unconventional relationships- removing springtails from the hexapods, for instance- but this larger and more appropriate data set is basically textbook in its findings.  Funny how we spend hundreds of thousands of dollars and ten years of research to confirm that the crusty old taxonomists that none of the cool kids wanted to listen to had been right all along. Hexapods are a clade, bristletails are sister to the remaining insects, and silverfish are sister to the Pterygotes.
  • Some of the difficult relationships within the hexapods remain difficult. There’s a hint that Diplura and Collembola are sister, but that doesn’t hold in all analyses. And Paleoptera (Mayflies + Dragonflies) do form a clade, but support is still low.
  • The myriapods (centipedes + millipedes) changed position again- they’re now sister to the pancrustacea. Earlier results had them with the chelicerates.  I don’t have much to say here.  Nor can I say much about the Crustacea, as that’s a group I do not know particularly well.
  • Pity the chelicerate systematists.  Sixty two genes and the internal relationships of this important group (spiders, scorpions, mites, etc) remain an unresolved mush. It seems the modern lineages arose very quickly in time.

source: Regier et al 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature doi:10.1038/nature08742

15 thoughts on “The most ambitious arthropod phylogeny yet”

  1. I haven’t seen a phylogeny this awesome since Goloboff et al.’s (2009) 73 000 taxa-paper on Eukaryota. Come to think about it, this is much cooler as the gene-to-taxon ratio is much higher without compromising the taxon sampling.

    1. Oooh… thanks for mentioning that paper, haven’t seen it!

      Now, while their number of taxa is quite insane, the overall distribution thereof is rather abysmal. The much exagerrated emphasis on metazoa and viridiplantae makes the rest of the tree rather questionable. The vast majority of eukaryotes, by far, are neither metazoa nor viridiplantae. Also, the absense of Rhizarians makes me want to cry.

      That said, their metazoans and archaeplastids themselves should be reasonable…

      Now back to waging a crusade against all those cell biologists who STILL use the much outdated Woese tree for their eukaryotic phylogenies. Srsly, if I see microsporidia being ‘basal’ to all or most eukaryotes, and not in Fungi where they belong ONE MORE TIME…grrrrr! How hard is it to not be a whole decade out of date?

  2. “It seems the modern lineages arose very quickly in time.”

    I suppose this is a throwaway statement however, there are two problems with it:

    1) we can NOT know the speed of adaptive radiation in this or any other group so far back in time. Jeeze – you are discussing events more than 445 million years old. At best we get a peek at such events from what fossils we stumble upon.

    2) we can NOT know all that much about what lineages were involved vs those present at the time — and which were which to have sifted down into extant representatives. Again, we have some few fossilized representatives to draw inferences from, inferences which could well be erroneous due to “chance” of which individuals were found as fossils.

    Still, I agree that more data is better and its always nice to see science stumble along, lol.

    1. You’re right that we cannot know.

      However, we can certainly infer from the data we do have. And considering the short internodes and poor resolution in the tree, one likely explanation is that the modern chelicerate lineages diverged in time rapidly enough that little phylogenetic signal for those events remains at the genetic level.

      1. While [begrudgingly] conceding biobob’s point about the dangers of over-interpreting the fossil record, it is interesting that the earliest fossil records for most crown group arachnids cluster between 430 and 390 Mya (Silurian/Devonian) (see Dunlop and Selden 2009 for a recent review DOI:10.1007/s10493-009-9247-1). Most of these fossils possess synapomorphies that allow them to be assigned to extant orders–at least according to the experts.

        In part, this reflects a few localities that yield unusually well-preserved arthropod fossils (notably the Rhynie chert), but the geologically “simultaneous” appearance of these extant orders in the fossil record is consistent with the genetic evidence pointing toward a relatively rapid radiation — and this itself is coincident with molecular and fossil evidence for the relatively rapid radiation of terrestrial plants and the first appearances of other terrestrial arthropod groups roughly around 430 Ma. All very circumstantial to be sure, but still quite interesting.

        Okay back to the reptiles.

      2. So the argument goes – lol – and we have demonstrated experimentally that genetic markers (adaptations/mutations) propagate thru populations in as little as 25 generations (see work of D. Pimentel’s students). Certainly it would be possible for lineages to ‘radiate’ in thousands or tens of thousands of years vs millions and I am inclined to think they HAVE. However, we humans do NOT KNOW as much as many of ‘us’ think and less than so many believe – hehe.

        Just the fact that one set of DNA analysis yields one set of results and ANOTHER set of DNA analysis yields A DIFFERENT result should set off your alarms. Personally, I have come to the conclusion that any DNA analysis equating/transmogrification to time is utter bullcrap. Just ponder LaMarkism vs Epigenetics for a clue to the state of our genetics “knowing”.

        They can get back to me after they sequence DNA, RNA etc all 1 million plus arthropoda with repeatable statistical analysis into a cogent schema/theory. After all, the exception makes the rule, as we always say in evolution.

  3. So all bugs came from crustaceans. Cool. And reptiles used to rule the earth. It amazes me how a chance event can lead to the dominance of a lifeform for millions of years.

    Large meteor strikes are statistically predictable to the extent that one extends the sample size, and are not random in that sense. But within the chronological grasp of the human psyche, I hope you’ll allow me the concept of random apocalypse.

    So many animal kingdoms wiped out. So many yet to come. So we enjoy our blogs, our pretty pictures, and our moments of rapture. And we take our place with the other carbons in the oil of the future.


  4. I’ve been puzzling over this paper for the last couple of days. It is true that the mandibulate taxa look well resolved, but as you note, the more interesting chelicerates look pitiful – or should I say full of pittfalls.

    I’m glad to see that these guys and gals actually managed to get genes from one mite from each of the major lineages, and like most molecular phylogenies that do so, found no evidence to support mite monophyly. Since I can’t rationalise a monophyletic Acari from morphology, I consider the question unresolved, and of course, tend to like results that support my gut feeling that mites are a grade of evolution. Note, the figure you have posted shows only a single mite – so it is misleading. Fgure 1 is hard to read, but shows the relationships better.

    The taxon sampling within the chelicerates lineages is not very impressive, but I am impressed that Jeff Shultz was willing to go with data that shot down his Acaromorpha, and even more unlikely groups such as Stomothecata. Always good to see someone following the data, rather than their pet theories.

  5. @warren

    “So many animal kingdoms wiped out. So many yet to come. So we enjoy our blogs, our pretty pictures, and our moments of rapture. And we take our place with the other carbons in the oil of the future.”

    That’s a very nice….

    after the carbon back to space dust…

    and around and around and around we go -oh -oh -oh -oh.

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