Long-term genetic vulnerability and recent erosion in the highly endangered Iberian lynx
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15462 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1653720.fastq.gz | Fastqsanger.gz | |||
| ERR1653730.fastq.gz | Fastqsanger.gz | |||
| ERR1653730_1.fastq.gz | Fastqsanger.gz | |||
| ERR1653730_2.fastq.gz | Fastqsanger.gz | |||
| ERR1653740.fastq.gz | Fastqsanger.gz |
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Project description:EXTREME GENOMIC EROSION AFTER RECURRENT DEMOGRAPHIC BOTTLENECKS IN THE HIGHLY ENDANGERED IBERIAN LYNX
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Project description:Iberian and Eurasian lynx 6x samples
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Project description:Whole genome shotgun resequencing of ancient samples of Iberian lynx
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Project description: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.
| S-EPMC5155386 | biostudies-literature
Project description:Hepatitis E virus (HEV) is an emerging zoonotic pathogen in Europe. In the Iberian Peninsula, wild boar (Sus scrofa) is considered the main wildlife reservoir of HEV. This wild ungulate shares habitat and resources with other potential HEV carriers in Iberian Mediterranean ecosystems, although information about the role of such sympatric species in the HEV epidemiological cycle is still very limited. The aims of the present large-scale, long-term study were: (1) to determine the seroprevalence and prevalence of HEV in both free-living and captive populations of the Iberian lynx (Lynx pardinus), the most endangered felid in the world; (2) to determine potential risk factors associated with HEV exposure in this species and (3) to evaluate the dynamics of seropositivity in longitudinally sampled animals during the study period. Between 2010 and 2021, serum samples from 275 Iberian lynxes were collected in free-ranging and captive populations across the Iberian Peninsula. Forty-four of the 275 lynxes were also longitudinally sampled during the study period. A double-antigen sandwich ELISA was used to test for the presence of antibodies against HEV. A subset of seropositive samples was analysed by Western blot (WB) assay to confirm exposure to HEV. In addition, serum, liver and/or faecal samples from 367 individuals were tested for orthohepevirus RNA by RT-PCR. A total of 50 (18.2%; 95% CI: 14.1-23.2) of the 275 animals analysed had anti-HEV antibodies by ELISA. Exposure to HEV was confirmed by WB in most of the ELISA-positive Iberian lynxes analysed. Significantly higher seroprevalence was found in captive (33.6%) compared to free-ranging (7.4%) individuals. Within captive population, the GEE model identified 'age' (senile, adult and subadult) as risk a factor potentially associated with HEV exposure in the Iberian lynx. Thirteen (29.5%) of 44 longitudinally surveyed individuals seroconverted against HEV during the study period. HEV RNA was detected in the faeces of one (1/364; 0.3%; 95% CI: 0.0-0.8) free-ranging adult animal sampled in 2021. Phylogenetic analysis showed that the sequenced strain belongs to HEV-3f subtype and shared a high nucleotide sequence identity (97-99.6%) with human HEV-3f sequences from Spain and France. To the best of the authors' knowledge, this is the first survey study on HEV in the Iberian lynx and the first molecular report of HEV-A infection in free-ranging felines. Our results indicate high exposure to HEV-3 in Iberian lynx populations, particularly those kept in captivity. The serological results suggest widespread but not homogeneous circulation of HEV in Iberian lynx populations. Further studies are required to assess the epidemiological role of this endangered species as a potential spillover host of HEV.
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Project description:SignificanceThe dynamics of deleterious variation under contrasting demographic scenarios remain poorly understood in spite of their relevance in evolutionary and conservation terms. Here we apply a genomic approach to study differences in the burden of deleterious alleles between the endangered Iberian lynx (Lynx pardinus) and the widespread Eurasian lynx (Lynx lynx). Our analysis unveils a significantly lower deleterious burden in the former species that should be ascribed to genetic purging, that is, to the increased opportunities of selection against recessive homozygotes due to the inbreeding caused by its smaller population size, as illustrated by our analytical predictions. This research provides theoretical and empirical evidence on the evolutionary relevance of genetic purging under certain demographic conditions.
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Project description:A 6-month-old female Iberian lynx (Lynx pardinus) cub that was severely affected by mange died in September 2016 in the Montes de Toledo (Spain) with crusts and fissures on its face, outer ears, nipples and footpads. The body condition of the cub was very poor, and it also had a mandibular abscess and a severely ankylosed luxation on its left knee. After confirming that the origin of the deceased cub's dermal lesions was Sarcoptes scabiei, the subsequent search for ectoparasites and a comparison of histopathological and immunohistochemical findings in all sympatric lynxes handled (n?=?30) and submitted for necropsy (n?=?4) during 2016 and 2017 revealed the presence of S. scabiei mites and/or milder mange compatible lesions in five members of her family group, which was treated against mange together with two exposed contiguous family groups. An ELISA developed by the authors showed the presence of antibodies against S. scabiei in the deceased female cub and one brother. The presence of concomitant immunosuppressive factors in the dead female cub and the results obtained for the other sympatric lynxes studied since 2016 suggest that S. scabiei had a limited effect on immune-competent Iberian lynxes in the local population of the Montes de Toledo. However, a different evolution and relevance of sarcoptic mange in different populations-or even in the same one in the presence of immunosuppressive factors-cannot be ruled out, thus confirming the need for further research in order to attain a complete comprehension of the epidemiology and the real threat that this ectoparasitic disease may imply for L. pardinus.
| S-EPMC7087905 | biostudies-literature