Data from: Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ

Date Published: September 18, 2017

DOI: https://doi.org/10.5061/dryad.3j218

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Title iqtree_ml
Downloaded 6 times
Description RADseq aDNA phylogeny
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Title iqtree_ultrafast_bootstrap_consensus
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Description RADseq aDNA ultrafastbootstraps
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Title FigTree_xDNA_gapped_and_ungapped_data_included
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Description RADseq xDNA chronogram
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Title FigTree_mcmctree_independent_rates
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Description RADseq aDNA chronogram
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Title boot_chrX
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Description RADseq xDNA ultrafastbootstraps
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Title iqtree_chrX
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Description RADseq xDNA phylogeny
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Title Genotypes_only_male_chrX_based_on_allelic_depth
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Description Script to generate a haploid chromosome X genotype from a vcf file based on allelic coverage. Command line format is in comments in the script.
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Title Performs_ABBA_BABA_on_populations
Downloaded 5 times
Description Perl script to calculate fDM and D statistics (two types of ABBABABA statistics) from a tab delimited input file. Command line format is in comments in the script.
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Title Performs_ABBA_BABA_on_populations_onlychrX
Downloaded 3 times
Description Script to calculate fDM and D statistic from chromosome X data in a tab delimited file. Command line format is in comments in the script.
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Title nonrecal_filtered_chr1_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr1
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Title nonrecal_filtered_chr2_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr2
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Title nonrecal_filtered_chr3_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr3
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Title nonrecal_filtered_chr4_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr4
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Title nonrecal_filtered_chr5_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr5
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Title nonrecal_filtered_chr6_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr6
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Title nonrecal_filtered_chr7_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr7
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Title nonrecal_filtered_chr8_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr8
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Title nonrecal_filtered_chr9_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr9
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Title nonrecal_filtered_chr10_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr10
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Title nonrecal_filtered_chr11_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr11
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Title nonrecal_filtered_chr12_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr12
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Title nonrecal_filtered_chr13_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr13
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Title nonrecal_filtered_chr14_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr14
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Title nonrecal_filtered_chr15_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr15
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Title nonrecal_filtered_chr16_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr16
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Title nonrecal_filtered_chr17_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr17
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Title nonrecal_filtered_chr18_final.vcf.gz_norepeat.vcf
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Description HiSeqX aDNA vcf, repeats removed, chr18
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Title nonrecal_filtered_chr19_final.vcf.gz_norepeat.vcf
Downloaded 14 times
Description HiSeqX aDNA vcf, repeats removed, chr19
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Title nonrecal_filtered_chr20_final.vcf.gz_norepeat.vcf
Description HiSeqX aDNA vcf, repeats removed, chr20
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Title nonrecal_filtered_chrX_final.vcf.gz_norepeat.vcf
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Description HiSeqX chrX vcf file, repeats excluded, diploid genotypes
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Title nonrecal_filtered_chrX_final.vcf.gz_norepeat_nomalehets.vcf
Downloaded 2 times
Description HiSeqX chrX vcf file, repeats excluded, male hets excluded, diploid genotypes
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Title GenotypeVCFs_noBSQR_filtered_aDNA_only.vcf
Downloaded 2 times
Description RADseq aDNA vcf
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Title GenotypeVCFs_noBSQR_filtered_xDNA_only.vcf
Downloaded 2 times
Description RADseq chrX vcf
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Title GenotypeVCFs_noBSQR_filtered_aDNA_only.vcf.gz.tab_with_baboon_and_human
Downloaded 1 time
Description Autosomal RADseq alignment with human, baboon,and rhesus outgroups
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Title GenotypeVCFs_noBSQR_filtered_xDNA_only_genotyped_based_on_depth_with_baboon_and_human
Downloaded 1 time
Description chrX RADseq alignment with human, baboon,and rhesus outgroups
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Title README
Downloaded 5 times
Description README file; this is a summary of the files in this accession.
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When using this data, please cite the original publication:

Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ (2017) Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. Royal Society Open Science 4(10): 170351. https://doi.org/10.1098/rsos.170351

Additionally, please cite the Dryad data package:

Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ (2017) Data from: Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. Dryad Digital Repository. https://doi.org/10.5061/dryad.3j218
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