Dataset Information

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

ABSTRACT: Genomic 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.We 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.The 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.

SUBMITTER: Abascal F

PROVIDER: S-EPMC5155386 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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

Abascal Federico F Corvelo André A Cruz Fernando F Villanueva-Cañas José L JL Vlasova Anna A Marcet-Houben Marina M Martínez-Cruz Begoña B Cheng Jade Yu JY Prieto Pablo P Quesada Víctor V Quilez Javier J Li Gang G García Francisca F Rubio-Camarillo Miriam M Frias Leonor L Ribeca Paolo P Capella-Gutiérrez Salvador S Rodríguez José M JM Câmara Francisco F Lowy Ernesto E Cozzuto Luca L Erb Ionas I Tress Michael L ML Rodriguez-Ales Jose L JL Ruiz-Orera Jorge J Reverter Ferran F Casas-Marce Mireia M Soriano Laura L Arango Javier R JR Derdak Sophia S Galán Beatriz B Blanc Julie J Gut Marta M Lorente-Galdos Belen B Andrés-Nieto Marta M López-Otín Carlos C Valencia Alfonso A Gut Ivo I García José L JL Guigó Roderic R Murphy William J WJ Ruiz-Herrera Aurora A Marques-Bonet Tomas T Roma Guglielmo G Notredame Cedric C Mailund Thomas T Albà M Mar MM Gabaldón Toni T Alioto Tyler T Godoy José A JA

Genome biology 20161214 1

<h4>Background</h4>Genomic 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.<h4>Results</h4>We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, e ...[more]

PMID: 27964752

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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.

Project description:The Iberian lynx (Lynx pardinus) is considered the most endangered felid species in the world. In order to save this species, the Spanish authorities implemented a captive breeding program recruiting lynxes from the wild. In this context, a retrospective survey on prevalence of selected feline pathogens in free-ranging lynxes was initiated.We systematically analyzed the prevalence and importance of seven viral, one protozoan (Cytauxzoon felis), and several bacterial (e.g., hemotropic mycoplasma) infections in 77 of approximately 200 remaining free-ranging Iberian lynxes of the Doñana and Sierra Morena areas, in Southern Spain, between 2003 and 2007. With the exception of feline immunodeficiency virus (FIV), evidence of infection by all tested feline pathogens was found in Iberian lynxes. Fourteen lynxes were feline leukemia virus (FeLV) provirus-positive; eleven of these were antigenemic (FeLV p27 positive). All 14 animals tested negative for other viral infections. During a six-month period in 2007, six of the provirus-positive antigenemic lynxes died. Infection with FeLV but not with other infectious agents was associated with mortality (p<0.001). Sequencing of the FeLV surface glycoprotein gene revealed a common origin for ten of the eleven samples. The ten sequences were closely related to FeLV-A/61E, originally isolated from cats in the USA. Endogenous FeLV sequences were not detected.It was concluded that the FeLV infection most likely originated from domestic cats invading the lynx's habitats. Data available regarding the time frame, co-infections, and outcome of FeLV-infections suggest that, in contrast to the domestic cat, the FeLV strain affecting the lynxes in 2007 is highly virulent to this species. Our data argue strongly for vaccination of lynxes and domestic cats in and around lynx's habitats in order to prevent further spread of the virus as well as reduction the domestic cat population if the lynx population is to be maintained.

Project description:Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequences and activity characteristics of bacterial intra-cellular extracts, in wild Iberian lynx (Lynx pardinus) fecal samples. Bacterial signatures (14.43% of all of the Firmicutes reads and 6.36% of total reads) related to the uncultured anaerobic commensals Anaeroplasma spp., which are typically found in ovine and bovine rumen, were first identified. The lynx gut was further characterized by an over-representation of 'presumptive' aquaporin aqpZ genes and genes encoding 'active' lysosomal-like digestive enzymes that are possibly needed to acquire glycerol, sugars and amino acids from glycoproteins, glyco(amino)lipids, glyco(amino)glycans and nucleoside diphosphate sugars. Lynx gut was highly enriched (28% of the total glycosidases) in genes encoding ?-amylase and related enzymes, although it exhibited low rate of enzymatic activity indicative of starch degradation. The preponderance of ?-xylosidase activity in protein extracts further suggests lynx gut microbes being most active for the metabolism of ?-xylose containing plant N-glycans, although ?-xylosidases sequences constituted only 1.5% of total glycosidases. These collective and unique bacterial, genetic and enzymatic activity signatures suggest that the wild lynx gut microbiota not only harbors gene sets underpinning sugar uptake from primary animal tissues (with the monotypic dietary profile of the wild lynx consisting of 80-100% wild rabbits) but also for the hydrolysis of prey-derived plant biomass. Although, the present investigation corresponds to a single sample and some of the statements should be considered qualitative, the data most likely suggests a tighter, more coordinated and complex evolutionary and nutritional ecology scenario of carnivore gut microbial communities than has been previously assumed.

Project description:The restoration of Iberian lynx (Lynx pardinus) populations in Extremadura (Southwestern Spain) have been carried out since 2014. One of the measures to ensure the success of this program is to examine the effects that diseases may have on reintroduction. Since diseases may be greatly located at certain sites because of the specific ecological requirements of the pathogens and/or vectors, reintroduced individuals may present a risk of infection once released. To determine which pathogens the reintroduced individuals may encounter, we performed a molecular and sero-epidemiological survey in reintroduced and wild-born lynxes. From 2015 to 2019, 69 Iberian lynxes (40 reintroduced and 29 wild-born) were sampled and screened against 10 viral, bacterial and piroplasmid agents. In parallel, 195 sympatric carnivores from the families Canidae, Felidae, Viverridae, Herpestidae and Mustelidae were tested against current or past infections to six common canine/feline viruses. In the Iberian lynx, low contact rates of active infection were obtained for the feline leukemia provirus (FeLV: 1.5%; 1/67), feline parvovirus (FPV: 1.5%; 1/67) and Cytauxzoon sp. (6.7%; 1/15). We also confirmed the emergence of Aujeszky's disease (suid herpesvirus-1) in this population (SuHV-1: 11.8%; 2/17). Evidence of previous exposure was detected for canine distemper virus (CDV: 5.8%; 3/52), feline coronavirus (1.9%; 1/52), FPV (7.7%; 1/13) and feline calicivirus (FCV: 5.3%; 1/19). From 25 recovered lynx carcasses, we could confirm infectious etiology involvement in the death of four individuals (SuHV-1 in two individuals, coinfection of Cytauxzoon spp. and Aeromonas veronii in one lynx and a Streptococcus canis myositis in another lynx). We confirmed the circulation of CDV, FPV, FeLV, FCV and the feline immunodeficiency virus within the sympatric carnivore community. Due to the low contact rate of infectious agents in such a small, endangered population, we recommend continuing a disease surveillance program to determine the prognostic factors of survival, understand the role that disease may play during the reintroduction and anticipate disease outbreaks that may pose a risk for the entire reintroduced population.

Dataset Information

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

Publications

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

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