When taxonomy meets genomics: lessons from a common songbird

Abstract

Taxonomy is being increasingly informed by genomics. Traditionally, taxonomy has relied extensively on phenotypic traits for the identification and delimitation of species, though with a growing influence from molecular phylogenetics in recent decades. Now, genomics opens up new and more powerful tools for analysing the evolutionary history and relatedness among species, as well as understanding the genetic basis for phenotypic traits and their role in reproductive isolation. New insights gained from genomics will therefore have major effects on taxonomic classifications and species delimitation. How a genomics approach can inform a flawed taxonomy is nicely exemplified by Mason & Taylor () in this issue of Molecular Ecology. They studied redpolls, which comprise a genus (Acanthis) of fringillid finches with a wide distribution in the Holarctic region, and whose species taxonomy has been a matter of much controversy for decades (Fig. ). Current authoritative checklists classify them into one, two or three species, and five or six subspecies, based largely on geographical differences in phenotypic traits. Previous studies, including a recent one of the subspecies on Iceland (Amouret et al. ), have found no evidence of differentiation between these taxa in conventional molecular markers. The lack of genetic structure has been interpreted as incomplete lineage sorting among rapidly evolving lineages. Now Mason & Taylor (), using a large data set of genomewide SNPs, verify that they all belong to a single gene pool with a common evolutionary history, and with little or no geographical structuring. They also show that phenotypic traits used in taxonomic classifications (plumage and bill morphology) are closely associated with polygenic patterns of gene expression, presumably driven by ecological selection on a few regulatory genes. Several lessons can be learned from this study. Perhaps the most important one for taxonomy is the risk of taxonomic inflation resulting from overemphasizing phenotypic traits under local adaptation and ignoring a lack of phylogenetic signal in molecular markers.

Keywords: adaptation; birds; hybridization; natural selection and contemporary evolution; phylogeography; speciation.