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

• Main Authors: Koepfli, Klaus-Peter, Pollinger, John, Godinho, Raquel, Robinson, Jacqueline, Lea, Amanda, Hendricks, Sarah, Schweizer, Rena M., Thalmann, Olaf, Silva, Pedro, Fan, Zhenxin, Yurchenko, Andrey A., Dobrynin, Pavel, Makunin, Alexey, Cahill, James A., Shapiro, Beth, Álvares, Francisco, Brito, José C., Geffen, Eli, Leonard, Jennifer A., Helgen, Kristofer M., Johnson, Warren E., O'Brien, Stephen J., Van Valkenburgh, Blaire, Wayne, Robert K.
• Format: Dataset
• Language: English
• Published: Dryad 2016
• Subjects: Canidae; Canis aureus; Canis simensis; Canis latrans; Canis lupus
• Online Access: https://dx.doi.org/10.5061/dryad.3b77f; https://datadryad.org/stash/dataset/doi:10.5061/dryad.3b77f

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and ... : File 1_Genbank accessions list for cytochrome b and mitochondrial genomesGenbank 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.File 1_Genbank accessions list_cytb and mitochondrial genomes_v2.xlsxFile 2_Primers for 20 nuclear gene segmentsGene symbol and name, primer sequences, and description of the 20 nuclear gene segments used in the study.Primers_20 nuclear gene segments.xlsxFile 3 Best-fitting models for nuclear gene segmentsBest-fitting models_nuclear gene segments.xlsxFile 4 Sequence characteristicsLength (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.Sequence characteristics.xlsxFile 5 Microsatellite results_genetic diversity_populationsMean ...