bioRxiv ScienceSearch

Biology subjects

Yamasaki, M.

Publications and source records attributed to Yamasaki, M..

2 recordsLinked to original sources

Seasonal and annual fluctuations of deer populations estimated by a Bayesian state-space model

Deer overabundance is a contributing factor in the degradation of plant communities and ecosystems worldwide. The management and conservation of the deer-affected ecosystems requires us to urgently grasp deer population trends and to identify the factors that affect them. In this study, we developed a Bayesian state-space model to estimate the population dynamics of sika deer (Cervus nippon) in a cool-temperate forest in Japan, where wolves (Canis lupus hodophilax) are extinct. The model was based on field data collected from block count surveys, road count surveys by vehicles, mortality surveys during the winter, and nuisance control for 12 years (2007-2018). We clarified the seasonal and annual fluctuation of the deer population. We found two peaks of deer abundance (2007 and 2010) over 12 years. In 2011 the estimated deer abundance decreased drastically and has remained at a low level then. The deer population increased from spring to autumn and decreased from autumn to winter in most years. The seasonal fluctuation we detected could reflect the seasonal migration pattern of deer and the population recruitment through fawn births in early summer. In our model, snowfall accumulation, which can be a lethal factor for deer, may have slightly affected their mortality during the winter. Although we could not detect a direct effect of snow on population dynamics, snowfall decrease due to global warming may decelerate the winter migration of deer; subsequently, deer staying on-site may intensively forage evergreen perennial plants during the winter season. The nuisance control affected population dynamics. Even in wildlife protection areas and national parks where hunting is regulated, nuisance control could be effective in buffering the effect of deer browsing on forest ecosystems.

ecology

Choosing the optimal population for a genome-wide association study: a simulation using whole-genome sequences from rice

A genome-wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS, e.g. population structure, sample size, and sequence analysis and field testing costs, need to be considered. Mixture populations containing subpopulations of different genetic backgrounds may be suitable populations. We conducted simulation experiments to see if a population with high genetic diversity, e.g., a diversity panel, should be added to a target population, especially when the target population harbors small genetic diversity. The target population was 112 accessions of Oryza sativa subsp. japonica, mainly developed in Japan. We combined the target population with three populations that had higher genetic diversities. These were 100 indica accessions, 100 japonica accessions, and 100 accessions with various genetic backgrounds. The results showed that the GWAS power with a mixture population was generally higher than with a separate population. Also, the GWAS optimal population varied depending on the fixation index FST of the quantitative trait nucleotide (QTN) and its polymorphism of QTN in each population. When a QTN is polymorphic in a target population, a target population combined with a higher diversity population improves the QTN detection power. Investigating FST and the expected heterozygosity He as factors influencing the detection power, we showed that SNPs with high FST or low He are less likely to be detected by GWAS with mixture populations. Sequenced/genotyped germplasm collections can improve the GWAS detection power by using a subset of them with a target population.\n\nCore ideas (3-5 impact statements, 85 char max for each)\n\n- Genome-wide association studies with mixture populations are expected to improve the detection power of novel genes due to the increase of the sample size although the influence of population structure is a concern.\n- When a quantitative trait nucleotide (QTN) is polymorphic in a target population, a combination of the target population and a population with higher diversity than the target population improves the detection power of the QTN.\n- We found that the fixation index (FST) and the expected heterozygosity (He) were strongly related to the detection power of QTNs.\n- Germplasm collections which have been already sequenced/genotyped are useful for improving the detection power of GWAS without any addition of sequence costs by using a subset of them with a target population.

genomics