A molecule study that includes ratfish and rats

Here’s a molecule study (Irisarri et al. (10 co-authors)
that includes select members of the Gnathostomata (jawed vertebrates going back to ratfish). Their abstract reports, “Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial.”

At least they are on the right track, with a wide gamut study. The LRT covers very few fish, but a long list tetrapods. Evidently the LRT was not on their radar. (sigh)

“We tested a new bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost-effective. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.”

Importance? Unfortunately you have to be a believer, because their RNA interrelationships can and cannot be verified by a competing analysis of traits (explained in detail below).

“Gene jackknifing of genomic data corroborates the robustness of our tree.”

Unfortunately, genomic data produces several false positives when compared to phenomic data.

Here we’ll compare results
to the large reptile tree (LRT, 1187 taxa), which goes back nearly as far in a morphological study and employs fossil taxa. I have often said that molecules produce false positives over large phylogenetic distances. Here that statement proves to be both true and false, depending on the node.

The LRT includes only bony vertebrates,
so sharks, rays and ratfish are not included as taxa in the LRT. Lungfish and most teleosts are also not included.

Where the Irisarri et al. tree matches the LRT:
Both trees:

  1. separate ray fin fish from lobe fin fish
  2. separate tetrapods from lobe fin fish
  3. separate amniotes from amphibians (only living taxa are tested)
  4. separate caecilians from salamanders + frogs
  5. separate turtles, mammals, archosaurs and lepidosaurs
  6. nest birds with crocs
  7. nest Sphenodon with squamates
  8. nest all mammals with other mammals, turtles with turtles, birds with birds, etc. etc.
  9. nest placental mammals with other placental mammals, apart from non-placental mammals
  10. nest palaegnath birds with palaeognath birds, apart from neognath birds
  11. nest placental mammals splitting from Monodelphis

Where the Irisarri et al. tree does not match the LRT:
The Isirarri et al. tree:

  1. separates mammal reptiles from all other reptiles
  2. separates turtles from lepidosaurs, instead nesting turtles with birds and crocs
  3. separates iguanids from Sphenodon, instead nesting iguanids and Elgaria (alligator lizard) with snakes
  4. separates geckos from snakes, instead nesting geckos with skinks
  5. separates the finch (Taeniopygia guttatafrom the chicken and turkey, instead nesting the finch as the basalmost neognath

The LRT:

  1. nests mammals with birds and crocs, not lepidosaurs
  2. nests turtles with lizards, not archosaurs
  3. nests geckos with snakes, not skinks
  4. nests iguanids at the base of all squamates, therefore closer to Sphenodon
  5. nests Elgaria with Cryptolacerta (Eocene) and Ophisaurus (extant, not tested by Irisarri et al)

You might remember
molecules brought us the clade Afrotheria, a clade that includes elephants, aardvarks and golden moles, among a larger list of unrelated taxa

At present a certain amount of faith
attends gene sequencing, a hope that similar genes will translate to the appearance of similar body parts and proportions. Often that faith is rewarded. Other times, it is not. While DNA testing has proven its validity within genera (in crime labs and ancestry searches), the possibility of a ‘false positive’ using gene sequencing over larger phylogenetic distances occurs too often.

Ultimately
if you want to see how evolution works in tetrapods, molecules work for some nodes, not for others, and excludes fossil taxa. For more consistent results that deliver gradual accumulations of traits in derived taxa, using every sort of tetrapod taxa (including fossils), try morphology. It’s the benchmark against which molecules succeed sometimes and fail other times. I cannot yet unravel the pattern of false positives vs. verified positives.

Perhaps the worst aspect of DNA analysis:
it is correct often enough that some well-meaning scientist consider it flawless. At present only one person on the planet has produced a competing trait analysis that shows DNA analysis is flawed…sometimes.

References
Irisarri I et al. 2017. Phylotranscriptomic consolidation of the jawed vertebrate time tree. Nature ecology & evolution 1: 1370–1378. doi:10.1038/s41559-017-0240-5

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