Speciation with gene flow in equids despite extensive chromosomal plasticity

Abstract

Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

Keywords: admixture; chromosomal rearrangements; equids; evolutionary genomics; speciation.

Fig. 1.

SNV overlap, heterozygosity, and inbreeding. (A) Number of SNVs identified with respect to horse, in millions. Smaller bars indicate the overlap with the other species sequenced in this study and the donkey (DON) from Orlando et al. (2). (B) Genome-wide distribution of heterozygosity values inferred from the θ-Watterson estimator in 50-kb blocks. The analysis was restricted to transversions for comparison with the QUA sample.

Fig. 2.

Equine phylogeny, selection scan, and karyotypic and mutational changes. (A) Inferred number of chromosome pairs for each ancestral node. (B) Phylogenetic chronogram of lineage divergence in equids based on a relaxed molecular clock. All nodes received 100% bootstrap support. The names of the genes showing evidence of positive selection are reported above the branches concerned. The numbers provided below branches refer to rates of gene loss and chromosome gains and losses, respectively. The numbers of chromosome pairs (dominant form) are indicated below species names.

Fig. 3.

PSMC demographic profiles for all extant equid species over the last 2 million years.

Fig. 4.

Proposed population model for equids. Events of gene flow between populations are represented by arrows with directionality if available. The exact timing of such events is not known at present. The dashed arrow indicates the result of a significant admixture test that likely reflects the consequence of the gene flow detected between E. a. somaliensis and E. grevyi. Divergence (time to the most recent common ancestor, TMRCA) and population split times are indicated by darker and lighter ends of the colored rectangles, respectively.

Fig. 5.

Karyotypic rearrangements and gene flow in equids. (A) An example of karyotypic rearrangement between positions 1,920,626 and 47,900,194 on the second horse chromosome. The filled segment encloses the area between two BAC markers from Musilova et al. (17). (B) Genetic distance (Upper) and D statistics (Δ_AB/T, Lower) across the genomic region showing a chromosomal rearrangement. The genetic distance is calculated within 200-kb nonoverlapping windows for all species pairs involved in the proposed SOM-GRE admixture event. The D statistics values are calculated within 1-Mb nonoverlapping windows for D(SOM,DON;X,TWI), where X is DON, KIA, ONA, or SOM.