A cryptic lineage is a genetically diverged but morphologically unrecognized variant of a known species. Clarifying cryptic lineage evolution is essential for quantifying species diversity. In sympatric cryptic lineage divergence compared with allopatric divergence, the forces of divergent selection and mating patterns override geographical isolation. Introgression, by supplying preadapted or neutral standing genetic variations, can promote sympatric cryptic lineage divergence via selection. However, most studies concentrated on extant species introgression, ignoring the genetic legacy of introgression from extinct or unsampled lineages (“ghost introgression”). Cycads are an ideal plant for studying the influence of ghost introgression because of their common interspecific gene flow and past high extinction rate. Here, we utilized reference‐based ddRADseq to clarify the role of ghost introgression in the evolution of a previously identified sympatric cryptic lineage in Cycas revoluta. After re‐evaluating the evolutionary independency of cryptic lineages, the group‐wise diverged single‐nucleotide polymorphisms among sympatric and allopatric lineages were compared and functionally annotated. Next, we employed an approximate Bayesian computation method for hypothesis testing to clarify the cryptic lineage evolution and ghost introgression effect. SNPs with the genomic signatures of ghost introgression were further annotated. Our results reconfirmed the evolutionary independency of cryptic lineage among C. revoluta and demonstrated that ghost introgression to the noncryptic lineage facilitated their divergence. Gene function related to heat stress and disease resistance implied ecological adaptation of the main extant populations of C. revoluta.

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.

Aim: Rapid global warming is threatening global biodiversity, and it will likely lead to varying degrees of local adaptation, particularly amongst plant species. Besides, rising temperatures frequently result in upslope distribution shifts towards climatic optima (i.e. the escalator effect) within a limited dispersal space, such as in insular environments. Here, we integrated ecological and genetic approaches to investigate how climate change will impact the genetic compositions and spatial distributions of Taiwan's endemic maple Acer caudatifolium.Location: Taiwan.Methods: We estimate the distribution range shifts of A. caudatifolium under climate change through species distribution modelling (SDM). We also use 368 genotyped samples to infer dispersal and genetic hotspots and quantify the contributions of geography/environments to genetic variations. We further assess the potential risk to A. caudatifolium under different climate warming scenarios.Results: We detected three genetic diversity hotspots near mountainous glacial refugia and two dispersal hotspots in northern Taiwan and the central‐to‐southern Central Mountain Range. Overall range reductions and an altitudinal upslope shift were observed in SDM. Using both linear and nonlinear regression approaches, we found that genetic variation was significantly associated with geographic distance and elevation‐related climatic variables. The potential risk analysis revealed that the northernmost summit‐dwelling populations were the most vulnerable. Furthermore, the major risk factor differed amongst populations: for central populations, temperature and precipitation jointly determined the potential risk, whereas precipitation was the only risk factor for northern and southern populations.Main conclusions: This case study demonstrates how various climate factors, mountain height and the availability of corridors jointly determine the demographic fates and sustainability of island maples in the face of climate change. This study also provided estimates of the implications of global warming, which can be conducive to developing appropriate conservation strategies.