Evolution of genetic diversity and local adaptation in the genus Apis

概要

Honeybee (the genus Apis) is an important bioresource that supports global food production through their various ecosystem services. However, in recent years, the honeybee decline due to the biological invasion of pathogens on a global scale has become a problem. Combined stressors such as climate change, pesticide use, and lack of plant resources also can influence population declines. Predicting the evolutionary response to environmental stresses of the genus Apis is important for promoting sustainable conservation and the agricultural use of honeybees. In this thesis, I examined the evolution of genetic diversity and local adaptation of the genus Apis in Asia using genomic data.

In chapter 1, to reveal the details of the phylogenetic relationship and evolution of subgenus Apis, I analyzed the complete mitochondrial genome of the Southeast Asian honeybee, A. koschevnikovi. A. koschevnikovi belonging to subgenus Apis is a cavity-nesting honeybee. The distribution of this species has been geographically restricted, mainly in Borneo, Malay Peninsula, and Sumatra. The mitochondrial genome of A. koschevnikovi was observed to be a circular molecule of approximately 15 kb and was similar to that of the other cavity-nesting honeybee species. It was predicted to contain 13 protein-coding, 24 tRNA, and two rRNA genes, along with one AT-rich control region, besides three tRNA-Met repeats. Phylogenetic analysis was performed using the sequences of 13 mitochondrial protein-coding genes, strongly supported the monophyletic species within each honeybee of subgenus Apis. The complete sequence of the A. koschevnikovi mitochondrial genome provides additional genetic tools for studying genetic diversity and local adaptation of the genus Apis.

In chapter 2, I performed the population genomics analyses of the Japanese honeybee, A. cerana japonica. This subspecies is the only native species in the genus Apis and has caught attention as a unique bioresource in Japan. Genetic structure using 105 individuals from all over the Japanese islands by ADMIXTURE and PCA showed that this subspecies is separated from the continental Chinese A. cerana. Furthermore, I found that populations in the North (Tohoku-Kanto-Chubu regions), Mid (Chugoku region), and South (Kyushu region) of Japan have different genetic divergence (Figs. 1A and 1B). In some regions, “Putative non-native” individuals were found. These individuals are likely to be related to the introgression of colonies suggested in recent years. Second, I conducted genome-wide scans to detect candidate genes associated with local adaptation by two different approaches: one focusing on population-specific divergence and the other on correlation with environmental factors (Fig. 1C). In population-specific divergence (using PBS: Population Branch Statistics), I detected candidate genes associated with circadian rhythm (Shaker), energy metabolism (GDPGP1, CBS), and immune function (HYPK, NPC2). In correlation with environmental factors (using LFMM), I detected candidate genes associated with nervous system (Sialin, NLG-3, CLUAP1) and skeleton (SGCZ, Obst-E, CPAP3-D). The candidate genes detected in this study are likely to relate to either local adaptation in different regions or adaptation to climatic environments. In a series of results, I revealed the genetic diversity and local adaptation of the genus Apis in Asia both inter and intraspecific scales. The use of genomic information was considered to be a very effective approach in understanding genetic diversity and local adaptation. Further genome-level analyses of each regional population are expected to uncover the more detailed evolutionary mechanism of the genus Apis.

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