Identifying long-term stable refugia for relict plant species in East Asia

Central China as LGM plant refugia: Insights from biome reconstruction for palaeoclimate information

The demonstration of survival of forest stands in relatively stable refugia during cold glacial stages has offered an increased understanding of the response of vegetation to climate change, but also provides insight into considerations for the conversation of biodiversity hotspots. However, refugia studies in China remain in question due to the lack of plant macrofossils, especially those of endemic and relict species. Palynology, while more broad brush, provides a method for exploring whether refugia occur, and can provide some details of palaeovegetation composition and temporal dynamics. Here, three pollen records derived from subalpine wetlands in central China, spanning the Last Glacial Maximum (LGM), have been coupled with biome and mean annual precipitation (MAP) reconstructions to identify the presence of trees that endured cold climate. The results indicated that some forest, including temperate deciduous broadleaf forest and cool mixed forest, survived the LGM at the three locations, and was thus at odds with the hypothesis that forests were replaced by herbs and grasses in central China at that time. Refugia favored by protection from cold air drainage and the availability of adequate water can explain the survival of the trees during otherwise harsh episodes. Our findings are consistent with other records from central China that argue for tree dominated refugia during the LGM.

Range dynamics of Anopheles mosquitoes in Africa suggest a significant increase in the malaria transmission risk

Despite a more than 100-year effort to combat malaria, it remains one of the most malignant infectious diseases globally, especially in Africa. Malaria is transmitted by several Anopheles mosquitoes. However, until now few studies have investigated future range dynamics of major An. mosquitoes in Africa through a unified scheme. Through a unified scheme, we developed 21 species distribution models to predict the range dynamics of 21 major An. species in Africa under future scenarios and also examined their overall range dynamic patterns mainly through suitability overlap index and range overlap index. Although future range dynamics varied substantially among the 21 An. species, we predicted large future range expansions for all 21 An. species, and increases in suitability overlap index were detected in more than 90% of the African continent for all future scenarios. Additionally, we predicted high range overlap index in West Africa, East Africa, South Sudan, Angola, and the Democratic Republic of the Congo under future scenarios. Although the relative impacts of land use, topography and climate variables on the range dynamics depended on species and spatial scale, climate played the strongest roles in the range dynamics of most species. Africa might face an increasing risk of malaria transmissions in the future, and better strategies are required to address this problem. Mitigating climate change and human disturbance of natural ecosystems might be essential to reduce the proliferation of An. species and the risk of malaria transmissions in Africa in the future. Our strategies against their impacts should be species-specific.

Forest Orchids under Future Climate Scenarios: Habitat Suitability Modelling to Inform Conservation Strategies

Orchidaceae is one of the largest and most diverse families of flowering plants in the world but also one of the most threatened. Climate change is a global driver of plant distribution and may be the cause of their disappearance in some regions. Forest orchids are associated with specific biotic and abiotic environmental factors, that influence their local presence/absence. Changes in these conditions can lead to significant differences in species distribution. We studied three forest orchids belonging to different genera (Cephalanthera, Epipactis and Limodorum) for their potential current and future distribution in a protected area (PA) of the Northern Apennines. A Habitat Suitability Model was constructed for each species based on presence-only data and the Maximum Entropy algorithm (MaxEnt) was used for the modelling. Climatic, edaphic, topographic, anthropogenic and land cover variables were used as environmental predictors and processed in the model. The aim is to identify the environmental factors that most influence the current species distribution and the areas that are likely to contain habitats suitable for providing refuge for forest orchids and ensuring their survival under future scenarios. This will allow PA authorities to decide whether to invest more resources in conserving areas that are potential refuges for threatened species.

Estimating bee distributions and their functional range to map important areas for protecting bee species and their functions

The decline of wild bee populations causes the decline of bee-pollinated plant populations through the deterioration of pollination services. Since high bee species richness generally involves high functional group diversity, protecting areas of high bee species richness will help to maintain pollination services for plants. However, those areas do not always include the habitats of bee species with specialized functions that expand the range of plants being pollinated. To map important areas for protecting native bee species and their functions, we estimated the distributions and functional range of 13 bumble bee species and 1 honey bee species in Japan. The distributions were estimated from an ensemble of six species distribution models using bee occurrence data and environmental data. The functional range of bee species was estimated by combining the estimated distributions and proboscis length, which frequently corresponds to the floral shape of the plant species they pollinate. The estimated species richness was high in western Hokkaido and the estimated functional range was wide in central Honshu. Our method is useful to see whether areas important for high species richness of pollinators differ from those for rare species or their functions.

The Influence of Climate Change on the Distribution of Hibiscus mutabilis in China: MaxEnt Model-Based Prediction

Our study utilized 374 geographical distribution records of H. mutabilis and 19 bioclimatic factors, employing the MaxEnt model and the Geographic Information System (ArcGIS). The key environmental variables influencing the suitable distribution areas of H. mutabilis were analyzed through the comprehensive contribution rate, permutation importance, and Pearson correlation coefficient. Based on this analysis, the contemporary and future suitable distribution areas and their extents were predicted. The results indicate that the key limiting factor affecting the suitable distribution areas of H. mutabilis is the precipitation of the driest month (bio14), with secondary factors being annual precipitation (bio12), annual mean temperature (bio1), and annual temperature range (bio7). Under contemporary climate conditions, the total suitable area for H. mutabilis is approximately 2,076,600 km2, primarily concentrated in the tropical and subtropical regions of southeastern China. Under low-to-medium-emission scenarios (SSP1-2.6, SSP2-4.5), the total suitable area of H. mutabilis shows a trend of first decreasing and then increasing compared to the current scenario. In contrast, under high-emission scenarios (SSP5-8.5), it exhibits a trend of first increasing and then decreasing. The spatial pattern changes indicate that the retention rate of suitable areas for H. mutabilis ranges from 95.28% to 99.28%, with the distribution centers primarily located in Hunan and Guizhou provinces, showing an overall migration trend towards the west and north. These findings suggest that H. mutabilis possesses a certain level of adaptability to climate change. However, it is crucial to consider regional drought and sudden drought events in practical cultivation and introduction processes. The results of our study provide a scientific basis for the rational cultivation management, conservation, and utilization of germplasm resources of H. mutabilis.

Shared phylogeographic patterns and environmental responses of co-distributed soybean pests: Insights from comparative phylogeographic studies of Riptortus pedestris and Riptortus linearis in the subtropics of East Asia

Comparative phylogeographic studies of closely related species sharing co-distribution areas can elucidate the role of shared historical factors and environmental changes in shaping their phylogeographic pattern. The bean bugs, Riptortus pedestris and Riptortus linearis, which both inhabit subtropical regions in East Asia, are recognized as highly destructive soybean pests. Many previous studies have investigated the biological characteristics, pheromones, chemicals and control mechanisms of these two pests, but few studies have explored their phylogeographic patterns and underlying factors. In this study, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) dataset to investigate phylogeographic patterns and construct ecological niche models (ENM) for both Riptortus species. Our findings revealed similar niche occupancies and population genetic structures between the two species, with each comprising two phylogeographic lineages (i.e., the mainland China and the Indochina Peninsula clades) that diverged approximately 0.1 and 0.3 million years ago, respectively. This divergence likely resulted from the combined effects of temperatures variation and geographical barriers in the mountainous regions of Southwest China. Further demographic history and ENM analyses suggested that both pests underwent rapid expansion prior to the Last Glacial Maximum (LGM). Furthermore, ENM predicts a northward shift of both pests into new soybean-producing regions due to global warming. Our study indicated that co-distribution soybean pests with overlapping ecological niches and similar life histories in subtropical regions of East Asia exhibit congruent phylogeographic and demographic patterns in response to shared historical biogeographic drivers.

Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

BACKGROUND

Relict species are important for enhancing the understanding of modern biogeographic distribution patterns. Although both geological and climatic changes since the Cenozoic have affected the relict flora in East Asia, the contributions of geographical processes remain unclear. In this study, we employed restriction-site associated DNA sequencing (RAD-seq) and shallow genome sequencing data, in conjunction with ecological niche modeling (ENM), to investigate the spatial genetic patterns and population differentiation history of the relict species Rehderodendron kwangtungense Chun.

RESULTS

A total of 138 individuals from 16 populations were collected, largely covering the natural distribution of R. kwangtungense. The genetic diversity within the R. kwangtungense populations was extremely low (HO = 0.048 ± 0.019; HE = 0.033 ± 0.011). Mantel tests revealed isolation-by-distance pattern (R2 = 0.38, P < 0.001), and AMOVA analysis showed that the genetic variation of R. kwangtungense occurs mainly between populations (86.88%, K = 7). Between 23 and 21 Ma, R. kwangtungense underwent a period of rapid differentiation that coincided with the rise of the Himalayas and the establishment of the East Asian monsoon. According to ENM and population demographic history, the suitable area and effective population size of R. kwangtungense decreased sharply during the glacial period and expanded after the last glacial maximum (LGM).

CONCLUSION

Our study shows that the distribution pattern of southern China mountain relict flora may have developed during the panplain stage between the middle Oligocene and the early Miocene. Then, the flora later fragmented under the force of orogenesis, including intermittent uplift during the Cenozoic Himalayan orogeny and the formation of abundant rainfall associated with the East Asian monsoon. The findings emphasized the predominant role of geographical processes in shaping relict plant distribution patterns.

Genetic diversity, phylogeography, and maternal origin of yak (Bos grunniens)

BACKGROUND

There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity.

RESULTS

A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979 ± 0.0039 and 0.00237 ± 0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328 Ma, and the differentiation time of clades (I and II) and III were 0.5654 Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks.

CONCLUSIONS

Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.

A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines

The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.

Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China

BACKGROUND

The eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions.

RESULTS

Sixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution.

CONCLUSIONS

Our results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.

Future Climate Change and Anthropogenic Disturbance Promote the Invasions of the World's Worst Invasive Insect Pests

Invasive insect pests adversely impact human welfare and global ecosystems. However, no studies have used a unified scheme to compare the range dynamics of the world's worst invasive insect pests. We investigated the future range shifts of 15 of the world's worst invasive insect pests. Although future range dynamics varied substantially among the 15 worst invasive insect pests, most exhibited large range expansions. Increases in the total habitat suitability occurred in more than ca. 85% of global terrestrial regions. The relative impacts of anthropogenic disturbance and climate variables on the range dynamics depended on the species and spatial scale. Aedes albopictus, Cinara cupressi, and Trogoderma granarium occurred four times in the top five largest potential ranges under four future climate scenarios. Anoplophora glabripennis, Aedes albopictus, and Co. formosanus were predicted to have the largest range expansions. An. glabripennis, Pl. manokwari, Co. formosanus, and So. invicta showed the largest range centroid shifts. More effective strategies will be required to prevent their range expansions. Although the strategies should be species-specific, mitigating anthropogenic disturbances and climate change will be essential to preventing future invasions. This study provides critical and novel insights for developing global strategies to combat the invasions of invasive insect pests in the future.

Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae

Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.

Origin and Early Evolution of Hydrocharitaceae and the Ancestral Role of Stratiotes

The combined morphological features of Stratiotes (Hydrocharitaceae) pollen, observed with light and electron microscopy, make it unique among all angiosperm pollen types and easy to identify. Unfortunately, the plant is (and most likely was) insect-pollinated and produces relatively few pollen grains per flower, contributing to its apparent absence in the paleopalynological record. Here, we present fossil Stratiotes pollen from the Eocene of Germany (Europe) and Kenya (Africa), representing the first reliable pre-Pleistocene pollen records of this genus worldwide and the only fossils of this family discovered so far in Africa. The fossil Stratiotes pollen grains are described and compared to pollen from a single modern species, Stratiotes aloides L. The paleophytogeographic significance and paleoecological aspects of these findings are discussed in relation to the Hydrocharitaceae fossil records and molecular phylogeny, as well as the present-day distribution patterns of its modern genera.

Spatial heterogeneity of neo- and paleo-endemism for plants in Madagascar

Madagascar is a biogeographically unique island with a remarkably high level of endemism. However, endemic taxa in Madagascar are massively threatened due to unprecedented pressures from anthropogenic habitat modification and climate change. A comprehensive phylogeny-based biodiversity evaluation of the island remains lacking. Here, we identify hotspots of taxonomic and phylogenetic plant diversity and neo- and paleo-endemism by generating a novel dated tree of life for the island. The tree is based on unprecedented sampling of 3,950 species (33% of the total known species) and 1,621 genera (93% of the total known genera and 69% of endemic genera) of Malagasy vascular plants. We find that island-endemic genera are concentrated in multiple lineages combining high taxonomic and phylogenetic diversity. Integrating phylogenetic and geographic distribution data, our results reveal that taxon richness and endemism are concentrated in the northern, eastern, and southeastern humid forests. Paleo-endemism centers are concentrated in humid eastern and central regions, whereas neo-endemism centers are concentrated in the dry and spiny forests in western and southern Madagascar. Our statistical analysis of endemic genera in each vegetation region supports a higher proportion of ancient endemic genera in the east but a higher proportion of recent endemic genera in the south and west. Overlaying centers of phylogenetic endemism with protected areas, we identify conservation gaps concentrated in western and southern Madagascar. These gaps should be incorporated into conservation strategies to aid the protection of multiple facets of biodiversity and their benefits to the Malagasy people.

Population genetic variation and geographic distribution of suitable areas of Coptis species in China

Introduction

The rhizomes of Coptis plants have been used in traditional Chinese medicine over 2000 years. Due to increasing market demand, the overexploitation of wild populations, habitat degradation and indiscriminate artificial cultivation of Coptis species have severely damaged the native germplasms of species in China.

Methods

Genome-wide simple-sequence repeat (SSR) markers were developed using the genomic data of C. chinensis. Population genetic diversity and structure of 345 Coptis accessions collected from 32 different populations were performed based on these SSRs. The distribution of suitable areas for three taxa in China was predicted and the effects of environmental variables on genetic diversity in relation to different population distributions were further analyzed.

Results

22 primer pairs were selected as clear, stable, and polymorphic SSR markers. These had an average of 16.41 alleles and an average polymorphism information content (PIC) value of 0.664. In the neighbor-joining (N-J) clustering analysis, the 345 individuals clustered into three groups, with C. chinensis, C. chinensis var. brevisepala and C. teeta being clearly separated. All C. chinensis accessions were further divided into four subgroups in the population structure analysis. The predicted distributions of suitable areas and the environmental variables shaping these distributions varied considerably among the three species.

Discussion

Overall, the amount of solar radiation, precipitation and altitude were the most important environmental variables influencing the distribution and genetic variation of three species. The findings will provide key information to guide the conservation of genetic resources and construction of a core reserve for species.

Responses of Three Pedicularis Species to Geological and Climatic Changes in the Qinling Mountains and Adjacent Areas in East Asia

The Qinling Mountains in East Asia serve as the geographical boundary between the north and south of China and are also indicative of climatic differences, resulting in rich ecological and species diversity. However, few studies have focused on the responses of plants to geological and climatic changes in the Qinling Mountains and adjacent regions. Therefore, we investigated the evolutionary origins and phylogenetic relationships of three Pedicularis species in there to provide molecular evidence for the origin and evolution of plant species. Ecological niche modeling was used to predict the geographic distributions of three Pedicularis species during the last interglacial period, the last glacial maximum period, and current and future periods, respectively. Furthermore, the distribution patterns of climate fluctuations and the niche dynamics framework were used to assess the equivalence or difference of niches among three Pedicularis species. The results revealed that the divergence of three Pedicularis species took place in the Miocene and Holocene periods, which was significantly associated with the large-scale uplifts of the Qinling Mountains and adjacent regions. In addition, the geographic distributions of three Pedicularis species have undergone a northward migration from the past to the future. The most important environmental variables affecting the geographic distributions of species were the mean diurnal range and annual mean temperature range. The niche divergence analysis suggested that the three Pedicularis species have similar ecological niches. Among them, P. giraldiana showed the highest niche breadth, covering nearly all of the climatic niche spaces of P. dissecta and P. bicolor. In summary, this study provides novel insights into the divergence and origins of three Pedicularis species and their responses to climate and geological changes in the Qinling Mountains and adjacent regions. The findings have also provided new perspectives for the conservation and management of Pedicularis species.

Salvia guidongensis sp. nov.: unraveling a critical evolutionary link in East Asian Salvia from Central China integrating morphology, phylogeny, and plastid genomics

Introduction

Salvia L., representing the largest genus within the mint family, is noted for its global distribution of approximately 1000 species, with East Asia, and particularly China, recognized as a critical center of diversity for the genus.

Methods

Our research was conducted through extensive fieldwork in Guidong County, Hunan Province, China, where we identified a previously undescribed species of Salvia. The identification process involved detailed morphological observations, phylogenetic analyses, and plastid genomics.

Results

The newly discovered species, Salvia guidongensis, exhibits unique characteristics not commonly observed in the East Asian lineage of Salvia, including dual floral colors within natural populations-either pale purple or pale yellow. Morphologically, while it shares similarities with members of sect. Glutinaria, S. guidongensis is distinct in its floral morphology, stature, and specific foliar traits. Phylogenetic analysis places S. guidongensis in a unique clade within the East Asian lineage of Salvia, suggesting it may serve as an important evolutionary link. Additionally, we explored the plastome features of S. guidongensis, comparing them with those of closely related species.

Discussion

The discovery of S. guidongensis not only entriches the taxonomic tapestry of Salvia but also provides critical insights into the biogeography and evolutionary pathways of the genus in East Asia. By integrating morphological and molecular data, we validate the novel status of S. guidongensis and highlight its significance in bridging taxonomic and evolutionary gaps within Sect. Glutinaria of Salvia.

Differential distribution shifts in two subregions of East Asian subtropical evergreen broadleaved forests-a case of Magnoliaceae

Aim

East Asian subtropical evergreen broad-leaved forests (EBLFs) are composed of western and eastern subregions with different topographical and environmental conditions. The distribution shifts over time of plants in the two subregions are predicted to be different, but the difference has seldom been investigated.

Methods

Potential distributions of 53 Magnoliaceae species (22 in the western and 31 in the eastern subregion) during the last glacial maximum (LGM), present, and the 2070s were predicted using MaxEnt based on 58 environmental variables. The changes in the distribution range size and centroid over time were analyzed. Species-level potential habitats were overlaid to uncover species diversity distribution, and the distributions over time were overlaid to discover long-term refugia.

Results

At present, the potential distributions are significantly larger than those shown by the occurrence points. During the LGM, 20/22 species in the western subregion experienced increases in range size through downwards and southward migrations, while decreases in range size in the eastern subregion (27/31 species) were accompanied by northward and eastward migrations. In the future, range size declines and northward shifts will both be found; northwestward shifts will exist in most (20/22 species) species in the western subregion, while both northwest- and northeastward shifts will occur in the eastern subregion. The diversity hotspots experienced a slight southward shift in the past and upwards to the mountain region in the future in the western subregion; in the eastern subregion, shrinks occurred in eastern China in the past and shrinks were shown in all regions in the future. Long-term refugia-preserving diversity was found in the mountains across the entire EBLFs region.

Main conclusions

Significant differences in distribution shifts from past to present and similar distribution shifts from present to future are revealed in the two subregions. Species diversity in both subregions experienced no significant shifts from past to future, and Magnoliaceae plants could be preserved in mountainous regions throughout the EBLFs.

Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens

Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan-Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine-rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest.

Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia

'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.

More than two-fifths of the protected land in a global biodiversity hotspot in southwest China is under intense human pressure

Habitat loss is the main threat to global biodiversity in the Anthropocene. To prevent this, protected areas are the most effective means for safeguarding biodiversity. However, extensive habitat protection under human pressure can undermine its effectiveness. Using the Hengduan Mountains, a global biodiversity hotspot in southwest China as an indicator, we assessed the extent and intensity of human pressure to highlight how these pressures have changed over time. We found that most ecoregions had high levels of intact habitat loss relative to areal protection by national nature reserves (NNRs). More than two-fifths of protected land is under intense human pressure, and lower elevation or smaller NNRs were subject to higher pressure. These increases have predominantly occurred in lower elevation NNRs, showing that elevation gradients correlate with increasing pressure. While protected areas are increasingly established, they are experiencing intense human pressure. Our findings provide useful insights for assessing resilience of protected areas and to prioritize areas where future conservation plans and actions should be focused in a changing world.

Approximate Bayesian computation and ecological niche models elucidate the demographic history and current fragmented population distribution of a Korean endemic shrub

Climatic fluctuations and geological events since the LGM are believed to have significantly impacted the population size, distribution, and mobility of many species that we observe today. In this paper, we determined the processes driving the phylogeographic structure of the Korean endemic white forsythia by combining the use of genome-wide SNPs and predicting paleoclimatic habitats during the LGM (21 kya), Early Holocene (10 kya), Mid-Holocene (6 kya), and Late Holocene (3 kya). Using a maximum of 1897 SNPs retrieved from 124 samples across nine wild populations, five environmental predictors, and the species' natural occurrence records, we aimed to infer the species' demographic history and reconstruct its possible paleodistributions with the use of approximate Bayesian computation and ecological niche models, respectively. Under this integrated framework, we found strong evidence for patterns of range shift and expansion, and population divergence events from the onset of the Holocene, resulting in the formation of its five distinct genetic units. The most highly supported model inferred that after the split of an ancestral population into the southern group and a larger central metapopulation lineage, the latter gave rise to the eastern and northern clusters, before finally dividing into two sub-central groups. While the use of molecular data allowed us to identify and refine the (phylo)genetic relationships of the species' lineages and populations, the use of ecological data helped us infer a past LGM refugium and the directions of post-glacial range dynamics. The time frames of these demographic events were shown to be congruent with climatic and geological events that affected the central Korean Peninsula during these periods. These findings gave us a better understanding of the consequences of past spatiotemporal factors that may have resulted in the current fragmented population distribution of this endangered plant.

Conservation priorities for endangered trees facing multiple threats around the world

Trees are vital to the survival of numerous species and to forest ecosystem functioning. However, the current distribution, vulnerability to extinction, and conservation priorities of globally endangered trees are not well known. We mapped the global distribution of 1686 tree species listed as endangered on the International Union for the Conservation of Nature Red List and identified conservation priority for them based on species richness, life-history traits, evolutionary distinctiveness, future climate change, and intensity of human activities. We also evaluated the impacts of various threats to these endangered tree species and evaluated the effectiveness of their protection based on the percentage of the species' range inside protected areas. The worldwide distribution of endangered trees, from the tropics through temperate zones, was uneven. Most endangered tree species were not protected in their native ranges, and only 153 species were fully protected. Hotspots of tree diversity occurred primarily in the tropics, and 79.06% of these were highly vulnerable to threats. We identified 253 areas of high priority for the conservation of endangered trees that are highly threatened and insufficiently protected. In particular, 43.42% of unprotected tree species in priority areas lacked recommended conservation measures or had no associated conservation plan. The priority conservation areas and unprotected trees we identified serve as a guideline for future management underpinning the post-2020 global biodiversity framework.

Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.

Ancient DNA reveals genetic admixture in China during tiger evolution

The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.

Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera

BACKGROUND AND AIMS

Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using a landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and to predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios.

METHODS

We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8244 single-nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype-environment association (GEA) methods. We further dissected the effect of geographical/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios.

KEY RESULTS

We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS) and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7-5.7 and 8.6-12.8 % of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variation to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations.

CONCLUSIONS

Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.

Incidence and evolutionary relevance of autotriploid cytotypes in a relict member of the genus Daphne (Thymelaeaceae)

Odd ploidy-level cytotypes in sexually reproducing species are considered a dead end due to absent or reduced fertility. If sterility is only partial, however, their contribution to the population gene pool can be augmented by longevity and clonal growth. To test this, we investigated the cytotype origin and spatial pattern, and pollen viability in three relict shrub species of the genus Daphne (Thymelaeaceae Juss.) in central Europe. Daphne cneorum subsp. cneorum is a widespread European species that has a broad ecological amplitude, whereas D. cneorum subsp. arbusculoides and D. arbuscula are narrow endemics of the western Pannonian Plain and the Western Carpathians, respectively. Our study confirmed that all three taxa are diploid. However, of more than a thousand analysed individuals of D. cneorum subsp. cneorum, five in four different populations were triploid. Our data indicate that these triploids most likely originate from recurrent autopolyploidization events caused by the fusion of reduced and unreduced gametes. High pollen viability was observed in all three taxa and in both diploid and triploid cytotypes, ranging from 65 to 100 %. Our study highlights the significant role of odd ploidy-level cytotypes in interploidy gene flow, calling for more research into their reproduction, genetic variability, and overall fitness. Interestingly, while the endemic D. arbuscula differs from D. cneorum based on genetic and genome size data, D. cneorum subsp. arbusculoides was indistinguishable from D. cneorum subsp. cneorum. However, our study reveals that the subspecies differ in the number of flowers per inflorescence. This is the first comprehensive cytogeographic study of this intriguing genus at a regional scale, and in spite of its karyological stability, it contributes to our understanding of genomic evolution in plant species with a wide ecological amplitude.

Incorporating global change reveals extinction risk beyond the current Red List

Global changes over the past few decades have caused species distribution shifts and triggered population declines and local extinctions of many species. The International Union for Conservation of Nature (IUCN) Red List of Threatened Species (Red List) is regarded as the most comprehensive tool for assessing species extinction risk and has been used at regional, national, and global scales. However, most Red Lists rely on the past and current status of species populations and distributions but do not adequately reflect the risks induced by future global changes. Using distribution maps of >4,000 endemic woody species in China, combined with ensembled species distribution models, we assessed the species threat levels under future climate and land-cover changes using the projected changes in species' suitable habitats and compared our updated Red List with China's existing Red List. We discover an increased number of threatened species in the updated Red List and increased threat levels of >50% of the existing threatened species compared with the existing one. Over 50% of the newly identified threatened species are not adequately covered by protected areas. The Yunnan-Guizhou Plateau, rather than the Hengduan Mountains, is the distribution center of threatened species on the updated Red Lists, as opposed to the threatened species on the existing Red List. Our findings suggest that using Red Lists without considering the impacts of future global changes will underestimate the extinction risks and lead to a biased estimate of conservation priorities, potentially limiting the ability to meet the Kunming-Montreal global conservation targets.

Climate change impacts the distribution of Quercus section Cyclobalanopsis (Fagaceae), a keystone lineage in East Asian evergreen broadleaved forests

East Asian evergreen broadleaved forests (EBFLs) harbor high species richness, but these ecosystems are severely impacted by global climate change and deforestation. Conserving and managing EBLFs requires understanding dominant tree distribution dynamics. In this study, we used 29 species in Quercus section Cyclobalanopsis-a keystone lineage in East Asian EBLFs-as proxies to predict EBLF distribution dynamics using species distribution models (SDMs). We examined climatic niche overlap, similarity, and equivalency among seven biogeographical regions' species using 'ecospat'. We also estimated the effectiveness of protected areas in the predicted range to elucidate priority conservation regions. Our results showed that the climatic niches of most geographical groups differ. The western species under the Indian summer monsoon regime were mainly impacted by temperature factors, whereas precipitation impacted the eastern species under the East Asian summer monsoon regime. Our simulation predicted a northward range expansion of section Cyclobalanopsis between 2081 and 2100, except for the ranges of the three Himalayan species analyzed, which might shrink significantly. The greatest shift of highly suitable areas was predicted for the species in the South Pacific, with a centroid shift of over 300 km. Remarkably, only 7.56% of suitable habitat is currently inside protected areas, and the percentage is predicted to continue declining in the future. To better conserve Asian EBLFs, establishing nature reserves in their northern distribution ranges, and transplanting the populations with predicted decreasing numbers and degraded habitats to their future highly suitable areas, should be high-priority objectives.

Historical development of karst evergreen broadleaved forests in East Asia has shaped the evolution of a hemiparasitic genus Brandisia (Orobanchaceae)

Brandisia is a shrubby genus of about eight species distributed basically in East Asian evergreen broadleaved forests (EBLFs), with distribution centers in the karst regions of Yunnan, Guizhou, and Guangxi in southwestern China. Based on the hemiparasitic and more or less liana habits of this genus, we hypothesized that its evolution and distribution were shaped by the development of EBLFs there. To test our hypothesis, the most comprehensive phylogenies of Brandisia hitherto were constructed based on plastome and nuclear loci (nrDNA, PHYA and PHYB); then divergence time and ancestral areas were inferred using the combined nuclear loci dataset. Phylogenetic analyses reconfirmed that Brandisia is a member of Orobanchaceae, with unstable placements caused by nuclear-plastid incongruences. Within Brandisia, three major clades were well supported, corresponding to the three subgenera based on morphology. Brandisia was inferred to have originated in the early Oligocene (32.69 Mya) in the Eastern Himalayas-SW China, followed by diversification in the early Miocene (19.45 Mya) in karst EBLFs. The differentiation dates of Brandisia were consistent with the origin of keystone species of EBLFs in this region (e.g., Fagaceae, Lauraceae, Theaceae, and Magnoliaceae) and the colonization of other characteristic groups (e.g., Gesneriaceae and Mahonia). These findings indicate that the distribution and evolution of Brandisia were facilitated by the rise of the karst EBLFs in East Asia. In addition, the woody and parasitic habits, and pollination characteristics of Brandisia may also be the important factors affecting its speciation and dispersal.

Genomic analyses reveal three phylogenetic species and their evolutionary histories in the big-headed turtle

The critically endangered big-headed turtle (Platysternon megacephalum) is currently classified into three subspecies. However, the classification is still controversial and their evolutionary histories are still unclear. Here, multiple genetic analyses consistently revealed three phylogenetic groups with substantial genetic divergences and distinct demographic histories, suggesting three phylogenetic species (P. megacephalum, P. peguense, and Baise clade). Phylogeographical analyses revealed that the Red River plains and Guangxi basins are largely coincident with the boundaries between the three phylogenetic species, highlighting the key role of lowland areas in driving speciation in the big-headed turtle. The Baise clade is characterized by high-linkage disequilibrium but the lowest effective population size, indicating that the cryptic phylogenetic species is more vulnerable to human activities and environmental disturbance, and urgently needs more protection. Our findings provide fundamental insights into the taxonomy and scientific conservation of the family Platysternidae.

The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis

Introduction

Whole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level.

Methods

In this study, based on the whole-genome resequencing data of 101 critically endangered Artocarpus nanchuanensis individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species.

Results

Whole-genome resequencing for A. nanchuanensis generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of A. nanchuanensis was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of A. nanchuanensis revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in Artocarpus nanchuanensis, especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of A. nanchuanensis will still maintain high suitability.

Discussion

Based on total analyses, we divided the populations of A. nanchuanensis into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of A. nanchuanensis and important insight into conservation genomics research.

Biogeographic diversification of Actaea (Ranunculaceae): Insights into the historical assembly of deciduous broad-leaved forests in the Northern Hemisphere

The deciduous broad-leaved forests (DBLFs) cover large temperate and subtropical high-altitude regions in the Northern Hemisphere. They are home to rich biodiversity, especially to numerous endemic and relict species. However, we know little about how this vegetation in the Northern Hemisphere has developed through time. Here, we used Actaea (Ranunculaceae), an herbaceous genus almost exclusively growing in the understory of the Northern Hemisphere DBLFs, to shed light on the historical assembly of this biome in the Northern Hemisphere. We present a complete species-level phylogenetic analysis of Actaea based on five plastid and nuclear loci. Using the phylogenetic framework, we estimated divergence times, ancestral ranges, and diversification rates. Phylogenetic analyses strongly support Actaea as monophyletic. Sections Podocarpae and Oligocarpae compose a clade, sister to all other Actaea. The sister relationship between sections Chloranthae and Souliea is strongly supported. Section Dichanthera is not monophyletic unless section Cimicifuga is included. Actaea originated in East Asia, likely the Qinghai-Tibet Plateau, in the late Paleocene (c. 57 Ma), and subsequently dispersed into North America in the middle Eocene (c. 43 Ma) via the Thulean bridge. Actaea reached Europe twice, Japan twice, and Taiwan once, and all these five colonization events occurred in the late Miocene-early Pliocene, a period when sea level dropped. Actaea began to diversify at c. 43 Ma. The section-level diversification took place at c. 27-37 Ma and the species-level diversification experienced accelerations twice, which occurred at c. 15 Ma and c. 5 Ma, respectively. Our findings suggest that the Northern Hemisphere DBLFs might have risen in the middle Eocene and further diversified in the late Eocene-Oligocene, middle Miocene and early Pliocene, in association with climatic deterioration during these four periods.

Forest characteristics, population structure and growth trends of threatened relict Pseudotsuga forrestii in China

Pseudotsuga forrestii is a relict evergreen coniferous tree species in Pinaceae endemic to China. P. forrestii tree numbers have greatly decreased due to deforestation, over-utilization and habitat degradation. Here we clarify P. forrestii community types, structure, species diversity, seedling recruitments and growth trends. We identified four P. forrestii community types: (1) Pseudotsuga forrestii - Quercus guyavifolia - Acer davidii evergreen coniferous and broad-leaved mixed forest; (2) Pseudotsuga forrestii - Pinus yunnanensis - Quercus guyavifolia evergreen coniferous and broad-leaved mixed forest; (3) Pseudotsuga forrestii evergreen coniferous forest; (4) Pseudotsuga forrestii - Abies georgei var. smithii evergreen coniferous forest. P. forrestii forests are characterized by both warm temperate and temperate affinities. Simpson diversity, Pielou evenness, Shannon-Wiener diversity indices ranged from 0.75 to 0.76, 0.74-0.81, and 1.62-1.93, respectively, with no significant differences among the four forest types. The forest stratification was multilayered. The canopy layer was generally 10-25 m tall, with the emergent layer reached 25-42 m. DBH and age structures of P. forrestii showed multimodal distributions. Its maximum age P. forrestii was 570 years with a DBH of 143 cm. The growth of annual ring width of P. forrestii was slow, and generally decreased with age, whereas the basal area at the breast height increased with age. Established seedlings/saplings were mainly found in unstable micro-habitats. Regeneration of P. forrestii depends on moderate natural disturbances. Finally, we provide recommendations for P. forrestii conservation.

East‒West genetic differentiation across the Indo-Burma hotspot: evidence from two closely related dioecious figs

BACKGROUND

Understanding biodiversity patterns and their underlying mechanisms is of interest to ecologists, biogeographers and conservationists and is critically important for conservation efforts. The Indo-Burma hotspot features high species diversity and endemism, yet it also faces significant threats and biodiversity losses; however, few studies have explored the genetic structure and underlying mechanisms of Indo-Burmese species. Here, we conducted a comparative phylogeographic analysis of two closely related dioecious Ficus species, F. hispida and F. heterostyla, based on wide and intensive population sampling across Indo-Burma ranges, using chloroplast (psbA-trnH, trnS-trnG) and nuclear microsatellite (nSSR) markers, as well as ecological niche modeling.

RESULTS

The results indicated large numbers of population-specific cpDNA haplotypes and nSSR alleles in the two species. F. hispida showed slightly higher chloroplast diversity but lower nuclear diversity than F. heterostyla. Low-altitude mountainous areas of northern Indo-Burma were revealed to have high genetic diversity and high habitat suitability, suggesting potential climate refugia and conservation priority areas. Strong phylogeographic structure and a marked east‒west differentiation pattern were observed in both species, due to the interactions between biotic and abiotic factors. Interspecific dissimilarities at fine-scale genetic structure and asynchronized historical dynamics of east‒west differentiation between species were also detected, which were attributed to different species-specific traits.

CONCLUSIONS

We confirm hypothesized predictions that interactions between biotic and abiotic factors largely determine the patterns of genetic diversity and phylogeographic structure of Indo-Burmese plants. The east‒west genetic differentiation pattern observed in two targeted figs can be generalized to some other Indo-Burmese plants. The results and findings of this work will contribute to the conservation of Indo-Burmese biodiversity and facilitate targeted conservation efforts for different species.

Global Protected Areas as refuges for amphibians and reptiles under climate change

Protected Areas (PAs) are the cornerstone of biodiversity conservation. Here, we collated distributional data for >14,000 (~70% of) species of amphibians and reptiles (herpetofauna) to perform a global assessment of the conservation effectiveness of PAs using species distribution models. Our analyses reveal that >91% of herpetofauna species are currently distributed in PAs, and that this proportion will remain unaltered under future climate change. Indeed, loss of species' distributional ranges will be lower inside PAs than outside them. Therefore, the proportion of effectively protected species is predicted to increase. However, over 7.8% of species currently occur outside PAs, and large spatial conservation gaps remain, mainly across tropical and subtropical moist broadleaf forests, and across non-high-income countries. We also predict that more than 300 amphibian and 500 reptile species may go extinct under climate change over the course of the ongoing century. Our study highlights the importance of PAs in providing herpetofauna with refuge from climate change, and suggests ways to optimize PAs to better conserve biodiversity worldwide.

Age-to-Glasgow Coma Scale score ratio predicts gastrointestinal bleeding in patients with primary intracerebral hemorrhage

Objective

Recent clinical studies have demonstrated that advanced age and low initial Glasgow Coma Scale (GCS) score were independent predictors of gastrointestinal bleeding (GIB) in patients with primary intracerebral hemorrhage (ICH). However, used singly, age and GCS score have their respective shortcomings in predicting the occurrence of GIB. This study aimed to investigate the association between the age-to-initial GCS score ratio (AGR) and the risk of GIB following ICH.

Methods

We conducted a single-center, retrospective observational study of consecutive patients presenting with spontaneous primary ICH at our hospital from January 2017 through January 2021. Patients who fulfilled the inclusion and exclusion criteria were categorized into GIB and non-GIB groups. Univariate and multivariate logistic regression analyses were implemented to identify the independent risk factors for the occurrence of GIB, and a multicollinearity test was performed. Furthermore, one-to-one matching was conducted to balance important patient characteristics by the groups' propensity score matching (PSM) analysis.

Results

A total of 786 consecutive patients fulfilled the inclusion/exclusion criteria for the study, and 64 (8.14%) patients experienced GIB after primary ICH. Univariate analysis revealed that patients with GIB were significantly older [64.0 (55.0-71.75) years vs. 57.0 (51.0-66.0) years, p = 0.001] and had a higher AGR [7.32 (5.24-8.96) vs. 5.40 (4.31-7.11), p < 0.001] and a lower initial GCS score [9.0 (7.0-11.0) vs. 11.0 (8.0-13.0), p < 0.001]. The multicollinearity test revealed that no multicollinearity was observed in the multivariable models. Multivariate analysis showed that the AGR was a significant independent predictor of GIB [odds ratio (OR) 1.155, 95% confidence interval (CI) 1.041-1.281, p = 0.007], as well as prior anticoagulation or antiplatelet therapy (OR 0.388, 95% CI 0.160-0.940, p = 0.036) and MV used >24 h (OR 0.462, 95% CI 0.252-0.848, p = 0.013). Receiver operating curve (ROC) analysis illustrated that the optimal cutoff value for the AGR as a predictor for GIB in patients with primary ICH was 6.759 [the area under the curve (AUC) was 0.713 with a corresponding sensitivity of 60.94% and specificity of 70.5%, 95% CI 0.680-0.745, p < 0.001]. After 1:1 PSM, the matched GIB group had significantly higher AGR levels compared with the matched non-GIB group [7.47(5.38-9.32) vs. 5.24(4.24-6.40), p <0.001]. The ROC analysis indicated an AUC of 0.747 (the sensitivity was 65.62%, and the specificity was 75.0%, 95% CI 0.662-0.819, p < 0.001) for AGR levels as an independent predictor of GIB in patients with ICH. In addition, AGR levels were statistically correlated with unfunctional 90-day outcomes.

Conclusion

A higher AGR was associated with an increased risk of GIB and unfunctional 90-day outcomes in patients with primary ICH.

Prehistoric pathways to Anthropocene adaptation: Evidence from the Red River Delta, Vietnam

Over the past twenty years, government advisory bodies have placed increasing emphasis on the need for adaptive measures in response to the effects of human-induced climate change. Integrated Assessment Models (IAMs), which incorporate macroeconomic and climate variables, feature prominently in advisory content, though they rarely draw on data from outside strictly constrained hypothetical systems. This has led to assertions that they are not well-suited to approximate complex systemic human-environment processes. Modular, interdisciplinary approaches have offered a way to address this shortcoming; however, beyond climate records, prehistoric data continue to be under-utilised in developing such models. In this paper we highlight the contribution that archaeology and palaeoecology can make to the development of the next generation IAMs that are expected to enhance provision for more local and pro-active adaptations to future climate change. We present data from one of Southeast Asia's most heavily developed river deltas: the Red River (Song Hong) Delta, in Vietnam and localised analysis from the Tràng An Landscape Complex World Heritage Site, on the delta's southern margin. Comparison is made between Shared Socio-economic Pathways (SSP) 5-8.5 and SSP2-4.5 emission projection models and the Mid-Holocene inundation of the Red River Basin. We highlight the value to taking a scientific long view of coastal evolution through an illustrative set of eight research foci where palaeo-data can bring new and localised empirical data to bear on future risk management planning. We proceed to demonstrate the applicability of palaeoenvironmental, zooarchaeological and historical evidence to management and the development of sustainable conservation strategies using Tràng An as a case study. In so doing, we further highlight the importance of knowledge exchange between scientific, corporate, non-governmental, local, and state stakeholders to achieve tangible results on the ground.

Riparian areas as a conservation priority under climate change

Identifying climatic refugia is important for long-term conservation planning under climate change. Riparian areas have the potential to provide climatic refugia for wildlife, but literature remains limited, especially for plants. This study was conducted with the purpose of identifying climatic refugia of plant biodiversity in the portion of the Mekong River Basin located in Xishuangbanna, China. We first predicted the current and future (2050s and 2070s) potential distribution of 50 threatened woody species in Xishuangbanna by using an ensemble of small models, then stacked the predictions for individual species to derive spatial biodiversity patterns within each 10 × 10 km grid cell. We then identified the top 17 % of the areas for spatial biodiversity patterns as biodiversity hotspots, with climatic refugia defined as areas that remained as biodiversity hotspots over time. Stepwise regression and linear correlation were applied to analyze the environmental correlations with spatial biodiversity patterns and the relationships between climatic refugia and river distribution, respectively. Our results showed potential upward and northward shifts in threatened woody species, with range contractions and expansions predicted. The spatial biodiversity patterns shift from southeast to northwest, and were influenced by temperature, precipitation, and elevation heterogeneity. Climatic refugia under climate change were related closely to river distribution in Xishuangbanna, with riparian areas identified that could provide climatic refugia. These refugial zones are recommended as priority conservation areas for mitigating the impacts of climate change on biodiversity. Our study confirmed that riparian areas could act as climatic refugia for plants and emphasizes the conservation prioritization of riparian areas within river basins for protecting biodiversity under climate change.

Threats, biodiversity drivers and restoration in temperate floodplain forests related to spatial scales

Floodplain forests offer a diversity of habitats and resources for a very wide range of plant and animal species. They also offer many benefits to humankind and are considered essential to the mitigation of the effects of climate change. Nevertheless, throughout the world they are suffering the most intense of anthropogenic pressures so are, of all ecosystems, among the most endangered. Here, we bring together and synthesise existing ecological understanding of the mechanisms underlying the high heterogeneity and diversity of temperate floodplain forests and of the pressures threatening their high biological value due to habitat homogenisation. Floodplain forests depend on the periodic disturbances under which they evolved, including fluvial dynamics, traditional management practices and the activities of herbivores. However, they have been heavily degraded by climate change, invasion of exotic species, river-flow regulation, landscape fragmentation, eutrophication and the cessation of traditional management. We can now observe two general trends in temperate floodplain forests: (1) Due to intensive landscape exploitation, they are now more open and thus prone to the spread of competitive species, including of invasive exotics and (2) Due to the cessation of traditional management, along with modified hydrological conditions, they are composed of species in the later successional stages (i.e., more shade-tolerant and mesic) while light-demanding species are quickly vanishing. Restoration practices have brought about contrasting results when restoration of floodplains to their natural states has been problematic. This is likely because of interplay between various natural and artificial processes not previously taken into proper consideration. We would like to draw attention to the fact that restoration projects or the preservation of existing floodplain forest ecosystems should combine the restoration of watercourses with the mitigation of other important threats acting at different scales of the landscape (spread of invasive species, eutrophication of watersheds and inappropriate forest management).

Monsoon intensification in East Asia triggered the evolution of its flora

INTRODUCTION

East Asia (EA), which falls within the region of the Asian monsoon that is composed of the East Asia monsoon (EAM) and the Indian monsoon (IM), is known for its high species diversity and endemism. This has been attributed to extreme physiographical heterogeneity in conjunction with climate and sea-level changes during the Pleistocene, this hypothesis has been widely proven by phylogeographic studies. Recently, dated phylogenies have indicated that the origins (stem age) of the flora occurred after the Oligocene-Miocene boundary and are related to the establishment of the EAM.

METHODS

Hence, this study further examined whether the strengthening of the monsoons triggered floral evolution via a meta-analysis of the tempo-spatial pattern of evolutionary radiation dates (crown ages) of 101 endemic seed plant genera.

RESULTS

Taxonomic diversification began during the late Eocene, whereas the accumulated number of diversifications did not significantly accelerate until the late Miocene. The distribution of the weighted mean and the average divergence times in the EAM, IM, or transitional regions all fall within the mid-late Miocene. Fossils of the Tertiary relict genera are mostly and widely distributed outside EA and only half of the earliest fossils in the EA region are not older than Miocene, while their divergence times are mostly after the late Miocene. The pattern of divergence time of monotypic and polytypic taxa suggest the climatic changes after the late Pliocene exert more influence on monotypic taxa.

DISCUSSION

The two key stages of floral evolution coincide with the intensifications of the EAM and IM, especially the summer monsoon which brings a humid climate. An integrated review of previous studies concerning flora, genus, and species levels further supports our suggestion that monsoon intensification in EA triggered the evolution of its flora.

The Effect of Environmental Factors on the Diversity of Crane Flies (Tipulidae) in Mountainous and Non-Mountainous Regions of the Qinghai-Tibet Plateau and Surrounding Areas

Tipulidae, one of the most diverse families of Diptera, is widely distributed in the world. The adults have weak flight ability, making it an ideal model for studying the formation of insect diversity. This study aims to explore the species diversity and endemism of Tipulidae in the Qinghai-Tibet Plateau and the surrounding areas, as well as analyze the relationships between the diversity pattern and 25 environmental factors in mountainous and non-mountainous regions. To this end, we collected 2589 datasets for the distribution of 1219 Tipulidae species, and found three areas with high diversities of Tipulidae around the QTP, including the Sikkim-Yadong area, Kamen River Basin, and Gongga Mountain. Further R, generalized additive model (GAM), and stepwise multiple regression analysis indicated that the richness and endemism of Tipulidae is mainly influenced by the warmest quarter precipitation and topographic heterogeneity in mountainous regions, but in non-mountainous regions, the richness is mostly affected by the precipitation seasonality, while there is no regularity in the relationship between endemism and environmental factors. In addition, the richness model in mountainous regions was in conformity with the results of GAM.

Diversification of East Asian subtropical evergreen broadleaved forests over the last 8 million years

The evolution of subtropical evergreen broadleaved forests (EBLFs) in East Asia is interesting while complicated. Genus‐level phylogenies indicate that the origins of EBLFs could trace back to the Oligocene–Miocene boundary or even the Eocene, while population‐level phylogeographic evidence suggests that they diversified after the Miocene, particularly in the Pleistocene. Here, we review the origins of dominant plant species to better understand the evolution of EBLFs. We compiled published estimates of the timing of origin of dominant species and diversification of evergreen relict genera from East Asian EBLFs. We also traced and visualized the evolution of EBLFs in the region using dated phylogenies and geographic distributions of the reviewed taxa. Most (76.1%) of the dominant species originated after the late Miocene, ca. 8 million years ago. Of the 10 evergreen relict genera, eight diverged near the late Miocene–Pliocene boundary or during the late Pliocene, and the remaining two diverged during the Pleistocene. Over the past 8 million years, geo‐climatic changes have triggered origins of most of the dominant EBLF species and provided refugia for evergreen relict genera. Three pulsed phases of evolution are suggested by genetic studies at the genus, species, and population levels. Fossil evidence and spatiotemporal investigations should be integrated to fully understand the evolution of EBLFs in East Asia.

Phylogeography of Himalrandia lichiangensis from the dry-hot valleys in Southwest China

Both changing tectonics and climate may shape the phylogeographic patterns of plant species. The dry-hot valleys in southwestern China harbor a high number of endemic plants. In this study, we investigated the evolutionary history and potential distribution of an endemic shrub Himalrandia lichiangensis (Rubiaceae), to evaluate the effects of tectonic and climatic processes on this thermophilic plant species from the dry-hot valleys. By sequencing DNA from four plastid non-coding regions (psbM-trnD, trnD-trnT, atpB-rbcL and accD-psaI) and the CAMX1F-CAMX2R region and ITS for 423 individuals from 23 populations, we investigated the genetic diversity, phylogeographical pattern and population dynamics of H. lichiangensis. We found a high degree of differentiation in H. lichiangensis during the middle Miocene (15-13 Myr), possibly triggered by the rapid tectonic uplift event in this period area. accompanied by frequent orogeneses in this period. This hypothesis is also supported by the association between genetic differentiation and altitudinal gradients among populations. The middle reach of the Jinsha River, which harbors the greatest genetic diversity, is most likely to have been a refugia for H. lichiangensis during Quaternary. We also detected a strong barrier effect between the Nanpan River and Jinsha River, suggesting the river system may play a role in geographical isolation between clades on both sides of the barrier. The Maximum Entropy Model (MaxEnt) results showed that future climate warming will lead to the niche expansion in some areas for H. lichiangensis but will also cause a scattered and fragmented distribution. Given the high among-population differentiation and no recent expansion detected in H. lichiangensis, its current phylogeographical pattern is possibly due to a long-term geographical barrier caused by uplifting mountains since the Miocene, as well as Quaternary climate refugia isolated also by high mountains. This study illustrated tectonic and climatic processes may have a continuous effect on plant phylogeography and offers insights into the origin of biodiversity and endemism in the dry-hot valleys of southwestern China.

Biotic colonization of subtropical East Asian caves through time

Caves are home to unique and fragile biotas with high levels of endemism. However, little is known about how the biotic colonization of caves has developed over time, especially in caves from middle and low latitudes. Subtropical East Asia holds the world's largest karst landform with numerous ancient caves, which harbor a high diversity of cave-dwelling organisms and are regarded as a biodiversity hotspot. Here, we assess the temporal dynamics of biotic colonization of subtropical East Asian caves through a multi-taxon analysis with representatives of green plants, animals, and fungi. We then investigate the consequences of paleonviromental changes on the colonization dynamics of these caves in combination with reconstructions of vegetation, temperature, and precipitation. We discover that 88% of cave colonization events occurred after the Oligocene-Miocene boundary, and organisms from the surrounding forest were a major source for subtropical East Asian cave biodiversity. Biotic colonization of subtropical East Asian caves during the Neogene was subject to periods of acceleration and decrease, in conjunction with large-scale, seasonal climatic changes and evolution of local forests. This study highlights the long-term evolutionary interaction between surface and cave biotas; our climate-vegetation-relict model proposed for the subtropical East Asian cave biota may help explain the evolutionary origins of other mid-latitude subterranean biotas.

Fingerprints of climatic changes through the late Cenozoic in southern Asian flora: Magnolia section Michelia (Magnoliaceae)

BACKGROUND AND AIMS

Ongoing global warming is a challenge for humankind. A series of drastic climatic changes have been proven to have occurred throughout the Cenozoic based on a variety of geological evidence, which helps to better understand our planet's future climate. Notably, extant biomes have recorded drastic environmental shifts. The climate in southern Asia, which hosts high biodiversity, is deeply impacted by the Asian monsoon. The origins and evolutionary dynamics of biomes occurring between the tropics and sub-tropics in southern Asia have probably been deeply impacted by climatic changes; however, these aspects remain poorly studied. We tested whether the evolutionary dynamics of the above biomes have recorded the drastic, late Cenozoic environmental shifts, by focusing on Magnolia section Michelia of the family Magnoliaceae.

METHODS

We established a fine time-calibrated phylogeny of M. section Michelia based on complete plastid genomes and inferred its ancestral ranges. Finally, we estimated the evolutionary dynamics of this section through time, determining its diversification rate and the dispersal events that occurred between tropical and sub-tropical areas.

KEY RESULTS

The tropical origin of M. section Michelia was dated to the late Oligocene; however, the diversification of its core group (i.e. M. section Michelia subsection Michelia) has occurred mainly from the late Miocene onward. Two key evolutionary shifts (dated approx. 8 and approx. 3 million years ago, respectively) were identified, each of them probably in response to drastic climatic changes.

CONCLUSION

Here, we inferred the underlying evolutionary dynamics of biomes in southern Asia, which probably reflect late Cenozoic climatic changes. The occurrence of modern Asian monsoons was probably fundamental for the origin of M. section Michelia; moreover, the occurrence of asymmetric dispersal events between the tropics and sub-tropics hint at an adaptation strategy of M. section Michelia to global cooling, in agreement with the tropical conservatism hypothesis.