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The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics., Trends in Genetics, 39 (7), ISSN:0168-9525

— The region of the Qinghai-Tibet Plateau hosts a remarkable biodiversity, including a plethora of endemics. There, the process of documenting biodiversity is still ongoing, and recently, an unusual plant of Gentiana section Frigida was discovered at Cuopu Lakes (Sichuan, China). Although Flora of China identified these specimens as G. algida based upon unmistakable traits (e.g. corolla colour and length, sessile flowers), it was obvious that the Sichuanese plants strongly differed morphologically from G. algida specimens from Siberia and North America. In order to clarify their relationships, we used an integrative approach, investigating not only morphological traits, but also phylogenetic relationships (based upon plastome and rDNA-cistron), as well as chloroplast structure. Whereas the rDNA-cistron phylogeny was poorly resolved, the plastome phylogeny was well supported in both Bayesian inference and maximum likelihood analyses. Our findings indicate that the samples of G. algida from Cuopu Lakes are morphologically and genetically distinct from those collected elsewhere, supporting the recognition of a new species, G. susanneae. The new species differs from G. purdomii (another similar species) by having sessile flowers, and from G. algida by being a generally much taller plant with more and longer flowers, and by having a smaller calyx. Gentiana susanneae clusters with other species from the region of the Qinghai-Tibet Plateau from which it differs morphologically, and is only distantly related to the G. algida/G. frigida clade, which stems from a dispersal event out of Tibet. Based upon these solid lines of evidence, G. susanneae is described and illustrated (drawings and photographs). In addition, a conservation assessment and an identification key modified from Flora of China are provided.

The Tibeto-Himalayan Region is famous for its geography, climatic influence, and exceptional and immense biodiversity. The “mountain-geobiodiversity hypothesis (MGH)” explores the interaction of topography, climate, and biology in the evolution of mountain biodiversity. We tested this hypothesis in the Himalayas and the Hengduan Mountains on a group of caddisflies that are endemic to this region. We investigated one caddisfly species pair from each mountain respectively, each pair containing one species inhabiting high elevation and one inhabiting low elevation. We incorporated genomic and ecological evidence to reveal population structure, demographic history, and potential habitat range dating back to the last glacial maximum (LGM) of each species. The results indicated that in both mountains, the high-elevation species showed strong local differentiation, while the low-elevation species were shaped by hydro-morphology indicating greater regional dispersal activity. Results of demographic history and species distribution modelling supported demographic expansions for all species during the LGM linked to an increase in potential habitats. Caddisfly species in the Himalayas generally exhibited an East-West oriented dispersal. Species from the Hengduan Mountains showed greater connectivity on the North-South orientation, suggesting that species have a higher chance to survive in the Hengduan Mountains by both in-situ displacement (along the elevational gradients) and long-distance dispersal (along the latitudinal gradients) during glaciation. Our study demonstrates that historical geodiversity and climate fluctuations interact and influence the diversification of caddisflies in the Tibeto-Himalayan Region, thus supporting the MGH.

Mountains are reservoirs for a tremendous biodiversity which was fostered by a suite of factors acting in concert throughout evolutionary times. These factors can be climatic, geological, or biotic, but the way they combine through time to generate diversity remains unknown. Here, we investigate these factors as correlates of diversification of three closely related sections of Gentiana in the European Alpine System. Based upon phylogenetic approaches coupled with divergence dating and ancestral state reconstructions, we attempted to identify the role of bedrock preferences, chromosome numbers coupled with relative genome sizes estimates, as well as morphological features through time. We also investigated extant climatic preferences using a heavily curated set of occurrence records individually selected for superior precision, and quantified rates of climatic niche evolution in each section. We found that a number of phylogenetic incongruences derail the identification of correlates of diversification, yet a number of patterns persist regardless of the topology considered. All the studied correlates are likely to have contributed to the diversification of Gentiana in Europe, however, their respective importance varied through time and across clades. Chromosomal variation and divergence of climatic preferences appear to correlate with diversification throughout the evolution of European Gentiana (Oligocene to present), whereas shifts in bedrock preferences appear to have been more defining during recent diversification (Pliocene). Overall, a complex interaction among climatic, geological and biotic attributes appear to have supported the diversification of Gentiana across the mountains of Europe, which based upon phylogenetic as well as other evidence, was probably also bolstered by hybridization.

Whole genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. It is thus imperative to select an appropriate reference genome and sequencing depth to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. To evaluate the effect of the choice of the reference genome and sequencing depth on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing depth (3.5×, 7.5× and 12×) in a population genomic study on two caddisfly species

Whole-genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. It is thus imperative to select an appropriate reference genome and sequencing coverage to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. To evaluate the effect of the choice of the reference genome and sequencing coverage on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing coverage (3.5x, 7.5x and 12x) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. tibetana. Using these 30 datasets (five reference genomes × three coverages × two target species), we estimated population genetic indices (inbreeding coefficient, nucleotide diversity, pairwise and genome-wide FST) based on variants and population structure (PCA and admixture) based on genotype likelihood estimates. The results showed that both distantly related reference genomes and lower sequencing coverage lead to degradation of resolution. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low coverage. Therefore, we conclude that population genetic studies would benefit from closely related reference genomes, especially as the costs of obtaining a high-quality reference genome continue to decrease. However, to determine a cost-efficient strategy for a specific population genomic study, a trade-off between reference genome relatedness and sequencing depth can be considered.

The genus Laoennea (Streptaxoidea, Diapheridae) was erected by Páll-Gergely, 2020. The type species, Laoennea carychioides Páll-Gergely, A. Reischütz & Maassen, 2020 is so far only known from the type locality cave in Laos. Herein, we describe a second species, Laoennea renouardisp. nov., from a nearby cave in the same karst region of Vientiane Province.

Background and AimsHosting several global biodiversity hotspots, the region of the Qinghai-Tibetan Plateau (QTP) is exceptionally species-rich and harbours a remarkable level of endemism. Yet, despite a growing number of studies, factors fostering divergence, speciation and ultimately diversity remain poorly understood for QTP alpine plants. This is particularly the case for the role of hybridization. Here, we explored the evolutionary history of three closely related Gentiana endemic species, and tested whether our results supported the mountain geo-biodiversity hypothesis (MGH).MethodsWe genotyped 69 populations across the QTP with one chloroplast marker and 12 nuclear microsatellite loci. We performed phylogeographical analysis, Bayesian clustering, approximate Bayesian computation and principal components analysis to explore their genetic relationship and evolutionary history. In addition, we modelled their distribution under different climates.Key ResultsEach species was composed of two geographically distinct clades, corresponding to the south-eastern and north-western parts of their distribution. Thus Gentiana veitchiorum and G. lawrencei var. farreri, which diverged recently, appear to have shared at least refugia in the past, from which their range expanded later on. Indeed, climatic niche modelling showed that both species went through continuous expansion from the Last Interglacial Maximum to the present day. Moreover, we have evidence of hybridization in the northwest clade of G. lawrencei var. farreri, which probably occurred in the refugium located on the plateau platform. Furthermore, phylogenetic and population genetic analyses suggested that G. dolichocalyx should be a geographically limited distinct species with low genetic differentiation from G. lawrencei var. farreri.ConclusionsClimatic fluctuations in the region of the QTP have played an important role in shaping the current genetic structure of G. lawrencei var. farreri and G. veitchiorum. We argue that a species pump effect did occur prior to the Last Interglacial Maximum, thus lending support to the MGH. However, our results do depart from expectations as suggested in the MGH for more recent distribution range and hybridization dynamics.

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.

SummaryEcological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and S. latifolia transplanted into the natural habitat of each species.We used reduced-representation sequencing and Bayesian Sparse Linear Mixed Models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat.Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. The direction of allelic effects was associated with allele frequency differences between the species: positive-effect alleles were often derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species.We conclude that ecological differentiation is governed and maintained by many loci with small, conditionally neutral effects. Conditional neutrality may result from differences in selection targets in the two habitats and provides hidden variation upon which selection can act. Polygenic architectures of adaptive differentiation are expected to be transient during lineage divergence and may therefore be unrelated to high genetic differentiation at the underlying loci.

Our objective is to analyse global‐scale patterns of mountain biodiversity and the driving forces leading to the observed patterns. More specifically, we test the ‘mountain geobiodiversity hypothesis’ (MGH) which is based on the assumption that it is not mountain‐uplift alone which drives the evolution of mountain biodiversity, but rather the combination of geodiversity evolution and Neogene and Pleistocene climate changes. We address the following questions: (a) Do areas of high geodiversity and high biodiversity in mountains overlap, that is can mountain geodiversity predict mountain biodiversity? (b) What is the role of Pleistocene climate change in shaping mountain biodiversity? (c) Did diversification rate shifts occur predominantly with the onset of more pronounced climate fluctuations in the late Neogene and Pleistocene fostering a ‘species pump’ effect, as predicted by the MGH?

BackgroundThe yield of commercially harvested “vegetable caterpillar” Ophiocordyceps sinensis has dramatically plummeted in the last few decades, while market demand has increased. Besides controlling the obvious overexploitation of this species, understanding how edaphic factors influence this system may improve the chances of successful cultivation and thus support the conservation of O. sinensis in the wild. Our study investigates how the presence/absence and the quality of O. sinensis may be linked to a series of edaphic factors pertinent to its microhabitat, including enzyme activity, nutrients, moisture, pH and nematode population. In order to provide a preliminary hypothesis on the relationships among edaphic factors and their influence on O. sinensis, we performed a principal component analysis and structural equation modelling despite limited replication. ResultsSoil samples containing O. sinensis were more moist and contained a higher concentration of nutrients and enzyme activity than control samples collected nearby, where the species was absent. Preliminary analyses indicated that enzyme activity may be crucial and appeared to be affected by a number of other soil factors. We found that O. sinensis would occupy microhabitats with a relatively higher soil fertility and a more persistent enzyme activity, where the values of total nitrogen and catalase are especially important. Otherwise, with the exception of organic matter and enzyme activity, mean values did not suggest any other factors potentially corresponding to a better quality of O. sinensis.ConclusionsBased on these preliminary findings and a further literature review, we formulated the first integrative hypothesis (network of interactions) on how soil factors may influence each other and O. sinensis. Finally, we indicate how this hypothesis may be tested in the future, in order to increase the chances for successful cultivation and thus promote the conservation and sustainable harvesting of O. sinensis.

The structure and sequence of plastid genomes is highly conserved across most land plants, except for a minority of lineages that show gene loss and genome degradation. Understanding the early stages of plastome degradation may provide crucial insights into the repeatability and predictability of genomic evolutionary trends. We investigated these trends in subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled, and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae and all main sections of the species‐rich genus Gentiana L. We reconstructed the phylogeny, estimated divergence times, investigated the phylogenetic distribution of putative gene losses, and related these to substitution rate shifts and species’ habitats. We obtained a strongly supported topology consistent with earlier studies, with all six genera in Gentianinae recovered as monophyletic and all main sections of Gentiana having full support. While closely related species have very similar plastomes in terms of size and structure, independent gene losses, particularly of the ndh complex, have occurred in multiple clades across the phylogeny. Gene loss was usually associated with a shift in the boundaries of the small single‐copy and inverted repeat regions. Substitution rates were variable between clades, with evidence for both elevated and decelerated rate shifts. Independent lineage‐specific loss of ndh genes occurred at a wide range of times, from Eocene to Pliocene. Our study illustrates that diverse degradation patterns shape the evolution of the plastid in this species‐rich plant group., This study traces plastome evolution of all main lineages of the species‐rich group Gentianinae, and shows lineage‐specific patterns of plastid degradation and shifts in substitution rates.

The Qinghai-Tibet Plateau sensu lato (QTP s.l.) harbors an exceptionally high biodiversity, especially at its southeastern margin: this area encompasses the Hengduan Mountains and the eastern Himalayas, which have been listed as biodiversity hotspots. To the contrary, the plateau interior (namely the Qinghai-Tibet Plateau sensu stricto, QTP s.s.) is relatively species-poor because of its particularly harsh climate. With contrasting geological histories and environmental conditions of the Hengduan Mountains, the Himalayas and the QTP s.s., it would be expected that floristic compositions and diversity patterns of these three regions would differ between each other. To compare the floristic diversity of these three regions, we assembled data on seed plant’s distribution in the three regions based on county-level mapping from published monographs and online databases, and we then analyzed their floristic features and species diversity patterns (horizontal and elevational). We found that the Hengduan Mountains hosted the most seed plant species (8,439), as expected. The highest percentage of shrub (22.88%) and tree species (9.80%) were in the Himalayas, whereas herbaceous species (81.50%) were relatively more prominent in the QTP s.s.. The Hengduan Mountains also had the most species-rich genera (10) with more than 50% of their total species diversity in China. Also, temperate genera dominated across these three regions, with a highest percentage (77.61%) within the QTP s.s.. Across the QTP s.l., species diversity gradually decreased from the southeastern part to the northwest, and most of seed plants were distributed in the southern and eastern margin of the Hengduan Mountains and East Himalayas. Along elevational gradients, species richness all demonstrated a hump-shape curve, but the most species-rich elevation zone differed for each type of life-form across the three regions. Our study sets a base for exploring the origin and evolution of mountain taxa, as well as provides a snapshot of the current plant distribution, which will certainly be modified by climate change.

Encompassing some of the major hotspots of biodiversity on Earth, large mountain systems have long held the attention of evolutionary biologists. The region of the Qinghai‐Tibet Plateau (QTP) is considered a biogeographic source for multiple colonization events into adjacent areas including the northern Palearctic. The faunal exchange between the QTP and adjacent regions could thus represent a one‐way street (“out of” the QTP). However, immigration into the QTP region has so far received only little attention, despite its potential to shape faunal and floral communities of the QTP. In this study, we investigated centers of origin and dispersal routes between the QTP, its forested margins and adjacent regions for five clades of alpine and montane birds of the passerine superfamily Passeroidea. We performed an ancestral area reconstruction using BioGeoBEARS and inferred a time‐calibrated backbone phylogeny for 279 taxa of Passeroidea. The oldest endemic species of the QTP was dated to the early Miocene (ca. 20 Ma). Several additional QTP endemics evolved in the mid to late Miocene (12–7 Ma). The inferred centers of origin and diversification for some of our target clades matched the “out of Tibet hypothesis’ or the “out of Himalayas hypothesis” for others they matched the “into Tibet hypothesis.” Three radiations included multiple independent Pleistocene colonization events to regions as distant as the Western Palearctic and the Nearctic. We conclude that faunal exchange between the QTP and adjacent regions was bidirectional through time, and the QTP region has thus harbored both centers of diversification and centers of immigration., The Qinghai‐Tibet Plateau (QTP) is considered a source region for colonization of adjacent areas such as the northern Palearctic. Using an ancestral area reconstruction approach on a phylogeny of 279 bird species, we suggest that faunal exchange between the QTP and adjacent regions was bidirectional through time and the QTP region has harbored both centers of diversification (for example of snowfinches) and centers of immigration.

While there is a general understanding of broadscale patterns of the region of the Qinghai-Tibet Plateau (QTP)'s biodiversity, this is largely reliant upon knowledge of species richness. Less known is the correlation between species richness and other measures of biodiversity, and how this correlation varies among different types of taxa. Using county-level seed plant data for the QTP region, we identified and compared regional species-rich areas, using six indices quantifying taxonomic, endemic and phylogenetic diversity for distinct plant types (trees, shrubs, herbs, endemic/non-endemic, alpine/non-alpine/non-alpine-endemic plants). We modelled diversity for each index and plant types using predictors of contemporary climate, topography and historical factors. We found a high congruence between species richness and phylogenetic diversity, which showed a consistent gradient from high values in the southeast to low values in the northwest. We confirm that this known pattern was largely associated with contemporary climatic and topographic predictors. There was a similarly high congruence of species-rich areas among plant types, except for alpine species. Strikingly, we identified species-rich areas which were previously unrecognized. Their identification largely derives from a low congruence between general patterns and patterns predicted by corrected weighted endemism. Nine of these species-rich areas are located where coverage in nature reserves is absent or inadequate, highlighting clear conservation gaps in the regional conservation strategy. Our study is the first to compare taxonomic, endemic and phylogenetic diversity for different plant types in the QTP region. Thus, it provides the essential bases for designing strategies for local to regional biodiversity conservation.

Two heterobranch species, Stylocheilus striatus (Quoy & Gaimard, 1825) (Anaspidea, Aplysiidae) and Pleurobranchusforskalii Rüppel & Leuckart, 1828 (Nudipleura, Pleurobranchidae) are reported for the first time for BazarutoIsland, Mozambique. Swarming behavior of Stylocheilus striatus, which was previously described for other localities,was also observed for the first time in the Bazaruto Archipelago. The sea slugs were photographed in situ and identifiedin sync with their species descriptions, photographic databases and the current literature.

A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes (orogenesis) and a biological response (diversification). Yet, a substantial delay (up to 30 Myr) between the start of orogenesis and diversification is often observed. Evolutionary biologists should therefore identify alternative drivers of diversification and maintenance of biodiversity in mountain systems. Using phylogenetic, biogeographic, and diversification rate analyses, we could identify two independent processes that most likely explain the diversity of the widespread genus Allium in the Qinghai–Tibet Plateau (QTP) region: (1) While the QTP-related taxa of the subgenus Melanocrommyum diversified in situ , (2) QTP-related taxa of other subgenera migrated into the QTP from multiple source areas. Furthermore, shifts in diversification rates within Allium could not be attributed spatially and temporally to the uplift history of the QTP region. Instead, global cooling and climate oscillations in the Quaternary were major contributors to increased speciation rates in three clades of Allium . Our study therefore adds to the growing evidence supporting the “mountain-geo-biodiversity hypothesis”, which highlights the role of climate oscillations for the diversification of mountain organisms.

The origin and evolution of alpine biota are not yet fully understood, particularly in the vast Asian mountain regions. In addition, in these regions, most studies have concentrated on taxa occurring in areas benefitting from relatively generous rainfall from the summer monsoon. In this study, we collected a large number of Oxytropis species throughout their distribution range, and investigated the taxonomy and evolution of this diverse legume genus, which also occurs in mountainous areas prone to drought. Using nuclear (ITS) and plastid (trnL‐F) markers, we reconstructed phylogenetic relationships within Oxytropis, conducting maximum parsimony, fasttree‐like, maximum likelihood, Bayesian, and BEAST analyses. We also used Anchored Hybrid Enrichment (AHE) to test the power of this method to resolve relationships among a small subset of Oxytropis species. For AHE, we sampled eight species and obtained 527 low‐copy and orthologous nuclear loci. We show that the taxonomy of this genus that radiated explosively in Asian mountains will remain recalcitrant based on conventional molecular methods. Because of a severe lack of resolution, none of the available taxonomic treatments for Oxytropis could either be confirmed or refuted based upon ITS and trnL‐F. Nevertheless, we confirm the status of several species, and identify morphological or genetic particularities for some groups of species. The AHE approach yielded a highly supported phylogenetic tree, suggesting that increased taxon sampling coupled with AHE methods promise advances in the study of the taxonomy and evolution of Oxytropis, thus providing further analytical opportunities, such as diversification rate and biogeographical analyses.

New species arise through the evolution of reproductive barriers between formerly interbreeding lineages. Yet, comprehensive assessments of potential reproductive barriers, which are needed to make inferences on processes driving speciation, are only available for a limited number of systems. In this study, we estimated individual and cumulative strengths of seven prezygotic and six postzygotic reproductive barriers between the recently diverged taxa Silene dioica (L.) Clairv. and S. latifolia Poiret using both published and new data. A combination of multiple partial reproductive barriers resulted in near‐complete reproductive isolation between S. dioica and S. latifolia, consistent with earlier estimates of gene flow between the taxa. Extrinsic barriers associated with adaptive ecological divergence were most important, while intrinsic postzygotic barriers had moderate individual strength but contributed only little to total reproductive isolation. These findings are in line with ecological divergence as driver of speciation. We further found extensive variation in extrinsic reproductive isolation, ranging from sites with very strong selection against migrants and hybrids to intermediate sites where substantial hybridization is possible. This situation may allow for, or even promote, heterogeneous genetic divergence.

Aim Geologically dynamic areas often harbour remarkable levels of biodiversity. Among other factors, mountain building is assumed to be a precondition for species radiation, and yet, the potential role of immigration as a source of biodiversity prior to radiation is often neglected. Here, we studied the biogeographical history of the large genus Saxifraga to unravel the role played by the Qinghai-Tibet Plateau (QTP) for the diversification of this genus and to understand factors that have led to the establishment of high biodiversity in and around this region. Location QTP and surrounding mountain ranges and worldwide distribution range of Saxifraga. Methods Using a total of 420 taxa (321 ingroup taxa) comprising more than 60% of extant Saxifraga species, we studied the evolutionary history of Saxifraga by performing phylogenetic analyses (maximum likelihood and Bayesian inference on nuclear ITS and plastid trnL–trnF, matK sequences), divergence time estimation (using uncorrelated log-normal clock models and four fossil constraints in beast) and ancestral range estimation (using BioGeoBEARS). Results Saxifraga originated in North America around 74 (64–83) Ma, dispersed to South America and northern Asia during its early diversification and colonized Europe and the QTP region by the Late Eocene. The QTP region was colonized several times independently, followed in some lineages by rapid radiations, temporally coinciding with recent uplifts of the Hengduan Mountains at the southeastern fringe of the QTP. Subsequently, several lineages dispersed out of Tibet. Main conclusions Immigration, recent rapid radiation and lineage persistence were all important processes for the establishment of a rich species stock of Saxifraga in the QTP region. Because floristic exchanges between the neighbouring areas and the QTP region were bi-directional, the spatio-temporal evolution of Saxifraga contrasts with the ‘out of QTP’ pattern, which has often been assumed for northern temperate plants.

Aim We investigated the historical biogeography and diversification of Gentiana L. (Gentianaceae). Our study depicts the origin and dispersal routes of this alpine genus, and the role of the uplift of the Qinghai–Tibet Plateau (QTP) and past climate changes as triggers for its diversification. Location Tibeto-Himalayan region and world-wide mountain habitats. Methods Our sampling represents more than 50% of the extant Gentiana species, including all sections across their entire geographical ranges. We investigated the evolutionary history of Gentiana using phylogenetic reconstructions (maximum likelihood and Bayesian inference) of ITS, atpB–rbcL and trnL–trnF sequences, as well as molecular dating with beast. We tested two approaches of ancestral area reconstructions (DEC, DIVA) in BioGeoBEARS and investigated diversification rates using BAMM. Results The common ancestor of Gentiana and subtribe Gentianinae lived in the QTP region at around 34 (25–45) million years ago (Ma), and 40 (29–52) Ma respectively. From the surroundings of the QTP, Gentiana lineages dispersed to eastern China, Taiwan, Europe, North and South America, Australia and New Guinea, from mid-Miocene onward (c. 15 Ma–present), with only one older dispersal event to Europe (c. 37–21 Ma). Diversification rates gradually increased over time, and two switches of diversification rates were identified in Gentianinae (c. 7 Ma, simultaneously in the Pneumonanthe/Cruciata lineage and in Tripterospermum). Main conclusions Gentiana existed in the QTP region throughout most of its uplift history following the India-Asia collision. This region acted as the primary source area for dispersals to many areas of the world. Because steady increase in diversification rates coincides with the extension of the QTP, we argue that the museum theory rather than the explosive radiation theory prevails for gentians in this region, although rare shifts of diversification rates are associated with niche shifts across the alpine/subalpine ecotone.

Two new varieties of Kuepferia pringlei D. Maity & S. K. Dey from north Sikkim (eastern Himalaya) are described, illustrated, and compared with closely related taxa of similar morphology. Details on its habitat, phenology and conservation status are provided. These previously undescribed varieties are most similar to, but distinct from, typical K. pringlei D. Maity & S. K. Dey, known from the eastern Himalaya. Both new taxa are compared with K. leucantha (Harry Sm. ex T.N. Ho & S.W. Liu) Adr.Favre.

Premise of the study Geological and climatic changes associated with the uplift of the Qinghai-Tibet Plateau (QTP) have been suggested as drivers for biological diversification locally and in neighboring regions. To test this hypothesis, we investigated the niche evolution of Tripterospermum (Gentianaceae) and related Asian genera through time. Methods We conducted Species Distribution Modeling using Maximum Entropy Modeling (MaxEnt). Furthermore, we performed stochastic character mapping and produced disparity-through-time plots, and examined putative key innovations using the binary state speciation and extinction approach (BISSE). Key results Kuepferia and Sinogentiana prefer the coolest and driest habitat, having rather conserved niches. Despite a tendency for niche evolution, Crawfurdia and Metagentiana are probably restricted to a narrow distribution range because of their poor dispersal ability. In contrast, Tripterospermum has the broadest niche and occurs under the warmest and wettest conditions. A higher degree of niche evolution and a more efficient dispersal mechanism allowed this genus to diversify more and occupy a broader distribution range. Conclusions The QTP genera producing dry capsules, whether displaying niche conservatism (Kuepferia and Sinogentiana) or a tendency for niche evolution (Crawfurdia and Metagentiana), are less species-rich and have a more restricted distribution than Tripterospermum (stronger niche evolution and berry-like fruits). The evolution of berry-like fruits corresponds to increased speciation rates, and could therefore be viewed as a key innovation. In contrast to the majority of studies on plants occurring around the QTP, we find that speciation was probably mediated by niche breadth and dispersal ability rather than geophysical changes.

Five years ago, the Panamanian evolutionary lineage (EL) C12 was uncovered along with four other ELs in an integrative phylogenetic investigation of worldwide Carychiidae. Since EL C12 lacked shell material post-molecular analysis to serve as a museum voucher, it remained undescribed. Now, after recent collection efforts of C12 and the congener, Carychiumzarzaae Jochum & Weigand, 2017 at their original Panamanian sites, C12 is morphologically described and formally assigned the name, Carychiumpanamaense Jochum, sp. n. In sync with recent taxonomic treatment of the genus, computed tomography (CT) is used in this work to differentiate shells of C.panamaensesp. n. from geographically-proximal, Caribbean, North and Central American congeners. Recent material of topotypic Carychiumjardineanum (Chitty, 1853) and undamaged C.zarzaae were additionally CT-scanned and assessed in the comparative analyses.