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.)

Winger BM, Hosner PA, Bravo GA, Cuervo AM, Aristizábal N, Cueto LE, Bates JM

Date Published: November 13, 2015

DOI: http://dx.doi.org/10.5061/dryad.q268m

 

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Title c85d10m7p3s7.phy
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Description Phylip sequence alignment of concatenated GBS loci underlying Fig. S2B
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Title c85d10m12p3s16.phy
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Description Phylip sequence alignment of concatenated GBS loci underlying Fig. S2A
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Title c85d10m8p3sALL.phy
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Description Phylip sequence alignment of concatenated GBS loci underlying Fig. 2B
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Title c85d5m8p3sALL.phy
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Description Phylip sequence alignment of concatenated GBS loci generated with a cluster depth of 5 or greater (phylogeny described, but not illustrated, in manuscript)
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Title RAxML_bipartitions.c85d8m8p3sALL.tree
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Description RAxML 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)
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Title RAxML_bipartitions.c85d10m7p3s7_b1000.tree
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Description RAxML tree file of GBS phylogeny in Fig. S2B
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Title RAxML_bipartitions.c85d10m8p3sALL_b1000.tree
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Description RAxML tree file of GBS phylogeny in Fig. 2B
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Title RAxML_bipartitions.c85d10m12p3s16_b1000.tree
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Description RAxML tree file of GBS phylogeny in Fig. S2A
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Title RAxML_bipartitions.ND2_10.6.15_b1000
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Description RAxML tree file of ND2 phylogeny in Fig. 2A
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Title c85d10m12p3s14.xml
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Description xml BEAST input file for SNAPP analysis
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Title ND2_BEAST_pp.log
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Description posterior distributions of BEAST analysis, used to produce Fig. 4
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Title ND2_forBEAST_3.10.15.trees
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Description Output tree files from BEAST analysis, used to produce MCC tree in Fig. 4
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Title c85d10m12p3s12_hyp.cast.vcf
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Description VCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4A)
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Title c85d10m12p3s12_hyp2.ER.vcf
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Description VCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4B)
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Title c85d10m14p3s14_hyp2.ER.CAsplit.vcf
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Description VCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4C) and to calculate Fst
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Title c85d10m11p3s11_all2.vcf
Downloaded 6 times
Description VCF file (output from pyRAD) used to calculate nucleotide diversity in VCFTools (Fig. S4D)
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When using this data, please cite the original publication:

Winger BM, Hosner PA, Bravo GA, Cuervo AM, Aristizábal N, Cueto LE, Bates JM (2015) Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.). Molecular Ecology 24(24): 6256–6277. http://dx.doi.org/10.1111/mec.13477

Additionally, please cite the Dryad data package:

Winger BM, Hosner PA, Bravo GA, Cuervo AM, Aristizábal N, Cueto LE, Bates JM (2015) 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.). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.q268m
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