Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA

Abstract

There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.

Insights from 180 years of mitochondrial variability in the endangered Mediterranean monk seal (Monachus monachus)

“…The ratio between haplotype numbers and the total number of samples (7/204 = 0.03) was the same as that reported in Karamanlidis et al (2016b) for 165 recent samples covering the current species' range. Such low levels of mitochondrial diversity correspond to levels observed in other mammalian species at the brink of extinction (Rosel and Rojas-Bracho 1999, Rosenbaum et al 2000, Weber et al 2000, Rodriguez et al 2011, Casas-Marce et al 2017.…”

“…The current pattern of low genetic diversity and population isolation observed in MMS is likely explained by a series of local, historical extinctions coupled with the effect of genetic drift on small breeding populations with already low levels of genetic diversity (as in the critically endangered Iberian lynx; Casas‐Marce et al . ). Such a scenario concurs with the conclusions of Pastor et al .…”

“…The use of historical samples allows for a direct assessment of genetic diversity loss over time (Rosenbaum et al 2000). In the case of genetically depauperate species under extinction risk, the analysis of historical samples may allow investigation of whether human activities have had a direct impact on the loss of genetic diversity (Matocq and Villablanca 2001, Wandeler et al 2007, Casas-Marce et al 2017.…”

“…, Casas‐Marce et al . ). To reach such an objective, access to historical specimens—notably from museum collections—is a critical step because such material often represents, especially in the case of endangered and/or elusive species, extinct or rare populations (Suarez and Tsutsui , Spurgin et al .…”

“…Because of the fragmented distribution of extant populations and their very low genetic diversity, scenarios for the demographic history of MMS and the time at which populations collapsed have remained speculative. In order to understand the ongoing process of a species' extinction, it is critical to take into account its past genetic diversity (e.g., Foote et al 2013, Casas-Marce et al 2017. To reach such an objective, access to historical specimens-notably from museum collections-is a critical step because such material often represents, especially in the case of endangered and/or elusive species, extinct or rare populations (Suarez andTsutsui 2004, Spurgin et al 2014).…”