Abstract: A full understanding of local adaptation at the genomic level will help to elucidate its role in the differentiation between closely related species. This study focused on rice seed bugs sister species (Leptocorisa chinensis and Leptocorisa oratoria), which are native to East Asia and are notorious pests targeting growing rice spikelets. East Asia is a region where diverse geology and fluctuating climate are known to have profound impacts on organisms. In this study, single nucleotide polymorphisms (SNPs) from double-digest restriction site-associated DNA sequencing and geographic distribution information were used to investigate phylogeography and assess the environmental contribution to genetic variation. We found clear genetic differentiation between sister species, but a lack of genetic structure within species because of their long-distance dispersal ability. The demographic model involved a scenario in which divergence in isolation (~0.6 Ma) was followed by secondary contact (~7 kya). The initial divergence may have been caused by the intensification of the East Asian monsoon during the Pleistocene climate oscillation. The historical demography indicated that the effective population size (N_e) showed an evident increase from 9 to 7 kya, which may be related to rice domestication and extensive human cultivation during the Holocene. We also detected a significant correlation between genetic and environmental distance, and the niche difference occupied between them. Temperature-related variables were ranked as the main factors for the difference, and 410 selective SNPs involved in adaptation were identified. The Nanling Mountains in southern China serve as a geographical boundary between them and act as an ecological barrier belt that promotes local environmental adaptation. Our study demonstrates that historical climate change and local adaptation by climate-imposed selection shape the phylogeographical patterns of sister species.

Key words: ddRAD, environmental‐related analysis, geographic distribution information, history demographic, rice cultivation.