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Retroposon evidence for an explosive radiation of Neoaves

A recent neontological paper that may be of interest to the DML:

Matzke A, Churnakov G, Berkes P, Arms EM, Kelsey D, Brosius J, Kriegs
JO, Schmitz J 2012 Retroposon insertion patterns of neoavian birds:
strong evidence for an extensive incomplete lineage sorting era. Mol
Biol Evol doi:10.1093/molbev/msr319


More than one hundred fifty million years ago the avian lineage
separated from that of other dinosaurs and later diversified into the
more than 10,000 species extant today. The early neoavian bird
radiations most likely occurred in the late Cretaceous (more than 65
Ma), but left behind few if any molecular signals of their archaic
evolutionary past. Retroposed elements, once established in an
ancestral population, are highly valuable, virtually homoplasy-free
markers of species evolution; after applying stringent orthology
criteria, their phylogenetically informative presence/absence patterns
are free of random noise and independent of evolutionary rate or
nucleotide composition effects. We screened for early neoavian
orthologous retroposon insertions and identified six markers with
conflicting presence/absence patterns; whereas six additional
retroposons established before or after the presumed major neoavian
radiation show consistent phylogenetic patterns. The exceptionally
conflicting retroposon presence/absence patterns of neoavian orders
are strong indicators of an extensive incomplete lineage sorting era,
potentially induced by an early rapid successive speciation of
ancestral Neoaves.

The neoavian tree presented is quite comb-like (consistently with the
inferred incomplete lineage sorting); however, there is some support
for the Charadriiformes/landbird node previously suggested by Hackett
et al. (2008).

David Černý