Data from: 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 clades, but were poorly resolved at nodes relevant for
biogeographic inference. By contrast, relationships inferred from GBS loci
were highly resolved and suggested a biogeographic history in which the
ancestor originated in the northern Andes and dispersed south. Our results
are consistent with a scenario of vicariant speciation wherein the range
of a widespread ancestor was fragmented as a result of geologic or
climatic change, rather than a stepping-stone series of dispersal events
across pre-existing barriers. However, our study also highlights
challenges of distinguishing dispersal-mediated speciation from static
vicariance. Our results further demonstrate the substantial evolutionary
timescale over which the diverse biota of the Andes was assembled.