Data from: Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species

Koepfli K, Pollinger J, Godinho R, Robinson J, Lea A, Hendricks S, Schweizer RM, Thalmann O, Silva P, Fan Z, Yurchenko AA, Dobrynin P, Makunin A, Cahill JA, Shapiro B, Álvares F, Brito JC, Geffen E, Leonard JA, Helgen KM, Johnson WE, O'Brien SJ, Van Valkenburgh B, Wayne RK

Date Published: August 17, 2015

DOI: http://dx.doi.org/10.5061/dryad.3b77f

 

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Title File 1_Genbank accessions list for cytochrome b and mitochondrial genomes
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Description Genbank accessions, species and source localities of sequences from previously published studies that were used in the cytochrome b (Cytb) and/or mitochondrial genome (mitogenome) phylogenetic analyses.
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Title File 2_Primers for 20 nuclear gene segments
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Description Gene symbol and name, primer sequences, and description of the 20 nuclear gene segments used in the study.
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Title File 3 Best-fitting models for nuclear gene segments
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Title File 4 Sequence characteristics
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Description Length (bp = base pairs), number of variable sites, number of parsimony-informative sites and mean empirical base frequency of the mitochondrial (CYTB and mitochondrial genome) and nuclear (20 individual loci and concatenated) data sets used in the phylogenetic analyses.
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Title File 5 Microsatellite results_genetic diversity_populations
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Description Mean genetic diversity indices for 38 autosomal microsatellite loci in four golden jackal populations plus gray wolves and dogs (n=128). Standard errors are given in parenthesis. N = number of individuals; Na = number of alleles; He = expected heterozygosity.
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Title File 6 Microsatellite results_genetic diversity_38 loci
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Description Number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He) and fixation index (Fis) computed as in Weir and Cockerham [S67] for each of the 38 microsatellites genotyped at four golden jackal populations, gray wolves and dogs. Deviations from Hardy-Weinberg expectations in each population are indicated with * (p<0.05).
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Title File 7 Microsatellite results_Likelihoods for genetic clusters
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Title File 8 Microsatellite results_Neighbor-joining genetic distance network
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Title File 9_D-statistics_plot
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Description D-statistic results for each D-statistic comparison done in the study.
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Title File 10_Morphology_Loadings for 45 craniodental measurements
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Description Loadings for 45 craniodental measurements included in PCA analysis.
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Title File 11_Morphology_Loadings for craniodental ratios
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Description Loadings for nine arcsine-transformed craniodental ratios included in PCA analysis
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When using this data, please cite the original publication:

Koepfli K, Pollinger J, Godinho R, Robinson J, Lea A, Hendricks S, Schweizer RM, Thalmann O, Silva P, Fan Z, Yurchenko AA, Dobrynin P, Makunin A, Cahill JA, Shapiro B, Álvares F, Brito JC, Geffen E, Leonard JA, Helgen KM, Johnson WE, O'Brien SJ, Van Valkenburgh B, Wayne RK (2015) Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species. Current Biology 25(16): 2158–2165. http://dx.doi.org/10.1016/j.cub.2015.06.060

Additionally, please cite the Dryad data package:

Koepfli K, Pollinger J, Godinho R, Robinson J, Lea A, Hendricks S, Schweizer RM, Thalmann O, Silva P, Fan Z, Yurchenko AA, Dobrynin P, Makunin A, Cahill JA, Shapiro B, Álvares F, Brito JC, Geffen E, Leonard JA, Helgen KM, Johnson WE, O'Brien SJ, Van Valkenburgh B, Wayne RK (2015) Data from: Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3b77f
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