Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)

In the Andes, humid-forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well-defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and to understand the assembly of species rich communities on Andean slopes. Here, we use mitochondrial DNA and thousands of short-read sequences generated with Genotyping-by-Sequencing (GBS) to examine the geographic history of speciation in a lineage of passerine birds found in the humid forest of the Andes, the “bay-backed” antpitta complex (Grallaria hypoleuca s. l). Mitochondrial DNA genealogies documented genetic structure among ...