Abstract
Disentangling the contribution of long‐term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key to assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns, and discuss the influence of long‐term isolation and/or more recent human‐driven changes. Our results show that Eurasian lynx populations shared a common history until 100,000 years ago, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times probably drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified in recent centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long‐term isolation argue for the restoration of lost population connectivity.
Highlights
Climatic oscillations and geological events have influenced the range of species and the size and connectivity of their populations, driving divergence and admixture processes that give rise to the biodiversity patterns we see today (Avise et al, 1987; Endler, 1977)
Our results indicate that the Eurasian lynx was genetically quite homogeneous at least until 100 kya, when lynx populations started diverging and the species entered a widespread and continuous demographic decline that affected the European populations in particular
Lower population sizes and increased fragmentation in the westernmost part of the distribution in more recent times probably drove the genetic differentiation between European populations that are otherwise geographically and ecologically close
Summary
Climatic oscillations and geological events have influenced the range of species and the size and connectivity of their populations, driving divergence and admixture processes that give rise to the biodiversity patterns we see today (Avise et al, 1987; Endler, 1977). The availability of new reference genomes is helping to overcome most of the limitations of classical genetic markers and to expand the range of questions that can be addressed, including the assessment of the relative influence of current (human-driven) and long-term evolutionary processes (Abascal et al, 2016; Feng et al, 2019; Li et al, 2014; Murchison et al, 2012). We addressed to what extent long-term isolation and/or recent human-driven changes have impacted the lynx populations by analysing: (a) the history of population size, divergence and admixture among lynx populations; and (b) the current patterns of genetic structure and diversity across its distributional range. We discuss the level of genetic support for the proposed subspecies and the implications for the conservation of its most endangered populations
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