DOI: 10.5061/dryad.3b77f
title: Data from: Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species

description: 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 Eurasian golden jackals and gray wolves. Our
 results provide consistent and robust evidence that populations of golden
 jackals from Africa and Eurasia represent distinct monophyletic lineages
 separated for more than one million years, sufficient to merit formal
 recognition as different species: C. anthus (African golden wolf) and C.
 aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a
 striking morphologic similarity between East African and Eurasian golden
 jackals, suggesting parallelism, which may have misled taxonomists and
 likely reflects uniquely intense interspecific competition in the East
 African carnivore guild. Our study shows how ecology can confound taxonomy
 if interspecific competition constrains size diversification.
description: 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 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.Microsatellite results_genetic
 diversity_populations.pdfFile 6 Microsatellite
 results_genetic diversity_38 lociNumber 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&lt;0.05).Microsatellite results_genetic
 diversity_38 loci.docxFile 7 Microsatellite
 results_Likelihoods for genetic clustersMicrosatellite results
 Likelihoods for genetic
 clusters.docxFile 8 Microsatellite
 results_Neighbor-joining genetic distance networkMicrosatellite
 results_Neighbor-joining genetic distance
 network.docxFile
 9_D-statistics_plotD-statistic results for
 each D-statistic comparison done in the study.D-statistics_plot.pdfFile 10_Morphology_Loadings for 45 craniodental measurementsLoadings for 45 craniodental measurements included in PCA analysis.Morphology_Loadings for 45 craniodental measurements.xlsFile 11_Morphology_Loadings for craniodental ratiosLoadings for nine arcsine-transformed craniodental ratios included in PCA analysisMorphology_Loadings for craniodental ratios.xls