Summary: The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction‐site associatedDNAsequencing (RAD‐seq) for 632 individuals representing nearly 250Quercusspecies to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000RAD‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.

Southwest China is one of the major global biodiversity hotspots. The Tanaka line, extending within southwestern China from its northwest to its southeast, is an important biogeographical boundary between the Sino-Japanese and Sino-Himalayan floristic regions. Understanding the evolutionary history of the regional keystone species would assist with both reconstructing historical vegetation dynamics and ongoing biodiversity management. In this research, we combined phylogeographic methodologies and species distribution models (SDMs) to investigate the spatial genetic patterns and distribution dynamics of Quercus kerrii, a dominant evergreen oak inhabiting southwest China lowland evergreen-broadleaved forests (EBLFs). A total of 403 individuals were sampled from 44 populations throughout southwest China. SDMs and mismatch distribution analysis indicated that Q. kerrii has undergone northward expansion since the Last Glacial Maximum (LGM). Quantitative analysis revealed that the range expansion of Q. kerrii since the LGM exceeded that of the sympatric mid-elevation species Quercus schottkyana, likely owing to their contrasting distribution elevations and habitat availabilities. The historical climate change since the LGM and the latitude gradient of the region played an important role in shaping the genetic diversity of Q. kerrii. The genetic differentiation index and genetic distance surface of Q. kerrii populations east of the Tanaka line exceeded those to its west. The long-term geographic isolation and environmental heterogeneity between the two sides of the Tanaka line might increase species divergence patterns and local adaptation. This study provides new insights into the historical dynamics of subtropical EBLFs and the changing biota of southwest China.

Understanding species response to climate change is essential for the conservation and utilization of species resources under rapid climate change in the future. In this study, the present and future suitable distribution range of Keteleeria davidiana, a tertiary relict gymnosperm, was predicted based on the maximum entropy model (MaxEnt). A total of 158 occurrence records were collected after removing the duplicated records. Six low-correlation climate variables were used to predict species distributions. The three key climate factors that affect the distribution of K. davidiana were temperature seasonality (34.96%), mean temperature of the coldest quarter (28.30%) and precipitation seasonality (13.58%). The most suitable zone of the temperature seasonality for K. davidiana was between 377.4 and 843.4. The highly suitable area was located in the mountainous regions of central and southeast China, which accounted for 13.39% of the whole study area. With climate warming in the future, the highly suitable distribution area of K. davidiana was estimated to decrease by 35% (SSP1-2.6 scenario) or 85% (SSP5-8.5 scenario). This study has provided a sufficient scientific basis for the future in situ and ex situ conservation of K. davidiana.