The potential drivers in forming avian biodiversity hotspots in the East Himalaya Mountains of Southwest China

Conservation implications of climatically heterogeneous areas for species diversity in a biodiversity hotspot

Climate heterogeneity is commonly associated with exceptionally high species richness, thus bolstering ecological resilience and maximizing long-term biodiversity benefits. However, few studies have been conducted to examine the implications of climatically heterogeneous areas (CHAs) for effective biodiversity conservation. In this study, we collected occurrence records of birds and vascular plants in a biodiversity hotspot in Yunnan, China, and delineated corresponding CHAs. The conservation effectiveness of CHAs for species diversity was demonstrated through a comparison of climate- and species-based prioritization schemes, incorporating surrogacy analysis and species representation. Despite significant spatial discrepancies with species-based conservation prioritization, we found that a prioritization scheme based on CHAs would effectively conserve more than 86.3% of Yunnan's birds and vascular plant species, regardless of spatial scale. The coverage of protected areas for priority conservation areas of two prioritization schemes is relatively low (<14.4%). Therefore, our study also underscores the significant conservation gaps for birds and vascular plants in Yunnan revealed by both prioritization schemes, with the latter emphasizing the crucial roles of mountainous regions, gorges, and particularly dry valleys along the Jinsha River and Yuanjiang River. These conservation gaps provide complementary and previously hidden potential conservation areas for the preservation of species diversity in Yunnan. Overall, our study demonstrates that incorporating CHAs into conservation prioritization represents a smart and effective approach for safeguarding species diversity, serving as a paradigm for integrating abiotic factors into conservation planning and providing valuable strategies to conserve species diversity in biodiversity hotspots.

Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones

A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation.

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.

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains

Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

The influence of climate oscillations and geological events on population differentiation of Camponotus japonicus in the Chinese mainland

Camponotus japonicus (Hymenoptera: Formicidae) is an omnivorous social insect which builds sizable colonies in sparse woodlands or cropland and spreads across multiple climatic zones in the Chinese mainland. This study aims to reveal the role of climate changes and geological events in driving the genetic structure of social insect populations by investigating the phylogenetics and historical demography of C. japonicus in the Chinese mainland. Phylogenetic analyses were conducted based on the mitochondria DNA dataset using MrBayes and IQ-TREE. We constructed a haplotype network, calculated analyses of molecular variance, estimated the divergence time, and reconstructed the maximum clade credibility tree. Mismatch distribution and Bayesian skyline plots were used to infer historical population fluctuations. Additionally, ecological niche modeling was employed to predict the potential distribution of the species during the present, mid-holocene, and last glacial maximum periods in the Chinese mainland. The phylogenetic tree and median-joining network analyses support the presence of four distinct lineages in C. japonicus. These lineages exhibit significant genetic differentiation and limited gene flow. The divergence among the four lineages began in the early Pleistocene, approximately 1.41 million years ago (Ma). Subsequently, the central lineage diverged from both the northern and southern lineages around 1.16 Ma, while the northern and southern lineages diverged from each other at approximately 1.07 Ma. Population expansion was observed in the southern, central, and northern lineages prior to the last glacial maximum, while the Yunnan-Sichuan lineage experienced a slight increase in population size in more recent times. The predicted distribution of the species corresponds well with the actual distribution. Furthermore, the current suitable habitat areas in northern Xinjiang, southern Tibet, and the southeast coastal regions have significantly decreased compared to the last glacial maximum and the mid-holocene periods. Our results suggest that climate oscillations and geological events play an important role in driving genetic patterns and differentiation of C. japonicus. Mountain barriers isolate populations from each other, hinder the flow of genes, and effectively prevent the spread of this species. But at the same time, it also formed refugia at low altitudes areas such as Qinling-Bashan Mountains and Yanshan-Taihang Mountains and provide suitable habitats during glaciation. This study provides a good model for understanding how complex climate changes and geological events affect population genetic differentiation of social insects in the Chinese mainland.

Climate Change Impacts on the Potential Distribution Pattern of Osphya (Coleoptera: Melandryidae), an Old but Small Beetle Group Distributed in the Northern Hemisphere

Exploring the development of species distribution patterns under climate change is the basis of biogeography and macroecology. However, under the background of global climate change, few studies focus on how the distribution pattern and the range of insects have or will change in response to long-term climate change. An old but small, Northern-Hemisphere-distributed beetle group Osphya is an ideal subject to conduct the study in this aspect. Here, based on a comprehensive geographic dataset, we analyzed the global distribution pattern of Osphya using ArcGIS techniques, which declared a discontinuous and uneven distribution pattern across the USA, Europe, and Asia. Furthermore, we predicted the suitable habitats of Osphya under different climate scenarios via the MaxEnt model. The results showed that the high suitability areas were always concentrated in the European Mediterranean and the western coast of USA, while a low suitability exhibited in Asia. Moreover, by integrating the analyses of biogeography and habitat suitability, we inferred that the Osphya species conservatively prefer a warm, stable, and rainy climate, and they tend to expand towards higher latitude in response to the climate warming from the past to future. These results are helpful in exploring the species diversity and protection of Osphya.

The Elevational Gradient of Bird Beta Diversity in the Meili Snow Mountains, Yunnan Province, China

Understanding the elevational patterns of beta diversity in mountain regions is a long-standing problem in biogeography and ecology. Previous research has generally focused on the taxonomy facet on a large scale, but was limited with regard to multi-facet beta diversity. Accordingly, we constructed a multi-dimensional (taxonomic/phylogenetic/functional) framework to analyze the underlying mechanisms of beta diversity. Within an approximately 2000 m altitudinal range (from 2027 m to 3944 m) along the eastern slope of the Meili Snow Mountains in Deqin County, Yunnan Province, China, we performed field surveys of breeding and non-breeding birds in September/2011 and May/2012, respectively. In total, 132 bird species were recorded during the fieldwork. The results indicated that taxonomic beta diversity contributed 56% of the bird species diversity, and its turnover process dominated the altitudinal pattern of taxon beta diversity; beta phylogenetic diversity contributed 42% of the bird phylogenetic diversity, and its turnover process also appeared to be stronger than the nestedness. For both taxonomy and phylogeny, the null models standardized measures (SES.β_sim/SES.β_sne/SES.β_sor) of paired dissimilarities between elevation zones all showed statistically significant differences (p ≤ 0.05) and were higher than expected (SES.β > 0). However, standardized functional beta diversity showed convergence along the elevational gradient with no significant change. Moreover, the functional beta diversity contributed 50% of the bird functional diversity; there was no significant difference between the turnover and the nestedness-resultant component. Based on these results, we discerned that taxonomic and phylogenetic beta diversity patterns among the elevational zone were overdispersed, which indicated that limiting similarity dominated the turnover process among the bird species and phylogenetic communities in the Meili Snow Mountains.

Adaptive evolution characteristics of mitochondrial genomes in genus Aparapotamon (Brachyura, Potamidae) of freshwater crabs

BACKGROUND

Aparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To study the molecular mechanisms of adaptive evolution in Aparapotamon, we performed evolutionary analyses, including morphological, geographical, and phylogenetic analyses and divergence time estimation. We sequenced the mitogenomes of Aparapotamon binchuanense and Aparapotamon huizeense for the first time and resequenced three other mitogenomes of Aparapotamon grahami and Aparapotamon gracilipedum. These sequences were combined with NCBI sequences to perform comparative mitogenome analysis of all 13 Aparapotamon species, revealing mitogenome arrangement and the characteristics of protein-coding and tRNA genes.

RESULTS

A new species classification scheme of the genus Aparapotamon has been detected and verified by different aspects, including geographical, morphological, phylogenetics and comparative mitogenome analyses. Imprints from adaptive evolution were discovered in the mitochondrial genomes of group A, including the same codon loss at position 416 of the ND6 gene and the unique arrangement pattern of the tRNA-Ile gene. Multiple tRNA genes conserved or involved in adaptive evolution were detected. Two genes associated with altitudinal adaptation, ATP8 and ND6, which experienced positive selection, were identified for the first time in freshwater crabs.

CONCLUSIONS

Geological movements of the Qinghai-Tibet Plateau and Hengduan Mountains likely strongly impacted the speciation and differentiation of the four Aparapotamon groups. After some group A species dispersed from the Hengduan Mountain Range, new evolutionary characteristics emerged in their mitochondrial genomes, facilitating adaptation to the low-altitude environment of China's second terrain tier. Ultimately, group A species spread to high latitudes along the upper reaches of the Yangtze River, showing faster evolutionary rates, higher species diversity and the widest distribution.

Four New Species of Larval Charletonia and Leptus (Acari: Trombidiformes: Erythraeidae), with a Checklist of the Two Genera and Their Hosts from China

Four new species, Charletonia rectangia Xu and Jin sp. nov., Leptus (Leptus) bomiensis Xu and Jin sp. nov., Leptus (Leptus) longisolenidionus Xu and Jin sp. nov., and Leptus (Leptus) striatus Xu and Jin sp. nov. are described and illustrated based on larvae. All four new species are from biodiversity hotspots, L. (L.) bomiensissp. nov. from the Eastern Himalayas biodiversity hotspot, while the other three species from the Indo-Burma biodiversity hotspot.

Myotis fimbriatus Virome, a Window to Virus Diversity and Evolution in the Genus Myotis

Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly on Rhinolophus bats that could be related to zoonotic events. However, other species of bats that are part of ecosystems identified as virus diversity hotspots have not been studied in-depth. We analyzed the virome of a group of Myotis fimbriatus bats collected from the Yunnan Province during 2020. The virome of M. fimbriatus revealed the presence of families of pathogenic viruses such as Coronavirus, Astrovirus, Mastadenovirus, and Picornavirus, among others. The viral sequences identified in M. fimbriatus were characterized by significant divergence from other known viral sequences of bat origin. Complex phylogenetic landscapes implying a tendency of co-specificity and relationships with viruses from other mammals characterize these groups. The most prevalent and abundant virus in M. fimbriatus individuals was an alphacoronavirus. The genome of this virus shows evidence of recombination and is likely the product of ancestral host-switch. The close phylogenetic and ecological relationship of some species of the Myotis genus in China may have played an important role in the emergence of this alphacoronavirus.

Cryptic species in a colorful genus: Integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species

Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study, we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic approach by combining multilocus, acoustic, plumage and morphometric analyses. Our results reveal that the isolated north-central Chinese populations of Tarsiger cyanurus, described as the subspecies albocoeruleus but usually considered invalid, is distinctive in genetics and vocalisation, but only marginally differentiated in morphology. We also found the Taiwan endemic T. indicus formosanus to be distinctive in genetics, song and morphology from T. i. indicus and T. i. yunnanensis of the Sino-Himalayan mountains. Moreover, Bayesian species delimitation using BPP suggests that both albocoeruleus and formosanus merit full species status. We propose their treatment as 'Qilian Bluetail' T. albocoeruleus and 'Taiwan Bush Robin' T. formosanus, respectively.

Systematic Review of the Genus Nalepa Reitter, 1887 (Coleoptera, Tenebrionidae, Blaptinae, Blaptini) from the Tibetan Plateau, with Description of Six New Species and Two Larvae

Simple Summary

The Tibetan Plateau is the largest and highest plateau in the world. The Tibetan Plateau is widely considered as a large natural experimental area for speciation; its uplift has facilitated allopatric speciation and diversification since the Miocene. In general, the Tibetan Plateau is known for its large number of endemic species. In this study, we revise the systematics of the endemic Tibetan genus Nalepa Reitter, 1887 (Blaptini tribe) and describe six new species based on larval and adult morphology and molecular data. We also provide a diagnostic key to the members of the genus Nalepa. Larvae were associated with the adults using a combined molecular species delimitation, and adult males and females are described and illustrated. Phylogenetic relationships of the members of the genus Nalepa are provided and discussed based on fragments of the mitochondrial and nuclear markers. Further, we applied molecular species delimitation methods to verify the taxonomic status of the new species. Lastly, the status of the genus Nalepa from the Tibetan Plateau is briefly discussed.

Abstract

Nalepa Reitter, 1887 is a monotypic genus of the tenebrionid tribe Blaptini and is endemic to the Tibetan Plateau. In this study, the genus Nalepa was reviewed using a combination of molecular and morphological datasets. Based on the results, six new species were described: N.acuminatasp. n., N. ovalifoliasp. n., N.politasp. n., N. quadratasp. n.,N.xinlongensissp. n., and N.yushuensissp. n. In addition, the larvae of N. cylindracea Reitter, 1887 and N. quadratasp. n. were described and associated with related adults using molecular approaches. This study provides valuable molecular and morphological data for phylogenetic studies.

Multi-Omics Approaches Revealed the Associations of Host Metabolism and Gut Microbiome With Phylogeny and Environmental Adaptation in Mountain Dragons

The molecular basis enabling the adaptation of animals to spatially heterogeneous environments is a critical clue for understanding the variation, formation, and maintenance of biodiversity in the context of global climate change. Mountain dragons (Agamidae: Diploderma) thrive in the Hengduan Mountain Region, a biodiversity hotspot and a typical spatially heterogeneous environment. Here, we compare the liver and muscle metabolome and gut microbiome of 11 geographical populations from three Diploderma species (D. iadinum, D. yulongsense, and D. vela) after 7 days acclimation in the same laboratory conditions. Amino acid metabolism, particularly the products of the glutathione cycle, accounted for major interspecies variations, implying its significance in genetic differentiation among mountain dragons. Notably, the cold-dwelling D. vela and D. yulongense populations tended to have higher glycerophosphate, glycerol-3-phosphocholine, and kinetin levels in their liver, higher carnosine levels in their muscle, and higher Lachnospiraceae levels in their gut. Phylogeny, net primary productivity (NPP), and the temperature had the highest explanation rate to the variations in muscle metabolome, liver metabolome, and gut microbiome, respectively, suggesting heterogeneity of biological systems in response to climatic variations. Therefore, we suggested that the organ heterogeneity in environmental responsiveness might be substantial for mountain dragons to thrive in complicated environments.

Assessing the Diversity and Distribution Pattern of the Speciose Genus Lycocerus (Coleoptera: Cantharidae) by the Global-Scale Data

Species richness patterns and endemism on the large-scale play a significant role in biogeography and biodiversity conservation. This study aimed to explore the diversity centers and endemic areas of a large cantharid genus Lycocerus, so as to test whether the hypothesis of montane and island systems biodiversity in previous studies was supported. In this study, a comprehensive species’ geographical database on the global scale consisting of 4,227 records for 324 Lycocerus species was compiled and analyzed. Species richness pattern was mapped into a grid-based map with a spatial resolution of 1° × 1° fishnet. An unbalanced pattern was identified, and it showed that the centers of species richness of Lycocerus were situated in Eastern Himalayas, Hengduan Mountains, Eastern Sichuan Mountains, Taiwan, and Japan. Further analyses based on two approaches, including parsimony analysis of endemicity (PAE) and endemicity analysis (EA), were applied to detect areas of endemism (AOEs) at three different grid sizes (1°, 1.5°, and 2°). Finally, a total of nine AOEs were detected, including five montane areas (Himalayan areas, Hengduan Mountains, South edge of China, Eastern China Mountains, and Eastern Sichuan Mountains), three islands (Taiwan Island, Japan, and Korean Peninsula), and one plateau (Shan Plateau), which were generally consistent with the species richness pattern. The results verify that montane and island systems have an essential role in promoting the formation of diversity centers and AOEs because of their complex topography, varied habitat and geological events.

Commensal microbiota and host metabolic divergence are associated with the adaptation of Diploderma vela to spatially heterogeneous environments

Heterogeneous environment adaptation is critical to understand the species evolution and response to climate change. However, how narrow-range species adapt to micro-geographic heterogeneity has been overlooked, and there is a lack of insights from metabolism and commensal microbiota. Here, we studied the environmental adaptation for 3 geographic populations (>40 km apart) of Diploderma vela, a lizard endemic to dry-hot valleys of the Hengduan Mountain Region. The climatic boundary caused a cooler, droughtier, and barren environment for northernmost population (RM) than the middle (QZK) and southernmost populations (FS). Correspondingly, significant divergences in liver and muscle metabolism and commensal microbiota were detected between RM and QZK or FS individuals, but not between QZK and FS individuals. Phospholipid composition, coenzyme level (i.e. pyridoxal and NAD⁺ ), and cholesterol metabolism (e.g. androgen and estriol synthesis) constituted the major metabolic difference between RM and QZK/FS groups. FS and QZK individuals kept abundant Proteobacteria and antifungal strains, while RM individuals maintained more Firmicutes and Bacteroidota. Strong associations existed between varied host metabolite and gut microbes. How were these interpopulation variations associated to the environment adaptation were discussed. These results provided some novel insights into the environmental adaptation and implicated the consequence of climate change on narrow-range species.

Ecological and evolutionary constraints on regional avifauna of passerines in China

Strong correlations between species diversity and climate have been widely observed, but the mechanism underlying this relationship is unclear. Here, we explored the causes of the richness-climate relationships among passerine birds in China by integrating tropical conservatism and diversification rate hypotheses using path models. We found that assemblages with higher species richness southwest of the Salween-Mekong-Pearl River Divide are phylogenetically overdispersed and have shorter mean root distances (MRDs), while species-rich regions northeast of this divide (e.g., north Hengduan Mountains-south Qinling Mountains) are phylogenetically clustered and have longer MRDs. The results of the path analyses showed that the direct effect of climatic factors on species richness was stronger than their indirect effects on species richness via phylogenetic relatedness, indicating that neither tropical conservatism nor diversification rate hypotheses can well explain the richness-climate relationship among passerines in China. However, when path analyses were conducted within subregions separately, we found that the tropical conservatism hypothesis was well supported in the southwestern Salween-Mekong-Pearl River Divide, while the diversification rate hypothesis could explain the richness-climate relationship well in the northeastern divide. We conclude that the diversity patterns of passerines in different subregions of the Eastern Himalayas-Mountains of Southwest China may be shaped by different evolutionary processes related to geological and climatic histories, which explains why the tropical conservatism or diversification rate hypothesis alone cannot fully explain the richness-climate relationships.

Shennongjia-Wushan Mountains-One cryptic glacial refugium introduced by the phylogeographical study of the Geometridae moth Ourapteryx szechuana Wehrli

The origin and evolution of biodiversity in the Shennongjia and Wushan Mountains, located in central China, are little known. In this study, we used Ourapteryx szechuana, which is widely distributed in China and northern Nepal, to explore whether these mountains acted as glacial refugia during climate oscillations of the Quaternary. In total, 192 samples of O. szechuana were collected throughout much of the distribution range. Phylogenetic analysis, molecular dating, demographic history reconstructions, and MAXENT were used to investigate the evolutionary history and differentiation mechanisms and predict the potential species distributions during four different periods. The phylogenetic tree and the star-like median-joining network strongly supported two reciprocally monophyletic and allopatric lineages. Lineage I was restricted to the Shennongjia and Wushan Mountains. The divergence time of O. szechuana from its sister species O. thibetaria was approximately 1.94 Ma. The differentiation processes of the two intraspecific lineages occurred at approximately 0.47 Ma. The demographic history reconstruction and the ecological niche model suggested that Lineage II experienced an expansion after the LGM (Last Glacial Maximum), whereas Lineage I did not experience any expansion. Our results suggested the Naynayxungla glaciation promoted the divergence of the two lineages by restricting them to different refugia. The valleys of the Shennongjia-Wushan Mountains may have kept stable and warm (thus ice-free) environments during Quaternary glaciations, allowing this region to act as a glacial refugia. Our studies show that the Shennongjia and Wushan Mountains are likely to be important but little studied glacial refugia for the insect and thus worthy of more attention.

A dataset on type specimens of hemipteran insects in China

Background

Type specimens are valuable resources for investigating and exploring biodiversity on Earth, which has high academic and conservation value. Hemipteran insects are one of the most important and diverse groups in Insecta and their type specimens have important reference value for many research fields. So far, the data on the type specimens of the Hemiptera in China have not been fully collated.

New information

Through extensive literature review, we have constructed a dataset of type specimens for the new species of hemipteran insects in China published from 1950 to 2017, which includes the data such as collection date, specimen gender, preservation institution and geographical distribution. A total of 6,583 type specimen records were collected, covering 3,783 new species belonging to 1,299 genera and 88 families. This dataset can support the international community in conducting research on taxonomy, biodiversity, evolution and pest management.

A multi-faceted comparative perspective on elevational beta-diversity: the patterns and their causes

The observed patterns and underlying mechanisms of elevational beta-diversity have been explored intensively, but multi-dimensional comparative studies remain scarce. Herein, across distinct beta-diversity components, dimensions and species groups, we designed a multi-faceted comparative framework aiming to reveal the general rules in the observed patterns and underlying causes of elevational beta-diversity. We have found that: first, the turnover process dominated altitudinal patterns of species beta-diversity (β_sim > β_sne), whereas the nestedness process appeared relatively more important for elevational trait dissimilarity (β_funcsim < β_funcsne); second, the taxonomic turnover was relative higher than its phylogenetic and functional analogues (β_sim > β_phylosim/β_funcsim), conversely, nestedness-resultant trait dissimilarity tended to be higher than the taxonomic and phylogenetic measures (β_funcsne > β_sne/β_phylosne); and third, as elevational distance increased, the contradicting dynamics of environmental filtering and limiting similarity have jointly led the elevational patterns of beta-diversity, especially at taxonomic dimension. Based on these findings, we infer that the species turnover among phylogenetic relatives sharing similar functional attributes appears to be the main cause of shaping the altitudinal patterns of multi-dimensional beta-diversity. Owing to the methodological limitation in the randomization approach, currently, it remains extremely challenging to distinguish the influence of the neutral process from the offset between opposing niche-based processes. Despite the complexities and uncertainties during species assembling, with a multi-dimensional comparative perspective, this work offers us several important commonalities of elevational beta-diversity dynamics.

Southeast Asia as One of World’s Primary Sources of Biotic Recolonization Following Anthropocene Extinctions

The plight of Southeast Asia’s animals, plants and ecosystems in the face of unsustainable exploitation and habitat destruction has been illustrated in several recent studies, despite often falling outside the global discourse on global conservation priorities. Here, we collate biogeographic and phylogenetic information to argue that this beleaguered region is one of world’s primary macrorefugia, and possibly its best chance of regaining its natural biodiversity distribution patterns after the current Anthropocene upheaval. The region uniquely combines top diversity values in (a) ancient lineage diversity and (b) cosmopolitan lineage diversity, suggesting that it has acted in the past as a biodiversity museum and source of global colonization. This is at least partly due to the interplay between latitudinal diversity gradients and continental connectivity patterns. However, the peak values in South China/North Indochina for cosmopolitan tetrapods and their sister lineages suggest that a key feature is also the availability of diverse climatic conditions. In particular, the north-south orientation of the mountain ranges here has allowed for rapid recolonization within the region following past climatic changes, resulting in high survival values and overall exceptional relict lineage diversity. From this starting point, global colonization occurred on multiple occasions. It is hoped that, with urgent action, the region can once again fulfill this function.

Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.

Global conservation of species' niches

Environmental change is rapidly accelerating, and many species will need to adapt to survive¹. Ensuring that protected areas cover populations across a broad range of environmental conditions could safeguard the processes that lead to such adaptations^1-3. However, international conservation policies have largely neglected these considerations when setting targets for the expansion of protected areas⁴. Here we show that-of 19,937 vertebrate species globally^5-8-the representation of environmental conditions across their habitats in protected areas (hereafter, niche representation) is inadequate for 4,836 (93.1%) amphibian, 8,653 (89.5%) bird and 4,608 (90.9%) terrestrial mammal species. Expanding existing protected areas to cover these gaps would encompass 33.8% of the total land surface-exceeding the current target of 17% that has been adopted by governments. Priority locations for expanding the system of protected areas to improve niche representation occur in global biodiversity hotspots⁹, including Colombia, Papua New Guinea, South Africa and southwest China, as well as across most of the major land masses of the Earth. Conversely, we also show that planning for the expansion of protected areas without explicitly considering environmental conditions would marginally reduce the land area required to 30.7%, but that this would lead to inadequate niche representation for 7,798 (39.1%) species. As the governments of the world prepare to renegotiate global conservation targets, policymakers have the opportunity to help to maintain the adaptive potential of species by considering niche representation within protected areas^1,2.

Phylogeography of Dendrolimus punctatus (Lepidoptera: Lasiocampidae): Population differentiation and last glacial maximum survival

Although the Masson pine moth, Dendrolimus punctatus, is one of the most destructive forest pest insects and is an endemic condition in China, we still do not fully understand the patterns of how its distribution range varies in response to Quaternary climatic oscillations. Here, we sequenced one maternally inherited mitochondrial gene (COI) and biparentally inherited nuclear data (ITS1 and ITS2) among 23 natural populations across the entire range of the species in China. A total of 51 mitotypes and 38 ribotypes were separately obtained using mtDNA and ITS1 data. Furthermore, significant phylogeographical structure (N ST > G ST, p < 0.01) were detected. The spatial distribution of mitotypes implied that two distinct groups existed in the species: one in the southwest distribution, including 10 locations, and the other located in the northeast region of China. It is suggested, therefore, that each group was derived from ancestors that occupied different isolated refugia during previous periods, possibly last glacial maximum. Mismatch distribution and Bayesian population dynamics analysis suggested the population size underwent sudden expansion, which is consistent with the results of ecological niche modeling. As a typical phytophagous insect, the history of population expansion was in accordance with the host plants, providing abundant food resources and habitat. Intraspecific success rate of barcoding identification was lower than interspecific ones, indicating a level of difficulty in barcoding individuals from different populations. However, it still provides an early insight into the pattern of genetic diversity within a species.

OPEN RESEARCH BADGES

This article has been awarded an Open Data and Open Materials. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.2df87g2. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.

From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex

As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1-1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.

The roles of environment, space, and phylogeny in determining functional dispersion of rodents (Rodentia) in the Hengduan Mountains, China

The recently described trait-based approach is becoming widely popular for a mechanistic understanding of species coexistence. However, the greatest challenge in functional analyses is decomposing the contributions of different ecological and evolutionary processes (e.g., niche-based process, neutral process, and evolutionary process) in determining trait structure. Taking rodents (Rodentia) in the Hengduan Mountains as our study model, we aim to (1) quantify the vertical patterns of functional structure for head-body length (HL), tail/body ratio (TR), animal component in diet (ACD), and all traits; (2) disentangle the relative importance of different assembly processes (environment, space, and phylogeny) in structuring trait dispersion; and (3) assess the feasibility of Bergmann's rule and Allen's rule along elevational gradient. Our results have suggested that the vertical functional structure pattern varied across these three traits, indicating distinct functional roles in the community assembly process. These nonrandom vertical patterns of HL, TR, and terminal ACD have demonstrated these traits were dominated by different ecological process along environmental gradient. In variance partitioning, high proportion of the spatial variations in trait dispersion was explained by environmental and spatial models, which have provided supporting strong evidence for niche-based and neutral processes in leading species coexistence. Although the three traits all exhibited apparent phylogenetic signals, phylogenetic relationship within community failed to predict the spatial variations of functional dispersion, confirming the enormous inference of phylogenetic signals in predicting trait structure. By assessing the vertical patterns of HL and TR at order and family levels, we argued that functional adaptation along an environmental gradient is a surrogate of series of complex processes (e.g., environmental filtering, interspecific interaction, and neutral dispersal) acting on multiple functional axes, which results in inconsistence with the empirical rules along elevational gradient.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence in Four Endangered Notopterygium Herbs

Mountain uplift and climatic fluctuations are important driving forces that have affected the geographic distribution and population dynamics history of organisms. However, it is unclear how geological and climatic events might have affected the phylogeographic history and species divergence in high-alpine herbal plants. In this study, we analyzed the population demographic history and species differentiation of four endangered Notopterygium herbs on the high-altitude Qinghai-Tibetan Plateau (QTP) and adjacent areas. We combined phylogeographic analysis with species distribution modeling to detect the genetic variations in four Notopterygium species (N. incisum, N. franchetii, N. oviforme, and N. forrestii). In total, 559 individuals from 74 populations of the four species were analyzed based on three maternally inherited chloroplast fragments (matK, rbcL, and trnS-trnG) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-five chloroplast DNA (cpDNA) and 48 ITS haplotypes were identified in the four species. All of the cpDNA and ITS haplotypes were species-specific, except N. franchetii and N. oviforme shared one cpDNA haplotype, H32. Phylogenetic analysis suggested that all four species formed a monophyletic clade with high bootstrap support, where N. franchetii and N. oviforme were sisters. In addition, each Notopterygium species generated an individual clade that corresponded to their respective species in the ITS tree. Population dynamics analyses and species distribution modeling showed that the two widely distributed herbs N. incisum and N. franchetii exhibited obvious demographic expansions during the Pleistocene ice ages. Molecular dating suggested that the divergence of the four Notopterygium species occurred approximately between 3.6 and 1.2 Mya, and it was significantly associated with recent extensive uplifts of the QTP. Our results support the hypothesis that mountain uplift and Quaternary climatic oscillations profoundly shaped the population genetic divergence and demographic dynamics of Notopterygium species. The findings of this and previous studies provide important insights into the effects of QTP uplifts and climatic changes on phylogeography and species differentiation in high altitude mountainous areas. Our results may also facilitate the conservation of endangered herbaceous medicinal plants in the genus Notopterygium.

Phylogenetic position of the white-cheeked macaque (Macaca leucogenys), a newly described primate from southeastern Tibet

The white-cheeked macaque Macaca leucogenys is a recently described species that was only diagnosed based on photos, without any specimen measurements or molecular genetic diagnosis. Using DNA extracted from four newly collected skin specimens, we studied the genetic diversity and phylogenetic position of M. leucogenys using multilocus sequence data, including mitochondrial and Y chromosomal genes. Skin measurements of four individuals showed that the white-cheeked macaque is robust and larger than M. assamensis but is similar in body size to M. thibetana. Although the holotype male of M. leucogenys was observed to have a round glans penis in three photos and a 15-s video, the current phylogenetic analysis placed this species in the sinica group, which has a sagittate glans penis. Our results confirm full species status of M. leucogenys and indicate that this species might have diverged from its closest relatives c. 2.5million years ago. The mitochondrial gene tree showed that M. leucogenys is phylogenetically close to M. munzala and M. radiata within the sinica group; however, their relationships were unresolved by Y chromosomal phylogenies, which indicates possible historical episode of male introgression. Further studies using an integrative approach that combines morphological and ecological characterizations and population-based genome-wide analysis are needed to investigate divergence and reproductive isolation, which are very likely to elucidate mechanisms underlying these Asian macaque radiations.

DNA barcoding reveals a mysterious high species diversity of conifer-feeding aphids in the mountains of southwest China

The mountains of southwest China are one of the hot spots of biodiversity in the world. However, the high-altitude fauna that inhabit these mountains remain a mystery. In this study, the species diversity of the aphids of the genus Cinara from the high-altitude coniferous forests was first assessed, and then the processes and the mechanisms of speciation were discussed. Three hundreds and four aphid samples that contained 3040 individuals were collected during fourteen field surveys. The molecular clusters derived from the DNA barcodes were used to explore the species diversity. Notably, the aphid alpha-diversity was high, with as many as 94 candidate species, and furthermore, 86.2% of the species collected had not been previously recorded. The centers of aphid species richness corresponded to the distributional pattern of the diversity of the host conifer plant species. The divergence time revealed that following the uplift of the Qinghai-Tibetan Plateau during the Pleistocene, the changes in the climate, ecology and host habitats were likely the most important factors that drove the rapid process of evolutionary radiation in the aphids. Our findings revealed the high species diversity of the aphids with DNA barcoding.

Dispersal, niche, and isolation processes jointly explain species turnover patterns of nonvolant small mammals in a large mountainous region of China

Understanding the mechanisms that govern the spatial patterns of species turnover (beta diversity) has been one of the fundamental issues in biogeography. Species turnover is generally recognized as strong in mountainous regions, but the way in which different processes (dispersal, niche, and isolation) have shaped the spatial turnover patterns in mountainous regions remains largely unexplored. Here, we explore the directional and elevational patterns of species turnover for nonvolant small mammals in the Hengduan Mountains of southwest China and distinguish the relative roles of geographic distance, environmental distance, and geographic isolation on the patterns. The spatial turnover was assessed using the halving distance (km), which was the geographic distance that halved the similarity (Jaccard similarity) from its initial value. The halving distance was calculated for the linear, logarithmic, and exponential regression models between Jaccard similarity and geographic distance. We found that the east-west turnover is generally faster than the south-north turnover for high-latitudinal regions in the Hengduan Mountains and that this pattern corresponds to the geographic structure of the major mountain ranges and rivers that mainly extend in a south-north direction. There is an increasing trend of turnover toward the higher-elevation zones. Most of the variation in the Jaccard similarity could be explained by the pure effect of geographic distance and the joint effects of geographic distance, environmental distance, and average elevation difference. Our study indicates that dispersal, niche, and isolation processes are all important determinants of the spatial turnover patterns of nonvolant small mammals in the Hengduan Mountains. The spatial configuration of the landscape and geographic isolation can strongly influence the rate of species turnover in mountainous regions at multiple spatial scales.

Mysmenidae, a spider family newly recorded from Tibet (Arachnida, Araneae)

The spider family Mysmenidae is reported from Tibet for the first time. Two new species, Chanea voluta sp. n. (male and female) and Mysmena lulanga sp. n. (male and female) are found in eastern Tibet in high altitude. Morphological descriptions, diagnoses and comparative photos are provided for the two new species.