Given the sensitivity of mountain biodiversity to human pressure, it is essential to quantify changes in montane biological communities and contrast them with expectations based on potential drivers of change. This need is particularly pressing for biological groups representing important but little-studied fractions of biodiversity, such as insects. We analyze the temporal changes (between 1998 and 2015) of leaf beetle communities in an altitudinal gradient in the Sierra de Ancares (NW Spain). Our results show temporal changes in the composition of local communities, with a tendency to assemblage thermophilization, as well as a homogenization of the spatial turnover pattern, mostly driven by an increased similarity between communities at the lower and intermediate altitudes. These temporal changes in community composition and in the spatial structure of biodiversity were associated with upward shifts of the upper altitudinal limit of warm-adapted species and with downward shifts of the lower altitudinal limit of cold-adapted species. While this upward shift is consistent with expectations of climate change effects, the observed downward shift suggests a land-use change effect. Our results point to the joint effect of multiple factors (climate and land-use change) behind temporal changes of these leaf beetle communities, which result in compositional reorganization and biotic homogenization, rather than a mere coherent displacement toward higher altitudes. More generally, we show that understanding temporal change of biodiversity requires assessing multiple community-level metrics (e.g., variation in assemblage composition and/or changes in spatial turnover) for the detection of tendencies among the species-specific signals (e.g., altitudinal range shifts).

The geodiversity of rocky ecosystems includes diverse plant communities with specific names, but their continental-scale floristic identity and the knowledge on the role of macroclimate remain patchy. Here, we assessed the identity of plant communities in eastern Brazil across multiple types of rocky landscapes and evaluated the relative importance of climatic variables in constraining floristic differentiation. We provided lists of diagnostic species and an assessment of the conservation status of the identified floristic groups. We compiled a data set of 151 sites (4498 species) from rocky ecosystems, including campos rupestres, campos de altitude, granitic-gneiss lowland inselbergs, and limestone outcrops. We used unsupervised clustering analysis followed by ANOSIM to assess floristic groups among sites. We performed a random forest variable selection to test whether the identified floristic groups occupy distinct climatic spaces. Six groups (lithobiomes) segregated floristically according to lithology and climate. Alongside campos de altitude and limestone outcrops, inselbergs were divided according to the biome in which they occur (Atlantic Forest or Caatinga), and campos rupestres were largely segregated according to their lithological matrix (ironstone or quartzitic). Plant communities of Caatinga inselbergs were more similar to limestone outcrops, while Atlantic Forest inselbergs communities resembled campos de altitude. The composition of plant communities on outcrops seems to be largely constrained by lithology, but climatic factors are also meaningful for sites with similar lithology. The current network of protected areas does not cover these unique ecosystems and their floristic heterogeneity, with Caatinga inselbergs and limestone outcrops being the least protected.

Climate change is promoting global declines in plant diversity, which are expected to be more critical in islands or island-like ecosystems due to environmental constraints and isolation. The species' vulnerability to climate change (VUL) depends on their ability to cope with changes or mitigate them. Therefore, we investigate the influence of growth and dispersal strategies of species from the Sugarloaf Rock Complex, Brazil, an island-like ecosystem, on their niche breadth (NB), long-dispersal (LD) capacity, and geographical range (GR). Besides, we evaluate the potential use of these strategies as indicators of species' VUL. We found that rock specialists exhibit narrower NB, lower LD capacity, and a more restricted GR when compared to other species. We also found that 63% of rock specialists are found in conservation red-lists and they are more vulnerable to climate change than woody plants. Conversely, self-dispersed plants are expected to be less vulnerable to climate change when compared to species with other dispersal mechanisms. Species vulnerable to climate change are 14 times more likely to be included in conservation red lists, and it might indicate that the species' VUL might also describe the species' vulnerability to other anthropogenic threats. Still, we suggest conservation attention on some species that are expected to be vulnerable to climate change but were not yet included in conservation red lists. We advocate for more efforts to ensure the conservation aspects of different functional groups in which inselbergs might not only offer isolation but also a refuge opportunity.

Phylogenomics enhances our understanding of plant radiations in the biodiverse Andes. Our study focuses on Puya, primarily Andean and a part of the Bromeliaceae family. Using a phylogenomic framework based on the Angiosperms353 probe set for 80 species, we explored Puya′s phenotypic evolution and biogeography. Divergence time analyses and ancestral area estimations suggested that Puya originated in Central Coastal Chile around 9 million years ago (Ma). Subsequently, it dispersed to the dry valleys of the Central Andes and Puna regions between 5–8 Ma, leading to the emergence of major lineages. Key events in the last 2–4 million years include the recolonization of Chilean lowlands and dispersal to the northern Andes via Peru's Jalcas, facilitating passage through the Huancabamba depression. This event gave rise to the high-elevation Northern Andes clade. Using phylogenetic comparative methods, we tested the hypothesis that adaptation to the Andes' island-like high-elevation ecosystems was facilitated by unique leaf and floral traits, life history, and inflorescence morphology. Our findings suggest correlations between inflorescence axis compression, protective bract overlap, and high-elevation living, potentially preventing reproductive structure freezing. Semelparity evolved exclusively at high elevations, although its precise adaptive value remains uncertain. Our framework offers insights into Andean evolution, highlighting that lineages adapted to life in dry ecosystems can easily transition to high-elevation biomes. It also underscores how the island-like nature of high-elevation ecosystems influences phenotypic evolution rates. Moreover, it opens avenues to explore genetic mechanisms underlying adaptation to extreme mountain conditions.

Chinese Tajiks are an Indo-Iranian-speaking population in Xinjiang, northwest China. Although the complex demographic history has been characterized, the ancestral sources and genetic admixture of Indo-Iranian-speaking groups in this region remain poorly understood. We here provide the genome-wide genotyping data for over 700?000 single-nucleotide polymorphisms (SNPs) and mtDNA multiplex sequencing data in 64 Chinese male Tajik individuals from two dialect groups, Wakhi and Selekur. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, treemix, qpWave/qpAdm, Admixture-induced Linkage Disequilibrium for Evolutionary Relationships (ALDER), and Fst analyses to infer a fine-scale population genetic structure and admixture history. Our results reveal that Chinese Tajiks showed the closest affinity and similar genetic admixture pattern with ancient Xinjiang populations, especially Xinjiang samples in the historical era. Chinese Tajiks also have gene flow from European and Neolithic Iran farmers-related populations. We observed a genetic substructure in the two Tajik dialect groups. The Selekur-speaking group who lived in the county had more gene flow from East Asians than Wakhi-speaking people who inhabited the village. These results document the population movements contributed to the influx of diverse ancestries in the Xinjiang region.

Tsuga (hemlock) is a small genus of 10 extant species in the Pinaceae, with a disjunct distribution in East Asia and eastern and western North America. Reliable species-level identification of Tsuga fossils depends on the discovery of seed cones with intact bracts, but such cones are rare in the fossil record. Here we describe a new fossil species of hemlock as T. weichangensis sp. nov. based on exquisitely preserved seed cones with nearly complete bracts from the Lower Miocene of Weichang, Hebei Province, North China. This fossil species displays a mosaic of characters between Tsuga and Nothotsuga. The well-developed and slightly exserted bract scales of T. weichangensis are reminiscent of Nothotsuga, but other characters, such as nonleaved peduncles and tongue-shaped bract scales, in addition to monosaccate pollen found at the same fossil locality, suggest an affinity closer to Tsuga. Cladistic analysis based on 15 morphological characters and a molecular backbone constraint supports the assignment of these fossil cones to Tsuga rather than Nothotsuga, and places the fossil species of T. weichangensis in an unresolved polytomy within the genus Tsuga. The occurrence of Tsuga seed cone fossils indicate the paleoclimate in the Miocene of Weichang was warmer and more humid than today's climate, which is consistent with the paleoclimate reconstructed by paleopalynology.

Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19??. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.

China has the most numerous Danxia and Karst landscapes, which serve as special terrestrial islands harboring ample endemic species, though how did these endemic species spread among those isolated sites is still an unresolved issue. To address this question, we explored the phylogeographical structure and demographic history of Firmiana danxiaensis, a tree species endemic to Danxia and Karst landscapes. We collected 295 samples (28 populations) of F. danxiaensis. Plastid genomes were assembled for 25 representative samples. Sanger sequencing of four plastid regions and restriction-site-associated DNA sequencing were performed on the 28 populations. The phylogenetic tree constructed from plastid genomes and restriction site-associated DNA sequencing (RAD-seq) data supported that F. danxiaensis originated from Mount Danxia and Nanxiong Basin, spread to Karst landscapes near Yingde City, and then back to Danxia Mountain and the Nanxiong Basin. In the Nanxiong Basin, the latter arrivals captured the plastid of the former. Population analyses revealed strong population structure among and within Danxia and Karst landscapes, possibly due to low seed and pollen dispersal abilities of the species. The demographic and ecological niche modeling approaches suggested that F. danxiaensis have widely occurred in the southeast of China during the last glacial period, and later retreated to the cliffs of Danxia and Karst landscapes due to temperature rising and competition failure. The declining of the effective population size of the species throughout the postglacial period suggested that global warming, agriculture, and industrial civilizations could have affected the survival of this species, and more measures should be taken to conserve these species.

Clear species boundaries are crucial for plans and actions on biodiversity conservation. However, morphological similarities among allied species can result in taxonomic difficulties, thus impeding conservation efforts. In China, Cinnamomum japonicum Siebold is a well-known endangered plant, yet suffers from longstanding taxonomic issues. Here, we explicitly evaluate whether C. japonicum, C. chenii, and C. chekiangense are the same phylogenetic species on the basis of a multi-individual sampling strategy. We identified three sets of low-copy orthologous genes from 19 Lauraceae taxa for phylogenetic inferences. Both the concatenation and coalescent-based phylogenies supported that C. chenii individuals were embedded in the C. japonicum clade, indicating these two taxa are conspecific. Meanwhile, C. chekiangense accessions formed a monophyly which was not sister to C. japonicum. This result, together with the morphological differences that the leaves of C. japonicum are glabrous with a faveolate pattern of venation while those of C. chekiangense have trichomes and inevident lateral veins, led us to consider both as two distinct species. Based on 17 728 neutral single nucleotide polymorphisms (SNPs), the ADMIXTURE analysis suggested that the Chinese C. japonicum populations in Zhoushan Archipelago (=C. chenii) were genetically differentiated from the Japanese and Korean ones. Furthermore, ecological niche modeling predicted that the present distribution area of Chinese C. japonicum is likely to be unsuitable under global warming scenarios. Together with its limited distribution and genetic uniqueness, we recommend that Chinese C. japonicum deserves conservation priorities.

Polyploids are common in Camellia sect. Paracamellia, which contain many important oil crop species. However, their complex evolutionary history is largely unclear. In this study, 22 transcriptomes and 19 plastomes of related species of Camellia were sequenced and assembled, providing the most completed taxa sampling of Camellia sect. Oleifera and C. sect. Paracamellia. Phylogenetic trees were reconstructed with predicted single-copy nuclear genes and plastomes. Phylogenetic trees with nuclear genes demonstrated that C. sect. Oleifera should be merged into C. sect. Paracamellia. Cytonuclear discordance and network analyses suggested hybridizations among polyploid species and relatives. The divergence of major clades in C. sect. Paracamellia was dated to be during the middle to late Miocene from the ancestral Lingnan region, and a rapid diversification during the Quaternary was found, probably through hybridization and polyploidization. The tetraploid Camellia meiocarpa Hu may have originated from hybridization between closely related diploid species. The hexaploid Camellia oleifera C. Abel probably originated from hybridization between closely related diploid and tetraploid (e.g., C. meiocarpa) species. The octoploid Camellia vietnamensis T. C. Huang ex Hu could have originated from hybridization between hexaploid C. oleifera and the closely related diploid species. Hybridization and polyploidization played an important role in generating the rich variation of important fruit traits, especially increased fruit size in polyploid species.

The Ventilago Gaertn. (Rhamnaceae) is widely distributed in pantropical areas of Africa, Asia, and Australia. However, fossil records of this taxon are sparse, which limits understanding of the evolution and biogeographic history of the genus. In the present study, we report and describe two new fossil species of Ventilago, V. siwalika sp. nov. from the Miocene sediments of Himachal Pradesh, western Himalaya, and V. pliocenica sp. nov. from the Pliocene sediments of Jharkhand, eastern India based on single-winged samaras. Ventilago pliocenica is characterized by a prominent midvein, obtuse to sub-round apex with mucronate tip, longitudinal secondary veins extending the full length of the fruit, and reticulate nature of higher-order veins, the presence of equatorial rim, the hypanthium, and short pedicel. On the other hand, V. siwalika is characterized by a prominent midvein, obtuse to sub-round apex with mucronate tip, longitudinal secondary veins extending the full length of the fruit, and reticulate nature of higher-order veins. Our discovery represents the first unambiguous fossil record of single-winged samara of Ventilago from India and provides valuable insights into the evolution of this genus. In this paper, we also review its biogeographic history and add new information to understand its hypothetical migration route. Present and earlier records of Ventilago also suggest that this genus was a common forest element during Neogene (Miocene time) in Asia.

Eudicots exhibit diverse life forms and occupy a wide variety of habitats in the modern terrestrial ecosystems, and the diversification began during the Early Cretaceous; however, few Early Cretaceous fossils are preserved as multiorgan whole plants that can provide sufficient morphological characters for detailed phylogenetic assessment. Here, Fairlingtonia microgyna sp. nov. is reported from the upper Lower Cretaceous of Zhonggou Formation, Hanxia Section, Yumen City, western Gansu Province, Northwest China. The specimen is exceptionally preserved as multiorgan whole plant fossil with fibrous adventitious roots, simple and deeply dissected leaves, solitary and dehiscent capsular fruits attached to the creeping stems. As such, it was interpreted as a herbaceous eudicot. Phylogenetic analyses support a placement within the Papaveraceae, most likely in Papaveroideae, but there are obvious differences in morphological characteristics, which cannot confirm the systematic position within the Papaveraceae. Fossil records of Fairlingtonia from contemporaneous deposits (late Aptian to early Albian) in Northwest China and eastern North America provide direct evidence of the geographical radiation of Fairlingtonia on Laurasia. And the morphological characters of F. microgyna, including creeping leafy branches, fibrous adventitious roots, small and deeply dissected leaves as well as small capsular fruits with tiny seeds probably indicate that it was a colonizer of lake-shore environments under wet and bright conditions and possessed fast-growing and rapid propagation habitats, which allowed it to expand its geographic range with both sexual and asexual reproduction.

Gomphomastacinae is a grasshopper subfamily in Eumastacidae, with a morphology and distribution distinct from other subfamilies. The alpine genera of Gomphomastacinae that inhabit the Qinghai–Tibet Plateau in China show unique characteristics adapted to high-altitude life. However, their phylogenetic position and biogeographic history remain controversial. Thus, to determine the diversification history of these alpine genera and the origin of the subfamily, we obtained mitochondrial genome sequences from all seven Gomphomastacinae genera distributed in China. The reconstructed phylogeny was well supported and confirmed the phylogenetic position of Gomphomastacinae within Eumastacidae. Time calibration revealed a deep-time origin of the subfamily dating back to the Cretaceous period, and the diversification among alpine genera was also an ancient pre-Miocene event (30–50 Ma). Based on phylogeny and time estimates, the most likely biogeographic scenario is that Gomphomastacinae originated from an ancestral lineage that lived in East Gondwana and dispersed to Central and Western Asia through India. Subsequently, the alpine genera likely diverged along with the uplift of the Qinghai–Tibet Plateau and survived drastic climate change by in situ adaptation to high-altitude dwellings.