DOI: 10.5061/dryad.q268m
title: 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.)

description: 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.
description: c85d10m7p3s7.phyPhylip sequence alignment of concatenated GBS loci underlying Fig. S2Bc85d10m12p3s16.phyPhylip sequence alignment of concatenated GBS loci underlying Fig. S2Ac85d10m8p3sALL.phyPhylip sequence alignment of concatenated GBS loci underlying Fig. 2Bc85d5m8p3sALL.phyPhylip sequence alignment of concatenated GBS loci generated with a cluster depth of 5 or greater (phylogeny described, but not illustrated, in manuscript)RAxML_bipartitions.c85d8m8p3sALL.treeRAxML tree file of phylogeny built from GBS alignment in which loci had a stack depth of 5 or greater (phylogeny described, but not illustrated, in manuscript)RAxML_bipartitions.c85d5m8p3sALL.treeRAxML_bipartitions.c85d10m7p3s7_b1000.treeRAxML tree file of GBS phylogeny in Fig. S2BRAxML_bipartitions.c85d10m8p3sALL_b1000.treeRAxML tree file of GBS phylogeny in Fig. 2BRAxML_bipartitions.c85d10m12p3s16_b1000.treeRAxML tree file of GBS phylogeny in Fig. S2ARAxML_bipartitions.ND2_10.6.15_b1000RAxML tree file of ND2 phylogeny in Fig. 2Ac85d10m12p3s14.xmlxml BEAST input file for SNAPP analysisND2_BEAST_pp.logposterior distributions of BEAST analysis, used to produce Fig. 4ND2_forBEAST_3.10.15.logND2_forBEAST_3.10.15.treesOutput tree files from BEAST analysis, used to produce MCC tree in Fig. 4c85d10m12p3s12_hyp.cast.vcfVCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4A)c85d10m12p3s12_hyp2.ER.vcfVCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4B)c85d10m14p3s14_hyp2.ER.CAsplit.vcfVCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4C) and to calculate Fstc85d10m11p3s11_all2.vcfVCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4D)