Complex admixture preceded and followed the extinction of wisent in the wild

Abstract

Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe's largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.

Past climate changes, population dynamics and the origin of Bison in Europe

“…It is interesting to note that this radiation event could be coincident with the onset and intensification of high-latitude glacial cycles (100 kyr-periodicity) around 1.2-0.8 mya. Incomplete lineage sorting, however, does not preclude later sporadic introgression of nuclear DNA at any point up to the present owing to the persistent interfertility between these species, as evidenced by the detection in the wisent genome of ancient gene flow from B. p. taurus [35,36].…”

A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombinaandB. variegata)

“…Local ancestry tracts provide the most direct evidence for hybridisation, as they cannot be explained by incomplete lineage sorting or convergence (Rieseberg et al 2000). They have been used to infer the number of generations required to stabilise a hybrid sunflower species (Ungerer et al 1998), uncover the lack of F2 or deeper hybrid generations in a Populus hybrid zone (Christe et al 2016), compare the age of two separate hybrid zones of Lissotriton newts (Zieliński et al 2019), detect past episodes of hybridisation (Meier et al 2017;Węcek et al 2017;Duranton et al 2020), localise introgressed genomic segments (Huerta-Sánchez et al 2014;vonHoldt et al 2016), identify incompatible haplotype combinations in hybrid swordfish (Powell et al 2020), and monitor shifts in genome composition in experimental Drosophila populations (Matute et al 2020). The rapidly growing theoretical literature infers evolutionary processes from genome-wide local ancestry patterns, from the age of ancient admixture pulses (Harris and Nielsen 2013) to the onset of neutral mixing with continuous gene flow (Sedghifar et al 2015), adaptive introgression (Sachdeva and Barton 2018;Shchur et al 2019), and selection against deleterious allele combinations in hybrid zones (Sedghifar et al 2016;Hvala et al 2018).…”