Data from: Mechanisms of global diversification in the brown booby (Sula leucogaster) revealed by uniting statistical phylogeographic and multilocus phylogenetic methods

Recent theoretical and empirical research suggests that statistical models
based on coalescent theory can improve both phylogeographic and
phylogenetic inference. An approach that involves elements of both
statistical phylogeography (e.g., Isolation with Migration analyses) and
multilocus phylogenetic inference (e.g., *BEAST) may be particularly
useful when applied to populations with relatively old divergence times.
Here we use such an approach in the globally distributed brown booby (Sula
leucogaster). We sampled 215 individuals from all major breeding areas and
genotyped them at eight microsatellite and three nuclear intron loci. We
found that brown booby populations were highly differentiated and that
colonies can be grouped into four major genetic populations (Caribbean
Sea, Central Atlantic Ocean, Indo-Central Pacific, and Eastern Pacific).
These populations apparently diverged in the absence of gene flow and,
with one exception, currently exchange few to no migrants. The Eastern
Pacific population diverged from all other populations approximately one
million years ago [90% highest posterior density: 330 000 – 2 000 000
years ago] and exhibits a distinct male plumage, relative to other
populations. However, recent gene flow from the Indo-Central Pacific into
the Eastern Pacific appears to have occurred, suggesting that
approximately one million years of genetic isolation and divergence in
male plumage colour are not sufficient to prevent interbreeding. Gene flow
following secondary contact of the Indo-Central Pacific and Eastern
Pacific populations was not detected in previous mitochondrial DNA (mtDNA)
studies, and the contrast between the mtDNA results and our current
results highlights the advantage of a multilocus phylogeographic approach.