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.
File 1_Genbank accessions list for cytochrome b and mitochondrial genomes
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.
File 1_Genbank accessions list_cytb and mitochondrial genomes_v2.xlsx
File 2_Primers for 20 nuclear gene segments
Gene symbol and name, primer sequences, and description of the 20 nuclear gene segments used in the study.
Primers_20 nuclear gene segments.xlsx
File 3 Best-fitting models for nuclear gene segments
Best-fitting models_nuclear gene segments.xlsx
File 4 Sequence characteristics
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.
Sequence characteristics.xlsx
File 5 Microsatellite results_genetic diversity_populations
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.
Microsatellite results_genetic diversity_populations.pdf
File 6 Microsatellite results_genetic diversity_38 loci
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).
Microsatellite results_genetic diversity_38 loci.docx
File 7 Microsatellite results_Likelihoods for genetic clusters
Microsatellite results Likelihoods for genetic clusters.docx
File 8 Microsatellite results_Neighbor-joining genetic distance network
Microsatellite results_Neighbor-joining genetic distance network.docx
File 9_D-statistics_plot
D-statistic results for each D-statistic comparison done in the study.
D-statistics_plot.pdf
File 10_Morphology_Loadings for 45 craniodental measurements
Loadings for 45 craniodental measurements included in PCA analysis.
Morphology_Loadings for 45 craniodental measurements.xls
File 11_Morphology_Loadings for craniodental ratios
Loadings for nine arcsine-transformed craniodental ratios included in PCA analysis
Morphology_Loadings for craniodental ratios.xls