Genomics of a rapid radiation, and the promises and pitfalls of massive datasets

Postdoc Leo Campagna’s new paper on dissecting the complex demographic and phylogenetic history of the Sporophila seedeaters is just out in Molecular Ecology.  In addition to revealing new insights into this avian rapid radiation, Leo and his collaborators also make some useful but sobering points about the potential for spurious results in genome-scale datasets for which the number of loci screened is orders-of-magnitude greater than the number of organisms sampled.

Campagna L, Gronau I, Silveira LF, Siepel A, Lovette I (2015) Distinguishing Noise from Signal in Patterns of Genomic Divergence in a Highly Polymorphic Avian Radiation. Molecular Ecology. In press.

Abstract: Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated, or that may cross species barriers through introgressive hybridization. Here we use a reduced representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans.


Sporophila cinnamomea(MEC-15-0722)

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