The subfamily Dryadoideae (Rosaceae) includes the genera Dryas, Cercocarpus, Purshia, and Chamaebatia. Previous phylogenetic studies have recovered conflicting relationships among these genera between nuclear and chloroplast data. Here, we present a phylogenetic reconstruction of Dryadoideae based on broad sampling of taxa and low-copy nuclear data obtained through gene capture. These data were analyzed using the gene-tree summary method ASTRAL-IV and a concatenated analysis employing maximum likelihood. The results recovered Dryadoideae as a well-supported clade. Cercocarpus, Purshia, and Chamaebatia were each recovered as monophyletic, and the three sampled species of Dryas formed a clade. Both methods recovered the same intergeneric topology with high support. Dryas was recovered as the sister group to the other three genera. Chamaebatia and Purshia were recovered as sister, and Cercocarpus as the sister group to both. Nevertheless, a high degree of discordance was detected among the gene trees at some nodes that establish intergeneric relationships. This discordance seems to be compatible with biological processes such as incomplete lineage sorting. Additionally, morphological and foliar anatomy characters were mapped. This allowed for the identification of characteristics consistent with the phylogeny. For example, Dryas has a greater number of sepals and petals compared to the other genera. Cercocarpus, Chamaebatia, and Purshia share anatomical characteristics such as the presence of idioblasts and secondary growth on the primary vein. This work provides a well-supported phylogenetic hypothesis among the genera of Dryadoideae and contributes to understanding the evolution and diversification of the subfamily.
The phylogenetic placement of the herbaceous family Biebersteiniaceae, a monotypic lineage with an exceptionally low chromosome number (2n = 10), has remained contentious within the order Sapindales, particularly regarding the relationships among Biebersteiniaceae, Sapindaceae, and Nitrariaceae. To address this, we generated a chromosome-level genome assembly for Biebersteinia heterostemon. Phylogenetic analyses based on single-copy nuclear genes and plastome sequences yielded strongly conflicting topologies. In contrast, a species tree reconstructed from collinear genes supported a third, well-defined topology: Biebersteiniaceae is sister to a subclade comprising Anacardiaceae, Meliaceae, and Rutaceae that further is sister to the subclade comprising only Sapindaceae. We further reconstructed the ancestral karyotype of Sapindales and traced karyotype evolution across the order. Reconstruction of ancestral karyotypes revealed that Anacardiaceae, Meliaceae, and Rutaceae share a chromosomal fusion supporting their monophyly. Biebersteiniaceae shares an additional fusion with this subclade, supporting its sister relationship. Furthermore, Biebersteiniaceae, Anacardiaceae, Meliaceae, Rutaceae, and Sapindaceae share another fusion that is absent from Nitrariaceae, suggesting that Nitrariaceae represents the earliest-diverging lineage among these families. Our study demonstrates that integrated phylogenomics based on collinear genes and karyotype evolution can resolve long-standing deep phylogenetic conflicts where traditional analyses fail, providing a robust framework for understanding trait evolution.
The genus Nectogale, endemic to the Himalayas, Hengduan Mountains, and adjacent ranges, comprises highly specialized semi-aquatic shrews adapted to high-elevation streams. Its diversity has likely been underestimated because of limited sampling and morphological conservatism, leaving species limits and evolutionary relationships unresolved. Here, we combined whole–genome data with morphological evidence to delimit species, infer phylogenetic history, and test for introgression and demographic change. Our results support three species: Nectogale elegans, Nectogale sikhimensis, and a newly identified species, Nectogale jilongensis sp. nov. Divergence-time analyses indicated that the Nectogale lineage diverged from its sister genus in the Middle Miocene (∼14 Ma), followed by diversification between the Late Miocene (∼7 Ma) and Early Pliocene (∼4.5 Ma), broadly coinciding with Himalayan uplift and regional climatic transitions. Admixture analyses and D-statistics (ABBA–BABA tests) indicated significant introgression near species range boundaries, while pairwise sequentially Markovian coalescent (PSMC) analyses revealed contrasting population histories among the three lineages. These results highlight the role of contact zones in facilitating lineage divergence through gene flow, and suggest that regional environmental heterogeneity contributes to distinct evolutionary trajectories across the Himalayas. Our study revises Nectogale taxonomy and clarifies its evolutionary history, offering new insights into diversification in the Himalayan biodiversity hotspot.
