MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris)

Pokorny, Ina; Sharma, Reeta; Goyal, Surendra Prakash; Mishra, Sudanshu; Tiedemann, Ralph

doi:10.1007/s00251-010-0475-7

Cited by 33 publications

(38 citation statements)

References 52 publications

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“…However, we did not find signatures of long-term positive selection in the form of an increased d N /d S ratio at ABS for any MHC family. Contrastingly, such positive selection signals were previously described in analyses of MHCI in cheetah [30], bengal tiger [32] and leopard [31], and for MHCII-DRB in eight different Felidae lineages [28], cheetah [30], but not in bengal tiger [32], leopard [31] or Eurasian lynx [29]. Interestingly, for MHCI we found d S at the ABS to be much larger than d S at non-ABS, this indicates that the ABS regions are older than non-ABS and points to positive selection acting in presence of recurrent gene conversion events [45].…”

Section: Discussionmentioning

confidence: 95%

“…Also the transcripts from two different Iberian lynxes annotated as MHCI or MHCII-DRB by the Iberian lynx genome project [35] were included. Primers were designed in approximately the same regions as the ones used in previous studies on MHC variation in the Felidae to enable comparisons [28, 30–32]. More specifically, MHCI primers spanned bases 2 to 21 (forward) and 253 to 271 (reverse) of the human MHC class I exon 2 and MHC class II-DRB spanned bases 4 to 23 (forward) and 270 to 288 (reverse) of the human homologues [78–80].…”

Section: Methodsmentioning

confidence: 99%

“…In felids MHC genes have received special attention due to the role of domestic cat as a model for human diseases [24–27] and because of its possible impact on endangered wild felid conservation, including the paradigmatic case of the cheetah [18, 28–32]. …”

Section: Introductionmentioning

confidence: 99%

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Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

Marmesat

Schmidt

Saveljev³

et al. 2017

BMC Evol Biol

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BackgroundDemographic bottlenecks erode genetic diversity and may increase endangered species’ extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus.ResultsThe Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels.ConclusionsSpecies-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-1006-z) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 95%

Section: Methodsmentioning

confidence: 99%

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Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

Marmesat

Schmidt

Saveljev³

et al. 2017

BMC Evol Biol

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“…Arguably, it is difficult to estimate “ecological meaningful” genetic diversity by solely measuring the neutral genetic diversity. In a recent review of MHC diversity and viability in natural populations, each case study included at least some populations that had undergone a decrease in population size (i.e., like our study) (Radwan et al 2010). A majority of these case studies showed a significant positive correlation between neutral markers with MHC AR, contrary to our study.…”

Section: Discussionmentioning

confidence: 99%

Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?

Strand

Segelbacher

Quintela

et al. 2012

Ecology and Evolution

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The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here, we use both neutral and major histocompatibility complex (MHC) markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled 11 different populations; five continuous, three isolated, and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs) which both were found to be neutral, and two functional MHC genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented.

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“…For example, a total of 10 alleles (9 functional alleles and 1 pseudo-allele) were detected from 4 putative MHC class I loci in 108 Namibian cheetahs, averaging 2.5 alleles per locus [34]. While 13 putatively functional alleles and one pseudo-allele were found from at least 4 MHC class I loci in 16 highly endangered India Bengal tigers [35]. Furthermore, Aime -MHC class II genes also showed higher polymorphism relative to other endangered species [27].…”

Section: Discussionmentioning

confidence: 99%

Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda

Zhu

Wan

et al. 2013

BMC Evol Biol

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BackgroundEvaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units.ResultsOverall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated.ConclusionsThe giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend that a captive breeding program be considered for the Qinling panda population.

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MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris)

Cited by 33 publications

References 52 publications

Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?

Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda

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