Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Abstract

BackgroundGenomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.ResultsWe generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.ConclusionsThe genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1090-1) contains supplementary material, which is available to authorized users.

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts

“…The sustained negative population trends during the Holocene probably contribute to the signals of recent bottlenecks, such as reduced X/A ratios and high Tajima's D values that all populations show. Additionally, even the most diverse populations show values of genetic diversity similar to that of the severely bottlenecked Apennine brown bear (Benazzo et al, ), and only twice that of the extremely eroded sister‐species—the Iberian lynx (θ = 2.22 × 10 −4 , π = 2.6 × 10 −4 ; Abascal et al, ), whose values are comparable to the least diverse Eurasian lynx populations (Figure ). Still, differences in recent demography between populations, with European populations experiencing a severe reduction in population size throughout the Holocene and Asian populations usually maintaining a softer population decline, are reflected in current genetic patterns: European populations, especially westernmost ones, show larger genetic differentiation, increased drift parameters in treemix analysis, along with bottleneck signals and lower genome diversity.…”

“…PSMC, stairway plot and snep outputs were plotted, scaled to time and population sizes assuming a mean generation time of 5 years(Lucena-Perez et al, 2018) and a mutation rate per site per generation of 6 × 10 −9(Abascal et al, 2016).…”

Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (sectionProtobalanus)

“…We used an information‐theoretic model selection approach based on the Akaike's information criterion (AIC) to determine the probability of each model given the observed data (Burnham & Anderson, ; e.g. Abascal et al ., ; Thome & Carstens, ). After the maximum likelihood was estimated for each model in every replicate, we calculated the AIC scores as detailed in Thome & Carstens ().…”

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

“…Despite the difficulty in assessing the role of genetic factors in past extinctions of small populations, the causative link between low genetic and genomic variation, fitness reduction, and high extinction risk is supported by theoretical arguments and empirical evidence (24,(62)(63)(64)(65). Still, the long-term persistence of species at extremely low levels of genomic variation has also been documented (11,66).…”