Dataset Information

Genetic variation of mitochondrial DNA in Phalacrocorax carbo in Japan.

ABSTRACT: A Japanese resident bird, Phalacrocorax carbo hanedae (Japanese name: Kawa-u), was threatened with extinction due to deterioration of its habitat in the 1970s, but the population has since recovered thanks to environmental protection measures. This study analyzed the genetic diversity of 18 Kawa-u individuals living in the basins of the Abe and Warashina rivers in Shizuoka Prefecture, Japan. We obtained seven haplotypes of mitochondrial D-loop sequences and compared them with 49 European P. carbo D-loop haplotypes. We identified four new haplotypes but no clear genetic evidence distinguishing the Kawa-u as a distinct subspecies of P. carbo. Our results suggest the need for further surveillance of the P. carbo genetic lineage, regardless of the geographical distribution.

SUBMITTER: Ochiai Y

PROVIDER: S-EPMC7324818 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Genetic variation of mitochondrial DNA in Phalacrocorax carbo in Japan.

Ochiai Yoshitsugu Y Yoshikawa Yuko Y Takano Takashi T Mori Makoto M Hondo Ryo R Mochizuki Mariko M Ueda Fukiko F

The Journal of veterinary medical science 20200409 6

A Japanese resident bird, Phalacrocorax carbo hanedae (Japanese name: Kawa-u), was threatened with extinction due to deterioration of its habitat in the 1970s, but the population has since recovered thanks to environmental protection measures. This study analyzed the genetic diversity of 18 Kawa-u individuals living in the basins of the Abe and Warashina rivers in Shizuoka Prefecture, Japan. We obtained seven haplotypes of mitochondrial D-loop sequences and compared them with 49 European P. carb ...[more]

PMID: 32269195

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Project description:Managing wildlife populations for conservation, control or harvesting involves uncertainty. Nevertheless, decisions need to be made based on the available evidence. The two main sources of uncertainty in population modelling are parameter estimates and structural uncertainty. Structural uncertainty in models is not included as often as parameter uncertainty.We present an approach where parameter and structural uncertainty (strength of density dependence) is included within a model, using the over-wintering English population of cormorants Phalacrocorax carbo L. Because of the damage caused to inland fishery interests by cormorants, there was a change in UK government policy in autumn 2004, increasing the numbers of birds that can be shot under licence.A stochastic Monte Carlo annual population model was produced to examine the effect of changes to the numbers of birds shot each year. Indices of annual population size were converted to population estimates and used to determine annual growth rates and strength of density dependence.There is strong evidence for density dependence in the data, which suggests the population is currently slightly above carrying capacity, with a mean growth rate of 4-6% per annum. The 1300 birds shot under licence in 2004/05 represent about 4.5% of the English population, and if this level of culling continues, the population would be expected to decline by 9% by 2007, compared to the long-term average. The a priori preferred model, which included all uncertainty, gave predictions for 2004/05 and 2005/06 in close agreement with field data.The model was used to produce short-term population projections, with the understanding that Adaptive Resource Management (ARM) will be adopted to iteratively update the parameters and model each year, feeding back into the numbers of available licences.Synthesis and applications. We recommend the approach used in this study of including parameter and structural uncertainty within a single model, where possible, with the proportion of iterations that utilize a particular structure dependent on the weight of evidence for that structure. This will produce results with wider confidence intervals, but ensures that the evidence for any particular model is not over-interpreted.

Project description:Mitochondrial DNA copy number (mtDNA CN) has been shown to be highly heritable and associated with traits of interest in humans. However, studies are lacking in the literature for livestock species such as beef cattle. In this study, 2,371 individuals from a crossbred beef population comprising the Germplasm Evaluation program from the U.S. Meat Animal Research Center had samples of blood, leucocyte, or semen collected for low-pass sequencing (LPS) that resulted in both nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) sequence reads. Mitochondrial DNA CN was estimated based on the ratio of mtDNA to nuDNA coverages. Genetic parameters for mtDNA CN were estimated from an animal model based on a genomic relationship matrix (~87K SNP from the nuDNA). Different models were used to test the effects of tissue, sex, age at sample collection, heterosis, and breed composition. Maternal effects, assessed by fitting a maternal additive component and by fitting eleven SNP on the mtDNA, were also obtained. As previously reported, mtDNA haplotypes were used to classify individuals into Taurine haplogroups (T1, T2, T3/T4, and T5). Estimates of heritability when fitting fixed effects in addition to the intercept were moderate, ranging from 0.11 to 0.31 depending on the model. From a model ignoring contemporary group, semen samples had the lowest mtDNA CN, as expected, followed by blood and leucocyte samples (P ≤ 0.001). The effect of sex and the linear and quadratic effects of age were significant (P ≤ 0.02) depending on the model. When significant, females had greater mtDNA CN than males. The effects of heterosis and maternal heterosis were not significant (P ≥ 0.47). The estimates of maternal and mtDNA heritability were near zero (≤0.03). Most of the samples (98%) were classified as haplogroup T3. Variation was observed in the mtDNA within Taurine haplogroups, which enabled the identification of 24 haplotypes. These results suggest that mtDNA CN is under nuclear genetic control and would respond favorably to selection.

Dataset Information

Genetic variation of mitochondrial DNA in Phalacrocorax carbo in Japan.

Publications

Genetic variation of mitochondrial DNA in Phalacrocorax carbo in Japan.

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