Evolutionary history of endangered and relict tree species Dipteronia sinensis in response to geological and climatic events in the Qinling Mountains and adjacent areas

A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo," cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.

Modeling the potential distribution of the energy tree species Triadica sebifera in response to climate change in China

As an important woody oilseed species in China, Triadica sebifera is not only concerned with the substitution of traditional energy sources, but also plays a considerable role in coping with energy shortages. Accurately predicting the potential geographic distribution of Triadica sebifera in China and understanding its ecological needs are crucial for alleviating the energy crisis and effectively implementing energy substitution strategies. In this study, the potential geographic distribution of Triadica sebifera in China at contemporary and future periods was predicted based on the distribution data of Triadica sebifera in China and the environmental factor variables by Maxent model and ArcGIS software. The combination of important factors governing the potential geographic distribution of Triadica sebifera was assessed by the contribution of environmental factor variables. The accuracy of Maxent model's predictions was assessed by AUC values, TSS values and Kappa statistics. The results show that: High AUC and TSS values indicate high accuracy and performance of the model. The crucial environmental factors limiting the potential geographic distribution of Triadica sebifera are the temperature factor (mean air temperature of the driest quarter), precipitation factor (precipitation of the coldest quarter, precipitation of the wettest month), and the intensity of human activities (hf). The total suitable area for Triadica sebifera is 233.64 × 104 km2, primarily located in Yunnan, Sichuan, Hubei, Guizhou, Jiangxi, Guangdong province and Guangxi Zhuang Autonomous Region; its high suitability area is 30.89 × 104 km2, accounting for 13.22% of the total suitable area, mainly distributed in Jiangxi, Sichuan and Hunan provinces in the shape of a cake. Under the four typical greenhouse gas emission concentration patterns in the 2050s and 2070s, the areas of high and medium suitable areas for Triadica sebifera will increase, while the area of its low suitable area will decrease. However, the total suitable area will remain relatively unchanged. Its potential suitable habitats show a trend of shifting towards lower latitudes and southeast regions. The study predicted the pattern of Triadica sebifera under different climate change conditions, which can provide guidance for future cultivation of Triadica sebifera as well as for biofuel development and utilization.

Population genomics reveal deep divergence and strong geographical structure in gentians in the Hengduan Mountains

Understanding the evolutionary and ecological processes driving population differentiation and speciation can provide critical insights into the formation of biodiversity. Here, we examine the link between population genetic processes and biogeographic history underlying the generation of diversity in the Hengduan Mountains (HM), a region harboring a rich and dynamic flora. We used restriction site-associated DNA sequencing to generate 1,907 single-nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing diversification of G. hexaphylla in the HM. We find the G. hexaphylla complex is characterized by geographic genetic structure with clusters corresponding to the South, North and the central HM. Phylogenetic reconstruction and pairwise F _ST analyses showed deep differentiation between Southern and Northern populations in the HM. The population in Mount Taibai exhibited the highest genetic similarity to the North HM. Ancestral range estimation indicated that the G. hexaphylla complex originated in the central HM and then diverged in the Pliocene and the Early Pleistocene, before dispersing widely, resulting in the current distinct lineages. Overall, we found deep genomic differentiation in the G. hexaphylla complex corresponds to geographic barriers to dispersal in the HM and highlights a critical role of the uplift of the Daxue Mountains and subsequent climatic fluctuations underlying diversification. The colonization of G. hexaphylla in the Mount Taibai region suggests directional dispersal between the alpine flora of the Qinling Mountains and the HM.