“…Post-speciation gene flow is becoming progressively recognized as a frequent phenomenon and it has been fairly common among felids in general and lynxes in particular [6], including current occasional hybridization at sites of range overlap (e.g. Lynx rufus and Lynx canadensis [25]). Therefore, evidence for post-divergence gene flow is not sufficient by itself to question the species-level taxonomic status of the Iberian lynx; further characterization of the patterns, timing, and outcome of admixture will be needed to assess the level of post-zygotic reproductive isolation between these two lynxes.Fig.…”
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.
“…Post-speciation gene flow is becoming progressively recognized as a frequent phenomenon and it has been fairly common among felids in general and lynxes in particular [6], including current occasional hybridization at sites of range overlap (e.g. Lynx rufus and Lynx canadensis [25]). Therefore, evidence for post-divergence gene flow is not sufficient by itself to question the species-level taxonomic status of the Iberian lynx; further characterization of the patterns, timing, and outcome of admixture will be needed to assess the level of post-zygotic reproductive isolation between these two lynxes.Fig.…”
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.
“…Climate change is also expected to cause a northward shift in bobcat (Lynx rufus (Schreber, 1777)) distribution (Anderson and Lovallo 2003;Roberts and Crimmins 2010), increasing the area of sympatry of lynx and bobcat. This interspecies range overlap will threaten lynx population persistence at the southern extent of their range through competition (Peers et al 2013) and hybridization (Schwartz et al 2004;Homyack et al 2008;Koen et al 2014b). If the St. Lawrence River impedes bobcat gene flow as it does lynx, then it is possible that the river might protect the core of lynx range north of the St. Lawrence River by limiting northward expansion of the range of bobcats from south of the river.…”
Section: Discussionmentioning
confidence: 99%
“…The lynx from Quebec and Newfoundland and Labrador presented by Row et al (2012Row et al ( , 2014 are a subset of what we present here. Furthermore, all lynx samples presented here are a subset of those reported in Koen et al (2014b). We measured pelt length to categorize individuals as adult or juvenile (Quinn and Gardner 1984;Slough 1996).…”
Section: Sample Collection and Genetic Profilingmentioning
Landscape barriers to gene flow, such as rivers, can affect animal populations by limiting the potential for rescue of these isolated populations. We tested the riverine barrier hypothesis, predicting that the St. Lawrence River in eastern Canada would cause genetic divergence of Canada lynx (Lynx canadensis Kerr, 1792) populations by restricting dispersal and gene flow. We sampled 558 lynx from eastern Canada and genotyped these at 14 microsatellite loci. We found three genetic clusters, defined by the St. Lawrence River and the Strait of Belle Isle, a waterway separating Newfoundland from mainland Canada. However, these waterways were not absolute barriers, as we found 24 individuals that appeared to have crossed them. Peripheral populations of lynx are threatened in parts of Canada and the USA, and it is thought that these populations are maintained by immigration from the core. Our findings suggest that in eastern North America, rescue might be less likely because the St. Lawrence River restricts dispersal. We found that ice cover was often sufficient to allow lynx to walk across the ice in winter. If lynx used ice bridges in winter, then climate warming could cause a reduction in the extent and longevity of river and sea ice, further isolating these peripheral lynx populations.
“…One of the best documented felid hybrid zones is between the bobcat and Canada lynx, which share a broad trans-continental range overlap in North America that has likely persisted to varying degrees as climate fluctuated across time. Genetic studies have identified several populations where hybridization is common along the US/ Canada border (Schwartz et al 2004;Homyack et al 2008;Koen et al 2014). ABBA/BABA tests indicate ancient signatures of bobcat-Canada lynx gene flow (Table 1), consistent with an extended period of gene flow that continues to the present day.…”
Section: Felid Diversification and Evidence For Hybridizationmentioning
Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X-and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven postdivergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.
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