Reticulation, divergence, and the phylogeography–phylogenetics continuum


Edwards SV, Potter S, Schmitt CJ, Bragg JG, Moritz C. Reticulation, divergence, and the phylogeography–phylogenetics continuum. Proceedings of the National Academy of Sciences. 2016;113 :8025-8032.
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Phylogeography, and its extensions into comparative phylogeogra-
phy, have their roots in the layering of gene trees across geography,
a paradigm that was greatly facilitated by the nonrecombining, fast
evolution provided by animal mtDNA. As phylogeography moves
into the era of next-generation sequencing, the specter of reticula-
tion at several levels
within loci and genomes in the form of re-
combination and across populations and species in the form of
has raised its head with a prominence even greater
than glimpsed during the nuclear gene PCR era. Here we explore the
theme of reticulation in comparative phylogeography, speciation
analysis, and phylogenomics, and ask how the centrality of gene
trees has fared in the next-generation era. To frame these issues,
we first provide a snapshot of multilocus phylogeographic studies
across the Carpentarian Barrier, a prominent biogeographic barrier
dividing faunas spanning the monsoon tropics in northern Australia.
We find that divergence across this barrier is evident in most spe-
cies, but is heterogeneous in time and demographic history, often
reflecting the taxonomic distinctness of lineages spanning it. We
then discuss a variety of forces generating reticulate patterns in
phylogeography, including introgression, contact zones, and the
potential selection-driven outliers on next-generation molecular
markers. We emphasize the continued need for demographic models
incorporating reticulation at the level of genomes and populations,
and conclude that gene trees, whether explicit or implicit, should
continue to play a role in the future of phylogeography.

Last updated on 09/22/2016