Phylogeography unplugged: comparative surveys in the genomic era

Abstract

ABSTRACT.-In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the IndoPacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional ("unplugged") approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches.

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“…For example, Bowen et al (2014) suggest a progressive research program, whereby comparative genetic surveys of multiple species based on mtDNA or a few loci are used to identify questions, locations and species of interest, which can then be pursued using targeted population genomic investigations. Thus, although the data used within this thesis is restricted to mtDNA, it sets the stage for follow up studies using NGS methods.…”

“…Given that single--locus inference is still common for Indo--Pacific species (see discussion in Bowen et al 2014), the genealogical approaches used here make much more effective use of the high information content in the mitochondrial locus than do estimates of genetic structure. Moreover, FST methods as well as more explicit population genetic models such as Migrate (Beerli and Felsenstein also Bloomquist et al 2010).…”