Retroposon evidence for irresolvable regions in bird phylogeny (free pdf)

[David Černý <david.cerny1@gmail.com>]

A new follow-up to the Avian Phylogenomics Project analyses published
last December (see http://dml.cmnh.org/2014Dec/msg00049.html), which
makes use of the same data but arrives at novel conclusions. In
particular, the paper presents what might be the first direct evidence
for the presence of "hard" polytomies in the phylogeny of neoavian
birds, or perhaps even the Tree of Life in general:

Suh A, Smeds L, Ellegren H 2015 The dynamics of incomplete lineage
sorting across the ancient adaptive radiation of neoavian birds. PLoS
Biol 13(8): e1002224
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002224

The diversification of neoavian birds is one of the most rapid
adaptive radiations of extant organisms. Recent whole-genome sequence
analyses have much improved the resolution of the neoavian radiation
and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary,
yet the causes of the remaining genome-level irresolvabilities appear
unclear. Here we show that genome-level analyses of 2,118
retrotransposon presence/absence markers converge at a largely
consistent Neoaves phylogeny and detect a highly differential temporal
prevalence of incomplete lineage sorting (ILS), i.e., the persistence
of ancestral genetic variation as polymorphisms during speciation
events. We found that ILS-derived incongruences are spread over the
genome and involve 35% and 34% of the analyzed loci on the autosomes
and the Z chromosome, respectively. Surprisingly, Neoaves
diversification comprises three adaptive radiations, an initial
near-K-Pg super-radiation with highly discordant phylogenetic signals
from near-simultaneous speciation events, followed by two post-K-Pg
radiations of core landbirds and core waterbirds with much less
pronounced ILS. We provide evidence that, given the extreme level of
up to 100% ILS per branch in super-radiations, particularly rapid
speciation events may neither resemble a fully bifurcating tree nor
are they resolvable as such. As a consequence, their complex
demographic history is more accurately represented as local networks
within a species tree.

Synopsis:

Roberts RG 2015 Intractable tangles in the bird family tree. PLoS Biol
13(8): e1002225
http://journals.plos.org/plosbiology/article?id=info:doi/10.1371/journal.pbio.1002225


-- 
David Černý