Climate change is likely to alter the selective pressures that drive shifts in adaptive variation. For species with long life histories and low dispersion capacities, rapid climate change could impede the migration of beneficial alleles and their ability to track changing environments. Disentangling the processes of adaptive genetic variation in tree species has important implications for conservation and forest management. In this study, we used landscape genomic approaches and phenotypic data from range-wide sampling to investigate the adaptive genetic and phenotypic variation of the oak Quercus longinux, which is endemic in Taiwan. Among 2,000 single-nucleotide polymorphisms (SNPs) generated by double-digested restriction-site associated DNA (ddRAD) sequencing from 205 individuals, 35 drought- and freeze-resistance genes exhibited signatures of natural selection driven by various environmental pressures. GradientForest and redundancy analysis showed that these putative adaptive SNPs had elevated associations with climate and soil variations. The proportion of joint effects of demography, geology, and environments was high, indicating covariation of environmental gradients and colonization history. Compared with other populations, Q. longinux var. kuoi, a unique variety limited to southern Taiwan, exhibited substantial phenotypic, ecological, and adaptive divergence. Finally, we used the environmentally associated SNPs to estimate the genetic offset for each individual under different climate change scenarios, which revealed that edge populations in northern and southeastern Taiwan may be threatened by rising temperatures and reallocation of precipitation. Our study shed light on the pattern of environment-driven adaptation and provides prediction for future vulnerability of island oaks in subtropical and tropical regions. Keywordsclimate change, genetic offset, landscape genomics, local adaptation, natural selection, Quercus

Island habitats are natural laboratories that offer unique opportunities to study speciation mechanisms. Recent work indicates that both anagenetic and cladogenetic speciation processes, driven by allopatric and sympatric modes, contribute to island species diversity. However, clear evidence of local adaptation of endemic plant species on islands requires in-depth studies, which are scarce. This study underscores the importance of local adaptation in maintaining species entity by examining how adaptive introgression, hybridization, and local adaptation contribute to genetic variation in island species. Specifically, multilocus genome scanning of 51 nuclear genes was used to investigate the evolutionary relationships of the Scutellaria species complex on Taiwan Island and assess the role of in situ diversification in generating high endemism and genetic diversity. Recurrent interspecies introgressions were detected by phylogenetic networks and ABBA-BABA-based analysis, suggesting ongoing or recent speciation processes. Approximate Bayesian computation identified hybrid speciation in S. taiwanensis and S. hsiehii, with evidence of hybridization between more than two parental species. Genotype-environment association studies revealed that the influence of climate, particularly precipitation- and temperature-related factors, contributed to adaptive genetic divergence between species. Additionally, adaptive introgressions related to environmental pressures that may have facilitated the colonization of new island habitats were identified. This research illustrates how hybridization, introgression, and adaptation shaped the evolutionary histories and divergence of this island-endemic plant species complex and sheds light on the multifaceted mechanisms of speciation on semi-isolated islands.

Elucidating how demography and contemporary landscape features regulate functional connectivity and diversity is crucial to implementing effective conservation strategies, especially in highly fragmented landscapes. We analyzed the impacts of landscape features and demographic events on the dispersal and genetic structure of a locally endangered carnivore, the leopard cat (Prionailurus bengalensis), across subtropical Taiwan. We genotyped 184 samples from both human-impacted and natural habitats using 12 nuclear microsatellites and a mitochondrial marker. Bayesian analyses revealed a recent population decline within the past 200 years, and a current genetic hotspot appears to have arisen from interbreeding between previously diverged populations. Genetic clustering and resistance surface modeling support the notion that the population structure is influenced by manufactured linear and natural topographical features. We employed a landscape optimization procedure using two genetic distances to reveal that highways and elevation are the most significant barriers affecting leopard cat connectivity. Niche modeling indicated that low temperature is a primary factor limiting leopard cat occurrence, potentially explaining why their resistance to movement is positively correlated with elevation. Utilizing an ensemble approach, we predict that suitable leopard cat habitat will shrink northward and towards higher more rugged altitudes. Our study provides genetic evidence that anthropogenic landscape features compromise the connectivity and persistence of a vagile carnivore that is under severe pressure from habitat loss and human activities. Our findings serve as a model for landscape genetic studies of island carnivores in subtropical regions, aimed at understanding how manufactured landscapes affect intra-species diversity and dispersal.