Extremely low genetic variation in endangered Tatra chamois and evidence for hybridization with an introduced Alpine population

Zemanová, Barbora; Hájková, Petra; Hájek, Bedřich; Martínková, Natália; Mikulíček, Peter; Zima, Jan; Bryja, Josef

doi:10.1007/s10592-015-0696-2

Cited by 17 publications

(19 citation statements)

References 67 publications

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“…Many conservation genetics studies have compared heterozygosity among natural populations to evaluate individual inbreeding and the loss of genetic variation (e.g. Dobrynin et al., ; Gebremedhin et al., ; Li et al., ; Paetkau et al., ; Zemanová et al., ). A limitation of this approach is that mean heterozygosity will be reduced both in populations with recently reduced effective population size ( N e ) and in populations that have been small for a long time.…”

Section: Identifying Populations Where Inbreeding Depression Is Likelmentioning

confidence: 99%

Genomics advances the study of inbreeding depression in the wild

Kardos

Taylor

Ellegren

et al. 2016

Evolutionary Applications

217

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Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high‐throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.

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Section: Identifying Populations Where Inbreeding Depression Is Likelmentioning

confidence: 99%

Genomics advances the study of inbreeding depression in the wild

Kardos

Taylor

Ellegren

et al. 2016

Evolutionary Applications

217

270

View full text Add to dashboard Cite

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“…Exact length was required for the dominant sequence within a cluster. From previous work on this species [22,[27][28][29], we did not expect more than two DRB variants per individual, so we kept the "minimum dominant frequency" clustering threshold at default 25%. Variants with frequency lower than 1% within an amplicon were discarded.…”

Section: Mhc Genotyping By An Amplicon-based Ngs Approachmentioning

confidence: 99%

MHC Genotyping by SSCP and Amplicon-Based NGS Approach in Chamois

Stipoljev

Bužan

Rolečková

et al. 2020

Animals

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Genes of the major histocompatibility complex (MHC) code for cell surface proteins essential for adaptive immunity. They show the most outstanding genetic diversity in vertebrates, which has been connected with various fitness traits and thus with the long-term persistence of populations. In this study, polymorphism of the MHC class II DRB locus was investigated in chamois with Single-Strand Conformation Polymorphism (SSCP)/Sanger genotyping and Ion Torrent S5 next-generation sequencing (NGS). From eight identified DRB variants in 28 individuals, five had already been described, and three were new, undescribed alleles. With conventional SSCP/Sanger sequencing, we were able to detect seven alleles, all of which were also detected with NGS. We found inconsistencies in the individual genotypes between the two methods, which were mainly caused by allelic dropout in the SSCP/Sanger method. Six out of 28 individuals were falsely classified as homozygous with SSCP/Sanger analysis. Overall, 25% of the individuals were identified as genotyping discrepancies between the two methods. Our results show that NGS technologies are better performing in sequencing highly variable regions such as the MHC, and they also have a higher detection capacity, thus allowing a more accurate description of the genetic composition, which is crucial for evolutionary and population genetic studies.

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“…Subsequent analyses using microsatellites, sex‐determining region Y gene, major histocompatibility complex and mtDNA confirmed up to 19% of male‐biased introgressive hybridisation between the two subspecies (Zemanová et al. ). Finally, potential issues of hybridisation have been suggested to occur in the Chartreuse Massif in the French Alps, where the genetic identity of the endemic subspecies Rupicapra rupicapra cartusiana is put at risk by translocations of individuals of the Alpine subspecies for hunting purposes (Roucher ), although evidence of hybridisation is currently lacking.…”

Section: Resultsmentioning

confidence: 96%

“…Zemanová et al. () suggested that the effects might include the disruption of local genetic adaptations, outbreeding depression, local extinctions, the increase of genetic variation, and enhanced adaptability to environmental change in populations with reduced genetic diversity. Future research on the effects of hybridisation on fitness‐related traits is thus of paramount importance for planning appropriate conservation measures.…”

Section: Resultsmentioning

confidence: 99%

Hybridisation in European ungulates: an overview of the current status, causes, and consequences

et al. 2018

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Hybridisation and gene introgression are important sources of diversification, the relevance of which in the evolutionary processes is well recognised. Their fitness consequences in animal populations, however, are not sufficiently well understood, despite hybridisation rates becoming increasingly important worldwide following human‐related activities such as domestication, game management and habitat alteration. In Europe, the density and distribution of native ungulates have largely been influenced by humans since pre‐historic times. This, alongside the introduction of non‐native and domesticated species, may bear major consequences at the genetic and population levels. We provide an updated overview of recent hybridisation events in wild European ungulates; we describe their ecological drivers, extent, current distribution, potential consequences and proposed management strategies. We reviewed the scientific literature published between 2000 and 2018 and found that confirmed hybridisation was described in 75 of the 89 references we included, involving nearly all the species that we investigated. Most researchers relied on genetic information for hybrid identification, which often involved a domestic counterpart. However, introductions and translocations also led to crossbreeding between wild ungulate (sub)species. Only 43 papers provided management recommendations, mostly focused on preventing hybridisation and removing hybrids. Hybridisation proved to be relatively common in several ungulate taxa in Europe. Despite reported changes in phenotype and fitness‐related traits in some species, the consequences of hybridisation for adaptation, life history, and evolutionary potential remain largely unknown. The current conservation paradigm aims to prevent the spread of domestic or non‐native genes in native populations; accordingly, conservation plans should: 1) determine the genetic origin of possible source populations; 2) protect native populations from the risk of crossbreeding with non‐native ones, and 3) establish permanent monitoring.

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Extremely low genetic variation in endangered Tatra chamois and evidence for hybridization with an introduced Alpine population

Cited by 17 publications

References 67 publications

Genomics advances the study of inbreeding depression in the wild

Genomics advances the study of inbreeding depression in the wild

MHC Genotyping by SSCP and Amplicon-Based NGS Approach in Chamois

Hybridisation in European ungulates: an overview of the current status, causes, and consequences

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