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

Local Adaptation and Climate Change Vulnerability of the Relict Tree Species Taiwania cryptomerioides Provide Insights Into Its Conservation and Restoration

Rapid climate change is affecting biodiversity and threatening locally adapted species. Relict species are often confined to relatively narrow, discontinuous geographic ranges and provide excellent opportunities to study local adaptation and extinction. Understanding the adaptive genetic variation and genetic vulnerability of relict species under climate change is essential for their conservation and management efforts. Here, we applied a landscape genomics approach to investigate the population genetic structure and predict adaptive capacity to climatic change for Taiwania cryptomerioides Hayata, a vulnerable Tertiary relict tree species in China. We used restriction site-associated DNA sequencing on 122 individuals across 10 sampling sites. We found three genetic groups across the Chinese range of T. cryptomerioides: the southwest, central-eastern, and Taiwanese groups. We detected significant signals of isolation by environment and isolation by distance, with environment playing a more important role than geography in shaping spatial genetic variation in T. cryptomerioides. Moreover, some outliers were related to defense and stress responses, which could reflect the genomic basis of adaptation. Gradient forest (GF) analysis revealed that precipitation-related variables were important in driving adaptive variation in T. cryptomerioides. Ecological niche modeling and GF analysis revealed that the central-eastern populations were more vulnerable to future climate change than other populations, with range contractions and high genetic offsets, suggesting these populations may be at higher risk of decline or local extinction. These findings deepen our understanding of local adaptation and vulnerability to climate change in relict tree species and will guide conservation and restoration programs for T. cryptomerioides in the future.

Changes in the Suitable Habitat of the Smoke Tree (Cotinus coggygria Scop.), a Species with an East Asian-Tethyan Disjunction

The smoke tree (Cotinus coggygria Scop.) is a woody species mainly distributed in the Mediterranean region and East Asia, known for its high ecological and ornamental value. Investigation of changes in suitable habitats under different conditions can provide valuable insights with implications for predicting the distribution of C. coggygria. In this study, we employed a MaxEnt model to simulate the current, historical, and future suitable habitat of C. coggygria using distribution records and environmental variables. The results indicated that climatic variables had a much stronger impact on the suitable habitat of this species compared with soil and topographic variables, and bio11 (mean temperature of the coldest quarter) and bio12 (annual precipitation) played particularly important roles in determining the suitable habitat. The core distribution of C. coggygria exhibited an East Asian-Tethyan disjunction. During the glacial period (Last Glacial Maximum), C. coggygria in Europe was concentrated in the glacial refugia in southern Europe; its range was substantially smaller during the glacial period than during interglacial periods (mid-Holocene). In contrast, C. coggygria in East Asia survived in regions similar to those of the interglacial period. Future climate change led to a gradual northward expansion of suitable habitats for C. coggygria, and the area of suitable habitat was substantially larger in Europe than in East Asia. There were significant differences among the four climate scenarios in Europe, with minimal variation in East Asia. Our findings provide valuable insights into the contrasting effects of climate change on European and East Asian populations of C. coggygria, which enhances our understanding of Eurasian species with discontinuous distributions.

From α-to β-diversity: Understanding the historical, present, and future diversity patterns of Fagaceae in Southwestern China

Macroecological research aims to understand factors influencing species composition and diversity. Understanding the distribution patterns of species is essential for prioritizing areas for conservation. This study investigates the alpha (α) and beta (β) diversity facets of Fagaceae across past (historical), present, and future timelines in Southwestern China. We used over 11,000 geographical observations to predict the spatial patterns of the α- and β-diversity of 120 species. We modeled the α-diversity via stacking prediction using an individual species distribution model at 50 km × 50 km grid cells. We used Sørensen dissimilarity to quantify total β-diversity and its components - turnover (β SIM) and nestedness (β NES). We integrated climate variables along with topographic and plant trait predictors to understand the species diversity. Finally, simultaneous autoregression (SAR) model was used to evaluate the effects of predictor variables on the α- and β-diversity patterns. Our results indicate a projected decline in α-diversity and an increase in β-diversity in the future. The findings underscore that the species β SIM is a driving factor of differing species composition during the past and present periods, while β NES will be a dominant factor in the future. Similarly, climatic and topographic factors significantly influenced the α-diversity and the β-diversity. In the future, climatic variables will play a significant role in determining the diversity patterns. By closely studying how various species respond and adapt to these changes, we can gain valuable insights into the dynamics of ecosystems and the potential threats to biodiversity.

Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium

BACKGROUND AND AIMS

Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time.

METHODS

We used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events.

KEY RESULTS

All sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographical distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographical analysis suggested a Neotropical origin of the genus during the Oligocene (~30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (~22 Ma). The rapid radiation at the backbone probably occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the glacial cycles of the Pliocene-Quaternary may have contributed to further speciation and reticulate evolution within Cypripedium.

CONCLUSIONS

Our study provides novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

Out of and in East Asia: phylogeny, biogeography and diversification of Thalictroideae (Ranunculaceae) in the Northern Hemisphere

BACKGROUND AND AIMS

Understanding the biogeographical patterns and processes underlying the distribution of diversity within the Northern Hemisphere has fascinated botanists and biogeographers for over a century. However, as a well-known centre of species diversity in the Northern Hemisphere, whether East Asia acted as a source and/or a sink of plant diversity of the Northern Hemisphere remains unclear. Here, we used Thalictroideae, a subfamily widely distributed in the Northern Hemisphere with the majority of species in East Asia, to investigate the role of East Asia in shaping the biogeographical patterns of the Northern Hemisphere and to test whether East Asia acted as a museum or a cradle for herbaceous taxa.

METHODS

Based on six plastid and one nuclear DNA regions, we generated the most comprehensive phylogeny for Thalictroideae, including 217 taxa (~66 % species) from all ten of the currently recognized genera. Within this phylogenetic framework, we then estimated divergence times, ancestral ranges and diversification rates.

KEY RESULTS

The monophyletic Thalictroideae contains three major clades. All genera with more than one species are strongly supported as monophyletic except for Isopyrum, which is nested in Enemion. The most recent common ancestor of Thalictroideae occurred in East Asia in the late Eocene (~36 Mya). From the Miocene onwards, ≥46 dispersal events were inferred to be responsible for the current distribution of this subfamily. East Asian Thalictroideae lineages experienced a rapid accumulation at ~10 Mya.

CONCLUSIONS

The biogeographical patterns of Thalictroideae support the 'out of and in East Asia' hypothesis, i.e. East Asia is both a source and a sink of biodiversity of the Northern Hemisphere. The global cooling after the middle Miocene Climatic Optimum, combined with the exposed land bridges owing to sea-level decline, might jointly have caused the bidirectional plant exchanges between East Asia and other Northern Hemisphere regions. East Asia serves as evolutionary museums and cradles for the diversity of Thalictroideae and probably for other herbaceous lineages.

Predicting the Global Distribution of Nitraria L. Under Climate Change Based on Optimized MaxEnt Modeling

The genus of Nitraria L. are Tertiary-relict desert sand-fixing plants, which are an important forage and agricultural product, as well as an important source of medicinal and woody vegetable oil. In order to provide a theoretical basis for better protection and utilization of species in the Nitraria L., this study collected global distribution information within the Nitraria L., along with data on 29 environmental and climatic factors. The Maximum Entropy (MaxEnt) model was used to simulate the globally suitable distribution areas for Nitraria L. The results showed that the mean AUC value was 0.897, the TSS average value was 0.913, and the model prediction results were excellent. UV-B seasonality (UVB-2), UV-B of the lowest month (UVB-4), precipitation of the warmest quarter (bio18), the DEM (Digital Elevation Model), and annual precipitation (bio12) were the key variables affecting the distribution area of Nitraria L, with contributions of 54.4%, 11.1%, 8.3%, 7.4%, and 4.1%, respectively. The Nitraria L. plants are currently found mainly in Central Asia, North Africa, the neighboring Middle East, and parts of southern Australia and Siberia. In future scenarios, except for a small expansion of the 2030s scenario model Nitraria L., the potential suitable distribution areas showed a decreasing trend. The contraction area is mainly concentrated in South Asia, such as Afghanistan and Pakistan, North Africa, Libya, as well as in areas of low suitability in northern Australia, where there was also significant shrinkage. The areas of expansion are mainly concentrated in the Qinghai-Tibet Plateau to the Iranian plateau, and the Sahara Desert is also partly expanded. With rising Greenhouse gas concentrations, habitat fragmentation is becoming more severe. Center-of-mass migration results also suggest that the potential suitable area of Nitraria L. will shift northwestward in the future. This study can provide a theoretical basis for determining the scope of Nitraria L. habitat protection, population restoration, resource management and industrial development in local areas.

Lineage Differentiation and Genomic Vulnerability in a Relict Tree From Subtropical Forests

The subtropical forests of East Asia are renowned for their high plant diversity, particularly the abundance of ancient relict species. However, both the evolutionary history of these relict species and their capacity for resilience in the face of impending climatic changes remain unclear. Using whole-genome resequencing data, we investigated the lineage differentiation and demographic history of the relict and endangered tree, Bretschneidera sinensis (Akaniaceae). We employed a combination of population genomic and landscape genomic approaches to evaluate variation in mutation load and genomic offset, aiming to predict how different populations may respond to climate change. Our analysis revealed a profound genomic divergence between the East and West lineages, likely as the result of recurrent bottlenecks due to climatic fluctuations during the glacial period. Furthermore, we identified several genes potentially linked to growth characteristics and hypoxia response that had been subjected to positive selection during the lineage differentiation. Our assessment of genomic vulnerability uncovered a significantly higher mutation load and genomic offset in the edge populations of B. sinensis compared to their core counterparts. This implies that the edge populations are likely to experience the most significant impact from the predicted climate conditions. Overall, our research sheds light on the historical lineage differentiation and contemporary genomic vulnerability of B. sinensis. Broadening our understanding of the speciation history and future resilience of relict and endangered species such as B. sinensis, is crucial in developing effective conservation strategies in anticipation of future climatic changes.

Assessment of suitable region of Asparagus cochinchinensis (Lour.) Merr. under different climatic conditions in China by the MaxEnt model and HPLC analysis

Asparagus cochinchinensis is a member of the Asparagaceae family whose medicinal part is the dried root tuber. The distribution of A. cochinchinensis and its secondary metabolites are closely associated with environmental factors, such as climate and soil properties. By establishing and optimizing a maximum entropy model, we analyzed and predicted the distribution pattern and migration direction of suitable habitats for A. cochinchinensis and determined the main environmental factors affecting the accumulation of secondary metabolites. Under current climatic conditions, the area of suitable habitats for A. cochinchinensis (208.38 × 104 km2) accounts for 21.71% of the land area of China, and the areas of lowly, moderately, and highly suitable areas were 64.15 × 104 km2, 113.66 × 104 km2, and 30.57 × 104 km2, respectively. Under future climate scenarios, the total area of suitable habitats hardly changes. The area of highly suitable habitats significantly decreases under the SSP1-RCP2.6 scenario (to 83.22% of the current value) and the SSP3-RCP7 scenario (to 48.94% of the current value), but eventually increases to 112.86% of the current value under the SSP5-RCP8.5 scenario, which indicates that A. cochinchinensis might adapt better to a high-carbon-emissions scenario. Under different climate scenarios, low-impact areas mainly occur in southern China and will correspond 92.07% of the current suitable area. Highly suitable habitats primarily occur in the southeastern Sichuan Basin, northern Guangxi, eastern Guizhou, and western Hunan. HPLC analysis showed that the content of protodioscin (0.373%) and protogracillin (0.044%) in S2 was the highest. The total saponins contents of S1 and S2 were the highest, which were 35.6586 and 33.1262 mg/g, respectively. The total polysaccharide content of S9 was the highest (16.9467%). The total contents of saponins and polysaccharides in A. cochinchinensis were significantly, but oppositely, correlated with temperature, precipitation, and other factors. This study has identified environmental factors affecting the growth and quality of A. cochinchinensis, which has guiding significance for resource conservation and site selection for large-scale cultivation.

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.

First report on population status and potential distribution of Tylototritonsparreboomi Bernardes, Le, Nguyen, Pham, Pham, Nguyen, Rödder, Bonkowski & Ziegler, 2020 (Amphibia, Salamandridae) in Vietnam

The Sparreboom's Crocodile Newt (Tylototritonsparreboomi) is a recently discovered species of crocodile newts from Vietnam and it is currently known only from Sin Ho District in Lai Chau Province. Due to the limited information available on its population status and distribution, the species has been classified as Data Deficient in the IUCN Red List. As a result of our field surveys in 2021 and 2022 in north-western Vietnam, novel data on distribution and population status of and threats to this poorly-known species were collected. We combined the newly-discovered locations with previous occurrence records and used the data as input for modelling the potential distribution of the Sparreboom's Crocodile Newt. The results showed that the Sparreboom's Crocodile Newt's potential distribution encompasses areas in Lai Chau, Dien Bien and Son La Provinces, Vietnam, as well as a section in Jinping County, Yunnan Province, China. Based on the findings, we suggest that protected areas in the eastern side of Hoang Lien Mountain Range, such as Che Tao, Muong La, Hoang Lien - Van Ban and Bat Xat Nature Reserves and Hoang Lien National Park in Vietnam and Jinping Feishuling Nature Reserve in China be priority sites for the species conservation. Future research and conservation initiatives should prioritise efforts in such areas in an effort to find and protect new populations of the newt.

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.

An unprotected vulnerable relict subtropical conifer-Keteleeria evelyniana: Its forests, populations, growth and endangerment by invasive alien plant species in China

Relict subtropical coniferous forests in China face severe fragmentation, resulting in declining populations, and some are under significant threat from invasive alien species. Despite the crucial importance of understanding forest dynamics, knowledge gaps persist, particularly regarding the impact of invasive plants on vulnerable natives like Keteleeria evelyniana. In this study, we investigated the impact of invasive plants on the regeneration of forests dominated by K. evelyniana, a subtropical relict species in southwestern China. For this purpose, we characterized forest dynamics of 160 forest plots featuring K. evelyniana as the primary dominant species and determined whether the presence of invasive plants was correlated with regeneration of K. evelyniana. We identified four distinct forest types in which K. evelyniana was dominant. We found that radial growth of K. evelyniana trees is faster in younger age-classes today than it was for older trees at the same age. The population structure of K. evelyniana in each forest type exhibited a multimodal age-class distribution. However, three forest types lacked established saplings younger than 10 years old, a situation attributed to the dense coverage of the invasive alien Ageratina adenophora. This invasive species resulted in a reduction of understory species diversity. Additionally, our analysis uncovered a significant negative correlation in phylogenetic relatedness (net relatedness index) between native and invasive alien plant species in eastern Yunnan. This suggests closely related invasive species face heightened competition, hindering successful invasion. Taken together, our findings indicate that successful establishment and habitat restoration of K. evelyniana seedling/saplings require effective measures to control invasive plants.

Genetically- and environmentally-dependent processes drive interspecific and intraspecific divergence in the Chinese relict endemic genus Dipteronia

China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere. Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations. One of these relict lineages is Dipteronia, an oligotypic tree genus with a fossil record extending to the Paleocene. Here, we investigated the genetic variability, demographic dynamics and diversification patterns of the two currently recognized Dipteronia species (D ipteronia sinensis and D . dyeriana). Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions, two single copy nuclear genes and 15 simple sequence repeat loci. The genetic study was combined with niche comparison analyses on the environmental space, ecological niche modeling, and landscape connectivity analysis. We found that the two Dipteronia species have highly diverged both in genetic and ecological terms. Despite the incipient speciation processes that can be observed in D. sinensis, the occurrence of long-term stable refugia and, particularly, a dispersal corridor along Daba Shan-west Qinling, likely ensured its genetic and ecological integrity to date. Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic, but also provide insight into how Arcto-Tertiary relict plants in East Asia survived, evolved, and diversified.

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.

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.

Risk Factors and Spatiotemporal Distribution of Lumpy Skin Disease Occurrence in the Asian Continent during 2012-2022: An Ecological Niche Model

Lumpy skin disease (LSD) is an emerging transboundary infectious disease of animals with high morbidity and low mortality rates. The infection occurs in cattle, buffalo, and some closely related wild animals, with cattle and buffalo showing higher susceptibility than other species. The primary mode of disease transmission is the mechanical dispersion of bloodsucking insects. The disease symptoms, including animal fur damage, weight loss, decline in milk production, infertility, and miscarriage, lead to huge economic losses in regions and countries with LSD outbreaks. The present study aimed to analyze the incidence data of LSD in the Asian continent from January 2012 to September 2022, identify spatiotemporal clusters and risk factors of the disease, and establish a maximum entropy ecological niche model to predict high-risk areas for disease outbreaks. The studied variables included bioclimatic factors, land type, and population density. Following the screening process, 12 variables were included in the maximum entropy model. Among them, the variable contribution rates of cattle density, land cover, isothermality, buffalo density, and maximum temperature of the warmest month were 53.8%, 10.9%, 9.2%, 8.9%, and 8%, respectively. Accounting for more than 90% of the total variable contribution rate, these five variables were considered to be the important influencing factors of LSD outbreaks. According to the results, nine spatiotemporal clusters approximately matched the high-risk areas predicted by the model. The Caucasus region of Russia; the Russian border areas of Kazakhstan, Turkey, Syria, Lebanon, Palestine, and Israel; and the western regions of Iran, India, and Southeast Asia were predicted to be high-risk areas. Thus, this study provides the spatiotemporal clusters, risk factors, and high-risk areas of LSD outbreaks in the Asian continent, which can help formulate more effective disease prevention and control policies.

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.