Hybridizing hyenas and how to find them

Genomes of extant and extinct hyenas reveal a reticulated history.

Almost every study that uses genomic data to retrace the evolutionary history of particular species uncovers traces of hybridization. Hyenas are no exception. A recent paper in the journal Science Advances reported gene flow between African spotted hyenas and extinct Eurasian cave hyenas. Spotted hyenas (Crocuta crocuta) are large carnivores that currently occur in sub-Saharan Africa. Compared to their African cousins, cave hyenas have shorter limbs and blunter teeth, suggesting that they were mainly scavengers. Based on more suble morphological differences, cave hyenas have been split into European (spelaea) and Asian (ultima) subspecies.

The genomic data pointed to a deep divergence (about 2.5 million years ago) followed by bidirectional gene flow sometime before 475,000 years ago. The study nicely outlines the different analyses that led to this conclusion. Let’s have a look.


A Spotted Hyena © Alicave | Pixabay



We start with the mtDNA. Previous work with short mitocondrial fragments could not differentiate between spotted and cave hyenas. Using whole mitochondrial genomes did not markedly change this conclusion. The resulting evolutionary tree is a mixture of both hyenas, albeit with more resolution.

Perhaps nuclear DNA might help resolve this phylogenetic mess? The researchers constructed almost 500 phylogenetic trees based on DNA sequences of 2 million letters. Most of these trees supported a clear split between spotted hyenas and cave hyenas. The incongruence between nuclear and mitochondrial phylogenies already indicates that something interesting is happening here. Are we dealing with incomplete lineage sorting or hybridization?


Incongruence between mitochondrial and nuclear DNA. (A) Phylogenetic analyses of mtDNA could be discriminate between spotted hyena (blue) and cave hyena (red). (B) Nuclear DNA, however, pointed to a clear split between both hyena types (Africa vs. Europe and Asia). Adapted from: Westbury et al. 2020 Science Advances


D-statistics and Simulations

Next, the researchers turned to everyone’s favorite test for ancient gene flow: the D-statistic (see this blog post for more information). They used an adjusted version of the D-statistic that infers the direction of gene flow. Calculating this statistic for different genomic regions revealed several instances of gene flow between spotted hyenas and cave hyenas. However, the patterns of gene flow depended on the individual genomes that were being compared. These results can be explained in two ways: (1) multiple gene flow events into spotted hyenas or (2) a single admixture event was followed sorting of the cave hyena loci.

To figure out which explanation was more likely, another approach was added to the mix: a coalescent modelling excercise. The researchers used Fastsimcoal to explore different scenarios of gene flow. These analyses suggested that gene flow was mostly bidirectional but with more gene flow from Europe into Africa in more recent times (as shown in the figure below). Given that the spotted and cave hyenas with mitochondrial haplotype A diverged about 475,000 years ago, these gene flow events probably happened after this split. More research is needed to pinpoint the exact timing.


The most likely model of gene flow between spotted hyenas and cave hyenas. From: Westbury et al. 2020 Science Advances



The researchers nicely summarize their findings: “We suggest a bidirectional gene flow event between cave and spotted hyenas after the split of cave hyenas into the European and Asian lineages and a subsequent unidirectional gene flow event into northern spotted hyenas, followed by differential diffusion of the admixed loci within the other spotted hyena lineages”



Westbury, M.V. et al. (2020). Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena. Science Advances6(11), eaay0456.

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