Genome-Wide Evidence for Complex Hybridization and Demographic History in a Group of Cycas From China

Adaptive Distribution and Priority Protection of Endangered Species Cycas balansae

As an endangered species, the habitat of Cycas balansae (C. balansae) is subject to a variety of impacts, including climate change and human activities, and exploring its adaptive distribution and conservation areas under such conditions is crucial to protecting the ecological security of endangered species. In this study, we used the MaxEnt model and Marxan v4.0.6 to systematically evaluate the adaptive distribution and priority protection areas of the endangered species C. balansae. The results showed that the endangered species C. balansae is concentrated in Xishuangbanna and its surrounding zones in the southern Yunnan Province. The main factors affecting the distribution of C. balansae were temperature seasonality, mean temperature of the coldest quarter, isothermality, and precipitation of the warmest quarter, among which temperature was the dominant factor. Under different climate scenarios in the future, the adaptive distribution area of C. balansae showed a slight decrease, and the adaptive distribution showed a northward migration trend. The future climate distribution pattern is closely related to temperature seasonality and the mean temperature of the coldest quarter. In addition, the influence of anthropogenic disturbances on the distribution of C. balansae cannot be ignored. Currently, there is a large range of conservation vacancies for C. balansae, and it is recommended that Simao City be used as a priority conservation area. This study provides new insights for determining the priority conservation areas and conservation strategies for the endangered species C. balansae.

Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape

This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.

Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China

The role of geographical isolation and environmental adaptation in driving the differentiation and radiation of species has been a hotspot in evolutionary biology. The extremely complicated and fragmented geography of the mountainous region of Southwest China provides an excellent system for investigating the process of species divergence in heterogeneous habitats. Amorphophallus yunnanensis is a species of extreme habitat preference that resides mainly in the mountainous region of Southwest China. Here, we used restriction site-associated DNA sequencing (RAD-seq) to characterize the geographic pattern of genetic variation among 19 populations of A. yunnanensis as well as the genomic basis of environmental adaptation. A pattern of low population genetic diversity and high level of genetic differentiation was observed. The genomic data revealed a clear east-west genetic differentiation, with two distinct genetic lineages corresponding to the Guizhou plateau and Yunnan plateau, respectively. However, we discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Significant levels of isolation by distance along with isolation by environment were detected. Outlier tests and genome-environment association analyses identified 89 putatively adaptive loci that might play a role in environmental adaptation. Our results suggest that the genetic divergence of A. yunnanensis is attributed to geographical isolation together with divergent selection in the mountainous region of Southwest China.

Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum

BACKGROUND

Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs.

METHODS

In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level.

RESULTS

The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization.

CONCLUSIONS

Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.

Geographic factors and climatic fluctuation drive the genetic structure and demographic history of Cycas taiwaniana (Cycadaceae), an endemic endangered species to Hainan Island in China

Hainan Island had experienced several cold-warm and dry-humid fluctuations since the Late Pleistocene period, resulting in separating and connecting from the mainland several times with the cyclic rise and fall of sea level. The fluctuations can change the biota and ecological environment in the island. Cycas taiwaniana Carruthers is endemic to Hainan Island and is classified as endangered by the International Union for Conservation of Nature (IUCN). To comprehensively understand the genetic dynamics of C. taiwaniana, we sampled 12 wild populations in Hainan Island and one cultivated population in Fujian province, and analyzed the genetic diversity, genetic structure, and demographic history based on the molecular data. Results revealed that C. taiwaniana had relatively low genetic diversity and high genetic differentiation. Haplotypes of C. taiwaniana diversified during the Pleistocene based on the chloroplast DNA (cpDNA) and the concatenated nuclear DNA (nDNA) data. Genetic cluster analyses based on the microsatellite (SSR) data showed that the 12 wild populations were separated into three clusters which could be three evolutionary significant units (ESUs), indicating three basic units of protection were identified. Moreover, we also confirmed the cultivated population FJ derived from the DLS1-GSL clade. Demographic inference from different data was discordant, but overall, it uncovered that C. taiwaniana had experienced population contraction events twice during the Pleistocene and Holocene, and then expanded recently. Our study elucidated the population genetic characteristics of C. taiwaniana, and guided us to develop targeted conservation and management strategies for this endangered species.

Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China

Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.