Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena

Abstract

The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.

Fig. 1. Sampling distribution and mitogenomic timetree of the hyaenidae family.

(A) Map showing the geographic origins of our spotted and cave hyena samples. The color of the dot represents the age of the sample. (B) Dated Bayesian phylogenetic tree constructed using complete mitochondrial genomes and a strict molecular clock. Haplogroups are those previously defined in Rohland et al. (9). Red-colored labels show Pleistocene cave hyena and blue-colored labels show modern spotted hyena. The yellow star represents a putative mitochondrial introgression event of unknown direction. The Hyaena/Parahyaena node was fixed for fossil calibration (as indicated by the bone image), and Proteles was set as the outgroup. All major nodes had posterior probability values of 1 (fig. S1). Dark blue node bars show the 95% credibility interval of the divergence dating.

Fig. 2. Population structure analyses comparing nuclear genomic information from Pleistocene cave hyena and modern spotted hyena.

(A) PCA based on genome-wide SNPs. Red shaded area encompasses cave hyenas and blue shaded area encompasses spotted hyenas. (B) Densitree constructed using 2 Mbp sliding windows and a maximum likelihood approach. Light gray lines represent single phylogenetic trees produced from each window. Dark black lines represent the root canal as defined by Densitree. Sample name colors represent the previously defined mitochondrial haplogroups.

Fig. 3. PSMC demographic analyses of three modern spotted hyena nuclear genomes.

The y axis represents effective population size (×10,000), and the x axis represents millions of years before present. Faded lines show bootstrap values.

Fig. 4. D statistics results and a schematic overview of the divergence of and post-divergence gene flow between spotted and cave hyenas.

(A) D statistics results using two cave hyenas, one spotted hyena, and the striped hyena as outgroup. (B) D statistics results using two spotted hyenas, one cave hyena, and the striped hyena as outgroup. Filled circles show significant D scores while nonfilled circles show nonsignificant D scores. (C) Phylogenetic tree presenting the admixture events found between African spotted and Eurasian cave hyena. Blue color represents African inhabitancy and red color represents Eurasian inhabitancy. Arrows show the direction of gene flow events. (Illustration credit: Binia De Cahsan, https://sites.google.com/view/decahsanillustrations.)