Under climate fluctuation, species dispersal may be disturbed by terrain and local climate, resulting in uneven spatial-genetic structure. In addition, organisms at different latitudes may be differentially susceptible to climate change. Here, we tracked the seed dispersal of Acer caudatifolium using chloroplast DNA to explore the relationships of terrain and local climate heterogeneity with range shifts and demography in Taiwan. Our results showed that the extant populations have shifted upward and northward to the mountains since the Last Glacial Maximum. The distributional upshift of A. caudatifolium is in contrast to the downward expansion of its closest relative in Taiwan, A. morrisonense. The northern populations of A. caudatifolium have acquired multiple-source chlorotypes and harbor high genetic diversity. However, effective gene flow between the north and south is interrupted by topography, geographic distance, north-south differences in October rainfall, and other climate heterogeneities, blocking southward genetic rescue. In addition, winter monsoon-driven rainfall may cause regional differences in the phenological schedule, resulting in adaptive effects on the timing of range shift and the genetic draft of chlorotype distribution. Terrain, distance, and local climate also differentiate the northernmost populations from the others, supporting the previous taxonomic treatment of Acer kawakamii var. taitonmontanum as an independent variety.

Hybridization frequently occurs in plant species. With repeated backcross, the introgression may influence evolutionary trajectories through the entry of foreign genes. However, the genetic admixture via hybridization events is often confused with the ancestral polymorphism, especially in closely related species that have experienced similar evolutionary events. In Taiwan, two independent-originated endemic snakebark maples have contrasted postglacial range expansion routes: northward and upward expansion in Acer caudatifolium and downward expansion in A. morrisonense. The range expansion causes the current parapatric distribution, increasing the possibility of introgression. This study elucidates how their genetic variation reflects introgression and historical demography. With 17 EST-SSR markers among the intensely sampled 657 individuals, we confirmed that the genetic admixture between species mainly was attributed to recent introgression instead of common ancestral polymorphism. The secondary contact scenario inferred by approximate Bayesian computation suggested that A. morrisonense received more genetic variations from A. caudatifolium. Introgression occurred in colonized Taiwan around the early Last Glacial Period. Furthermore, the demography of A. caudatifolium was more severely affected by introgression than A. morrisonense, especially in the wavefront populations with high altitude range expansion, implying an altitude-related adaptive introgression. In contrast, A. morrisonense exhibited ubiquitous introgression independent of postglacial expansion, suggesting that introgression in A. morrisonense was neutral. In terms of different genetic consequences, introgression had different demographic impacts on species with different altitude expansion directions even under the same climate-change conditions within an island.

Fagaceae species predominate a diverse range of habitats in the northern hemisphere and are critical to the ecosystem and economy. The high morphological and genetic diversity of these species serves as the foundation for adaptation to environmental stress. To comprehend the diversity, an evolutionary viewpoint is required. However, we found extensive conflicts among gene trees at the genus level, resulting in inconclusive phylogenetic inferences based on various genetic markers. Unresolved phylogeny would affect taxonomy, biogeographic inference, and ancestral state. In this study, we aimed to look deeply into the source of phylogenetic discordance in Fagaceae. We sampled 65 species from six genera (Fagus, Lithocarpus, Quercus, Castanea, Castanopsis, and Notholithocarpus) and obtained 603,809 SNPs from transcriptome sequences. In addition to concatenated and coalescence-based approaches for phylogenetic inference, we also reconstructed 256 gene topologies to investigate conflict among nuclear genes. Our results show that the conflicts arise mainly from the relationship between Lithocarpus and Quercus, with approximately 34% of genes supporting the two genera as a sister group. We also try to understand why the genes of minority topologies are different from those of majority topologies. To answer the question, we performed a functional enrichment analysis to determine the function of the minority topological genes. According to the GO terms, their functions are primarily related to cellular structure or organelle. In the following step, we will investigate whether the main sources of discordance are introgression, incomplete lineage sorting, or selection.