Low genetic diversities in isolated populations of the Asian black bear (Ursus thibetanus) in Japan, in comparison with large stable populations

Ohnishi, Naoki; Saitoh, Takashi; Ishibashi, Yasuyuki; Oi, Toru

doi:10.1007/s10592-006-9281-z

Cited by 56 publications

(20 citation statements)

References 22 publications

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“…The habitat area of the Eastern Chugoku (SK), Kii Hanto (KH), and Shikoku (SK) units in western Japan are smaller than that of the WC unit. Since previous studies that examined genetic diversities of black bears by using mtDNA and microsatellite markers have suggested a lower level of genetic diversities in the populations of western Japan [6,8], MHC variation in these management units might be lower than that in the WC unit. Therefore, it is essential to investigate MHC variation in these units further by using an increased number of samples.…”

Section: Discussionmentioning

confidence: 99%

“…Sequences of the mtDNA control region indicated that the Japanese black bear could be divided genetically into three groups: western, eastern, and Shikoku/Kii-hanto populations [7,8]. Analyses of mtDNA and microsatellite markers [6,8] revealed lower genetic diversity and higher genetic differentiation in the western population than in the other populations. In fact, in most of the management units in western Japan the species has been designated as “endangered” in the Red Data Book of Japan [13] because of the fragmentation and isolation of their habitats.…”

Section: Introductionmentioning

confidence: 99%

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MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

et al. 2012

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BackgroundThe major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations.ResultsAmong 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected.ConclusionsThe low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that the Japanese black bears may also retain more potential resistance against pathogens than other endangered mammalian species. To prevent further decline of potential resistance against pathogens, a conservation policy for the Japanese black bear should be designed to maintain MHC rare variants in each local population.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

et al. 2012

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“…Such low genetic diversity could be caused by decreases in population size, population extinction, genetic drift, and habitat loss (Allentoft and Brien, 2010); factors that have been discussed previously in relation to amphibians (Murphy et al, 2000). Furthermore, some studies have proposed that isolated populations may have low genetic variation (Ohnishi et al, 2007). Urban development has also been a major cause of fragmented habitats.…”

Section: Genetic Diversitymentioning

confidence: 99%

Range-wide phylogeography and conservation genetics of a narrowly endemic stream salamander, Pachyhynobius shangchengensis (Caudata, Hynobiidae): implications for conservation

Wang¹,

Hu²,

Shi³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. The Shangcheng stout salamander (Pachyhynobius shangchengensis) is an endangered amphibian endemic to the Dabie Mountains, southeast China, and is currently threatened by habitat loss and illegal poaching. Here we used the mitochondrial DNA control region sequence (768 bp) to conduct a comprehensive investigation of genetic diversity, phylogeographic pattern, and demographic history of the species across its geographic distribution to assist its conservation. We concluded that the levels of genetic variation are relatively low in all four populations. Analysis of molecular variance indicated that the most likely phylogeographic pattern is [JGT] [KHJ] [TM, BYM]. Two distinct clades were identified in the phylogenetic tree of 28 haplotypes, corresponding to the two southern populations (TM, BYM) and two northern populations (JGT, KHJ). Significant population differentiation (F ST ) was detected among all populations. Among the four populations, historical demographic analyses (e.g., the g parameter, the Tajima D test, and the Fu Fs test) did not reveal definite information on population expansion except for the BYM population, which had undergone a strong population expansion event. Based on the analysis of a Bayesian skyline plot, the total population underwent a significant population fluctuation around 20 kya. This may have been triggered by the end of the last glacial maximum. In conclusion, the existence of three evolutionarily significant units (BMY-TM, KHJ, and JGT) and four management units (BMY, TM, KHJ, and JGT) is supported by our study.

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“…Demographic analysis can provide information on population trends and the life stages or sex most impacted by stressors (Dorcas et al 2007;Tatin et al 2009), while genetic analysis can quantify existing levels of genetic diversity and the timing of historic bottlenecks (Ramakrishnan et al 2005;Ohnishi et al 2007;Dixo et al 2009;Meyer et al 2009;Fluker et al 2010). However, recent demographic bottlenecks may not be accompanied by declines in genetic diversity in long-lived species; specifically, long generation time is thought to buffer reductions in genetic diversity (Kuo and Janzen 2004).…”

Section: Introductionmentioning

confidence: 99%

Demographic and genetic status of an isolated population of bog turtles (Glyptemys muhlenbergii): implications for managing small populations of long-lived animals

et al. 2011

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In this study, we sought to determine the population stability and genetic diversity of one isolated population of the federally-threatened bog turtle (Glyptemys muhlenbergii) in North Carolina. Using capture-recapture data, we estimated adult survival and population growth rate from 1992 to 2007. We found that the population decreased from an estimated 36 adult turtles in 1994 to approximately 11 adult turtles in 2007. We found a constant adult survival of 0.893 (SE = 0.018, 95% confidence interval, 0.853-0.924) between 1992 and 2007. Using 18 microsatellite markers, we compared the genetic status of this population with five other bog turtle populations. The target population displayed allelic richness (4.8 ± 0.5) and observed heterozygosity (0.619 ± 0.064) within the range of the other bog turtle populations. Coalescent analysis of population growth rate, effective population size, and timing of population structuring event also indicated the genetics of the target population were comparable to the other populations studied. Estimates of effective population size were a proportion of the census size in all populations except the target population, in which the effective population size was larger than the census size (30 turtles vs. 11 turtles). We attribute the high genetic diversity in the target population to the presence of multiple generations of old turtles. This study illustrates that the demographic status of populations of long-lived species may not be reflected genetically if a decline occurred recently. Consequently, the genetic integrity of populations of long-lived animals experiencing rapid demographic bottlenecks may be preserved through conservation efforts effective in addressing demographic problems.

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Low genetic diversities in isolated populations of the Asian black bear (Ursus thibetanus) in Japan, in comparison with large stable populations

Cited by 56 publications

References 22 publications

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

Range-wide phylogeography and conservation genetics of a narrowly endemic stream salamander, Pachyhynobius shangchengensis (Caudata, Hynobiidae): implications for conservation

Demographic and genetic status of an isolated population of bog turtles (Glyptemys muhlenbergii): implications for managing small populations of long-lived animals

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