Monday, February 8, 2016

The network of woodpeckers, etc

The world continues on its merry way, searching for fragments of the Tree of Life. That is, research papers continue to be published that give no credence to the possibility of reticulate evolutionary history, especially in zoology.

A recent case in point is this one:
Matthew J. Dufort (2016) An augmented supermatrix phylogeny of the avian family Picidae reveals uncertainty deep in the family tree. Molecular Phylogenetics and Evolution 94: 313–326.
The author constructed a supermatrix for 26 loci for 78 taxa of the bird family containing woodpeckers, piculets, and wrynecks. The author used an array of phylogenetic techniques, including the construction of maximum-likelihood "gene" trees, several different maximum-likelihood species trees, plus time trees. All of these methods pre-suppose that the evolutionary history of the species was strictly tree-like.

We can use an exploratory data analysis to evaluate how probable is this fundamental assumption. I constructed a SuperNetwork based on the 26 gene trees produced by the author, using the SplitsTree program, as shown here. The network is basically tree-like, with one major exception.

I have labeled only one taxon, which seems to be the culprit for the major non-tree-likeness. This species appears in 10 of the gene trees, being part of the Leiopicus group (as expected) in 7 of the rooted trees. It is unexpectedly related to the Picus group in two of the other rooted trees, and is close to Dryocopus in the remaining tree.

This network EDA does not, of course, imply the existence of reticulate evolution. It does, however, highlight a pattern of incongruence that requires explanation, if the history of these birds is to fully elucidated. Reticulate evolution remains one of the possible explanations, pending further investigation.

For an example of a network view of bird evolution, see:
Antonio Hernandez-Lopeza, Didier Raoult, Pierre Pontarotti (2013) Birds perching on bushes: networks to visualize conflicting phylogenetic signals during early avian radiation. Comptes Rendus Palevol 12: 333-337.

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