DOI: 10.1101/491688Dec 10, 2018Paper

Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

BioRxiv : the Preprint Server for Biology
Ethan LinckJohn Klicka

Abstract

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of a widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or sibling) lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidental...Continue Reading

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