Several attempts have been made to understand the population dynamics of fishery resources, such as tuna species using an integrated analysis model with multiple data sources. However, estimating absolute abundance levels in practical stock assessments remains a challenge. Close-kin mark–recapture (CKMR) methods provide information about the number of adults in a population using close-kinship pairs identified by genetic markers and statistical methods. In this study, we compared three methods for kinship identification using different algorithms in samples of wild Pacific bluefin tuna genotyped across 5,029 genome-wide single nucleotide polymorphisms in 4,108 samples. The fraRF method we developed employs pairwise identity-by-descent values as inputs for random-forest classification. The other two methods were CKMRsim and COLONY, which have been published and applied in several studies. These three methods were applied to the actual genotyping data with moderate missing genotypes, in addition to the pseudo-generated genotyping data for the simulation test. The simulation test mimicked genotyping data with physical linkage as well as genetic characteristics similar to those of actual samples. The three methods resulted in different numbers of inferred kinship pairs for both generated and actual data. Particularly for the half-sibling pairs, considerable number of false-positive and false-negative existed in the identification results. The differences in kinship identification results were interpreted based on a simulation test. This study may promote the understanding of behavior in each software when applying the software to SNP data with moderate missing genotypes as in the case of this study.

The Arabidopsis thaliana population has been exposed to unexperienced biotic and abiotic stresses as a result of range expansion or environmental change. To obtain a global picture of the genetic adaptations in the population history of A. thaliana, we constructed a database of the phenotypic-adaptations (p-adaptations) and gene expression-adaptations (e-adaptations). We analysed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes, and identified 650 p-adaptations and 3,925 e-adaptations (FDR=0.05). The population underwent large scale p-adaptations and e-adaptations along four lineages, the eastward migration to Central Asia and South Siberia, Russia, the northward migration to Sweden, the migration to Azerbaijan, and the migration of the German population to the United States. Extremely cold winters and short summers prolonged seed dormancy, and expanded the root system architecture. Low temperatures prolonged the growing season and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected for alleles underlying low heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The database of p-adaptations and e-adaptations, which complements studies focusing on specific aspects of adaptation, may be useful for future studies to understand the biological adaptations of A. thaliana throughout its population history.