Loss of allelic diversity in the MHC class II DQB gene in western populations of the Japanese black bear Ursus thibetanus japonicus

Ishibashi, Yasuyuki; Oi, Toru; Arimoto, Isao; Fujii, Takeshi; Mamiya, Kazuyori; Nishi, Nobusuke; Sawada, Seigo; Tado, Hiroyuki; Yamada, Takaki

doi:10.1007/s10592-016-0897-3

Cited by 6 publications

(4 citation statements)

References 51 publications

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“…High genetic diversity is widely regarded as a crucial aspect of a healthy and resilient population (Rivers, Brummitt, Nic Lughadha, & Meagher, ). A rapid reduction in population size and loss of allelic diversity and heterozygosity is a feature of many populations of conservation concern (Ishibashi et al, ). Measuring genetic diversity is therefore a priority in many conservation contexts (IUCN, ), but whole genome sequencing is the only method that can truly provide a complete measure of individual or population genetic diversity (Ng & Kirkness, ).…”

Section: Introductionmentioning

confidence: 99%

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

McLennan

Wright

Belov

et al. 2019

Molecular Ecology Resources

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Molecular markers are a useful tool allowing conservation and population managers to shed light on genetic processes affecting threatened populations. However, as technological advancements in molecular techniques continue to evolve, conservationists are frequently faced with new genetic markers, each with nuanced variation in their characteristics as well as advantages and disadvantages for informing various questions. We used a well‐studied population of Tasmanian devils (Sarcophilus harrisii) from Maria Island, Tasmania, to illustrate the issues associated with combining multiple genetic data sets and to help answer a question posed by many population managers: which data set will provide the most precise and accurate estimates of the population processes we are trying to measure? We analysed individual heterozygosity (as internal relatedness, IR) of 96 individuals, calculated using four genetic marker types (putatively neutral microsatellites, major histocompatibility complex‐linked microsatellites, reduced representation sequencing, and candidate region resequencing). We found no correlation in IR values across marker types, suggesting that various genetic markers reflect different aspects of genomic diversity. In addition, some marker types were more informative than others for conservation decision‐making. Reduced representation sequencing provided the highest precision (lowest error) for estimating population‐level genetic diversity, and most closely reflected genome‐wide heterozygosity both theoretically and empirically. Within the conservation context, our results highlight important considerations when choosing a molecular technique for wildlife genetics.

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Section: Introductionmentioning

confidence: 99%

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

McLennan

Wright

Belov

et al. 2019

Molecular Ecology Resources

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“…MHC is intimately linked with factors likely to affect individual fitness, population viability and evolutionary potential in changing environments. Thus, patterns of MHC diversity have been repeatedly used in a conservation context in populations of particular interest [19–22].…”

Section: Introductionmentioning

confidence: 99%

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore

et al. 2019

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Background Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf ( Canis lupus ) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci. Results Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection. Conclusion Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity. Electronic supplementary material The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.

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“…Indeed, heterozygosity of the Shikoku individual is lower than that of Nishi‐Izu individual in spite of higher sequencing coverage (Table 1), implying that their genetic diversity has been decreasing due to the isolation of this population from the mainland populations. Ishibashi et al (2017) reported that the number of the MHC gene alleles has become reduced rapidly in the Shikoku population in recent decades. Conservation of the Japanese black bear, particularly the Shikoku population, is an urgent issue to avoid extinction.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population history of the Japanese black bear (Ursus thibetanus japonicus) based on the genome‐wide analyses

Kishida

Ohashi

Komatsu

2022

Ecological Research

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The Japanese black bear (Ursus thibetanus japonicus) is a subspecies of the Asian black bear endemic to Mainland Japan. It has been reported that the extant Japanese bear population is genetically differentiated into several geographically restricted clusters with an estimated divergence time of 100,000–500,000 years ago. The ancestral population of the Japanese black bear migrated from the continent to the Japanese archipelago in the Pleistocene, and no interaction between continental and Japanese bear populations after their migration has been speculated. However, most of the previous studies are based only on mitochondrial DNA. Here, we sequenced the genome of a Japanese black bear and compared it with that of other Ursus individuals to evaluate the genetic status of this subspecies. We suggest that the Japanese black bear population is genetically almost uniform and has been structured only in recent 30,000 years. This inconsistency between mitochondria and nuclear DNA may be explained by the female philopatry and male‐mediated gene flow of this species. We also suggest ancestral admixture between the Japanese black bear and the Ussuri black bear (Ursus thibetanus ussuricus), implying a complex history of inter‐subspecies interactions of the Japanese black bears. Genomic evidence of ancient admixture between the Asian black bear and the American black bear (Ursus americanus) sheds new light on the population history of the Asian black bears. The genetic diversity of the Japanese black bears is remarkably lower compared to thaother bear populations, and conservation of this subspecies is an urgent issue.

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Loss of allelic diversity in the MHC class II DQB gene in western populations of the Japanese black bear Ursus thibetanus japonicus

Cited by 6 publications

References 51 publications

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

Too much of a good thing? Finding the most informative genetic data set to answer conservation questions

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore

Genetic diversity and population history of the Japanese black bear (Ursus thibetanus japonicus) based on the genome‐wide analyses

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