Dispersal modes affect Rhamnaceae diversification rates in a differentiated manner.

The evolution of dispersal modes has been proposed to promote the diversification of angiosperms. However, little is known about the relative impact of different dispersal modes on plant diversification. We test the association between dispersal modes and diversification rates using Rhamnaceae, the cosmopolitan buckthorn family, as a model. We found that species with diplochory have the highest diversification rates followed by those with myrmecochory and ballistic dispersal, while lineages dispersed by vertebrates and wind have relatively low diversification rates. The difference in diversification rates may be closely linked to the difference in dispersal distance and ecological interactions implied by each dispersal mode. Species which disperse over larger geographical distances may have much higher speciation rates due to the increased chance of establishing isolated populations due to geological barriers or habitat fragmentation. However, long-distance dispersal may also increase the chance of extinction. By contrast, species with short-distance dispersal modes may have low speciation rates. Complex interactions with the surrounding environment may, however, impact diversification rates positively by increasing plant survival and reproductive success.

The big four of plant taxonomy - a comparison of global checklists of vascular plant names.

Taxonomic checklists used to verify published plant names and identify synonyms are a cornerstone of biological research. Four global authoritative checklists for vascular plants exist: Leipzig Catalogue of Vascular Plants, World Checklist of Vascular Plants, World Flora Online (successor of The Plant List, TPL), and WorldPlants. We compared these four checklists in terms of size and differences across taxa. We matched taxon names of these checklists and TPL against each other, identified differences across checklists, and evaluated the consistency of accepted names linked to individual taxon names. We assessed geographic and phylogenetic patterns of variance. All checklists differed strongly compared with TPL and provided identical information on c. 60% of plant names. Geographically, differences in checklists increased from low to high latitudes. Phylogenetically, we detected strong variability across families. A comparison of name-matching performance on taxon names submitted to the functional trait database TRY, and a check of completeness of accepted names evaluated against an independent, expert-curated checklist of the family Meliaceae, showed a similar performance across checklists. This study raises awareness on the differences in data and approach across these checklists potentially impacting analyses. We propose ideas on the way forward exploring synergies and harmonizing the four global checklists.

Challenging Structure Elucidation of Lumnitzeralactone, an Ellagic Acid Derivative from the Mangrove Lumnitzera racemosa.

The previously undescribed natural product lumnitzeralactone (1), which represents a derivative of ellagic acid, was isolated from the anti-bacterial extract of the Indonesian mangrove species Lumnitzera racemosa Willd. The structure of lumnitzeralactone (1), a proton-deficient and highly challenging condensed aromatic ring system, was unambiguously elucidated by extensive spectroscopic analyses involving high-resolution mass spectrometry (HRMS), 1D 1H and 13C nuclear magnetic resonance spectroscopy (NMR), and 2D NMR (including 1,1-ADEQUATE and 1,n-ADEQUATE). Determination of the structure was supported by computer-assisted structure elucidation (CASE system applying ACD-SE), density functional theory (DFT) calculations, and a two-step chemical synthesis. Possible biosynthetic pathways involving mangrove-associated fungi have been suggested.

Evaluation of plant sources for antiinfective lead compound discovery by correlating phylogenetic, spatial, and bioactivity data.

Antibiotic resistance and viral diseases are rising around the world and are becoming major threats to global health, food security, and development. One measure that has been suggested to mitigate this crisis is the development of new antibiotics. Here, we provide a comprehensive evaluation of the phylogenetic and biogeographic patterns of antiinfective compounds from seed plants in one of the most species-rich regions on Earth and identify clades with naturally occurring substances potentially suitable for the development of new pharmaceutical compounds. Specifically, we combine taxonomic and phylogenetic data for >7,500 seed plant species from the flora of Java with >16,500 secondary metabolites and 6,255 georeferenced occurrence records to 1) identify clades in the phylogeny that are characterized by either an overrepresentation ("hot clades") or an underrepresentation ("cold clades") of antiinfective compounds and 2) assess the spatial patterns of plants with antiinfective compounds relative to total plant diversity across the region. Across the flora of Java, we identify 26 "hot clades" with plant species providing a high probability of finding antibiotic constituents. In addition, 24 "cold clades" constitute lineages with low numbers of reported activities but which have the potential to yield novel compounds. Spatial patterns of plant species and metabolite diversity are strongly correlated across Java, indicating that regions of highest species diversity afford the highest potential to discover novel natural products. Our results indicate that the combination of phylogenetic, spatial, and phytochemical information is a useful tool to guide the selection of taxa for efforts aimed at lead compound discovery.

Polyploidy promotes species diversification of Allium through ecological shifts.

Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.

Key innovations and climatic niche divergence as drivers of diversification in subtropical Gentianinae in southeastern and eastern Asia.

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.

An evaluation of taxonomic concepts of the widespread plant genus Aglaia and its allies across Wallace's Line (tribe Aglaieae, Meliaceae).

Similar to other species-rich taxa in the Indo-Australian Archipelago, taxonomy of the genus Aglaia (mahogany family, Meliaceae) remains problematic. This study aims to evaluate taxonomic concepts within Aglaia based on the largest dataset to-date. We analyzed sequences of 237 accessions of Aglaia and representatives of all other genera of the tribe Aglaieae, including nuclear ribosomal ITS, the trnL-trnF intron and intergenic spacer, the atpF intron and the petD region comprising the petB-petD spacer, the petD-5' exon and the petD intron (all but the first from the plastid genome). Our analyses were set both in maximum likelihood and Bayesian frameworks, which (1) supported paraphyly of Aglaia and Aphanamixis; (2) demonstrated polyphyly of previously described sections for Aglaia; and (3) suggested delimitation problems with 57% of the morphologically "variable species" and all "complex species". In general, there were more genetic entities than species described, which shows that the taxonomy of this group is more complex than has sometimes been previously assumed. For some species, morphological variation suggests the existence of more variants, subspecies or species within various taxa. Furthermore, our study detected additional phylogenetic entities that were geographically distinct, occurring on either side of Wallace's Line but not on both sides. The delineation of these inter-specific taxa needs further investigation by taking into account the morphological variation within and between populations across the entire distribution.

Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling.

Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow-contributes significantly to overall diversity within mountain systems, but the origins of alpine plant diversity are poorly understood. Here, we quantify the processes that generate alpine plant diversity and their changing dynamics through time in Saxifraga (Saxifragaceae), an angiosperm genus that occurs predominantly in mountain systems. We present a time-calibrated molecular phylogenetic tree for the genus that is inferred from 329 low-copy nuclear loci and incorporates 73% (407) of known species. We show that upslope biome shifts into the alpine zone are considerably more prevalent than dispersal of alpine specialists between regions, and that the rate of upslope biome shifts increased markedly in the last 5 Myr, a timeframe concordant with a cooling and fluctuating climate that is likely to have increased the extent of the alpine zone. Furthermore, alpine zone specialists have lower speciation rates than generalists that occur inside and outside the alpine zone, and major speciation rate increases within Saxifraga significantly pre-date increased rates of upslope biome shifts. Specialisation to the alpine zone is not therefore associated with speciation rate increases. Taken together, this study presents a quantified and broad scale perspective of processes underpinning alpine plant diversity.

Niche evolution through time and across continents: The story of Neotropical Cedrela (Meliaceae).

PREMISE OF THE STUDY: Climatic and geological changes have been considered as major drivers of biological diversification. However, it has been generally assumed that lineages retain common environmental affinities, suggesting a limited capacity to switch their climatic niche. We tested this assumption with a study of the evolution of climatic niches in the Neotropical tree genus Cedrela (Meliaceae). • METHODS: We combined distribution models of extant Cedrela with a dated molecular phylogeny based on one nuclear (ITS) and three plastid markers (psbA-trnH, trnS-G and psbB-T-N) to reconstruct the evolutionary dynamics of climatic niches. We calculated relative disparity of climatic tolerances over time to test for niche evolution within subclades or divergence between subclades and conservatism among closely related groups. Published fossil records and studies on paleosols were evaluated for the distribution and climatic conditions of extinct Cedrela. • KEY RESULTS: The fossil record of Cedrela suggested a major biome shift from paratropical conditions into warm-temperate seasonal climates in the Early Oligocene of western North America. In the Miocene, Cedrela extended from North America (John Day Formation, Oregon, USA) to southern Central America (Gatún, Panama). Diversification in the early evolutionary history was mainly driven by changes in precipitation. Temperature had an increasing impact on ecological diversification of the genus from the Miocene onwards. Sister-species comparisons revealed that recent speciation events may be related to divergence of climatic tolerances. • CONCLUSIONS: Our study highlights the complexity of climatic niche dynamics, and shows how conservatism and evolution have acted on different temporal scales and climatic parameters in Cedrela.

Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication.

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

Climate change will disproportionally affect the most genetically diverse lineages of a widespread African tree species.

Global climate change is proceeding at an alarming rate with major ecological and genetic consequences for biodiversity, particularly in drylands. The response of species to climate change may differ between intraspecific genetic groups, with major implications for conservation. We used molecular data from 10 nuclear and two chloroplast genomes to identify phylogeographic groups within 746 individuals from 29 populations of Senegalia senegal, a savannah tree species in sub-Saharan Africa. Three phylogroups are identified corresponding to Sudano-Sahelian, Zambezian and Southern African biogeographic regions in West, East and Southern Africa. Genetic diversity was highest in Southern and Zambesian and lowest in the Sudano-Sahelian phylogroups. Using species distribution modeling, we infer highly divergent future distributions of the phylogroups under three climate change scenarios. Climate change will lead to severe reductions of distribution area of the genetically diverse Zambezian (- 41-- 54%) and Southern (- 63-- 82%) phylogroups, but to an increase for the genetically depauperate Sudano-Sahelian (+ 7- + 26%) phylogroups. This study improves our understanding of the impact of climate change on the future distribution of this species. This knowledge is particularly useful for biodiversity management as the conservation of genetic resources needs to be considered in complementary strategies of in-situ conservation and assisted migration.

Two new species and a new species record of Aglaia (Meliaceae) from Indonesia.

Two new species of Aglaia from Indonesia are described, Aglaia monocaula restricted to West Papua, and Aglaia nyaruensis occurring on Borneo (Kalimantan, Brunei, Sabah and Sarawak). A phylogenetic analysis using nuclear ITS and ETS, and plastid rps15-ycf1 sequence data indicates that the two new species of Aglaia are also genetically distinct. Aglaia monocaula belongs to sectionAmoora, while A. nyaruensis is included in section Aglaia. A dichotomous key, drawings and three-locus DNA barcodes are provided as aids for the identification of the two new species of Aglaia. In addition, the geographic range of Aglaia mackiana (section Amoora) is expanded from a single previously known site in Papua New Guinea to West Papua, Indonesia.

Mountains as Evolutionary Arenas: Patterns, Emerging Approaches, Paradigm Shifts, and Their Implications for Plant Phylogeographic Research in the Tibeto-Himalayan Region.

Recently, the "mountain-geobiodiversity hypothesis" (MGH) was proposed as a key concept for explaining the high levels of biodiversity found in mountain systems of the Tibeto-Himalayan region (THR), which comprises the Qinghai-Tibetan Plateau, the Himalayas, and the biodiversity hotspot known as the "Mountains of Southwest China" (Hengduan Mountains region). In addition to the MGH, which covers the entire life span of a mountain system, a complementary concept, the so-called "flickering connectivity system" (FCS), was recently proposed for the period of the Quaternary. The FCS focuses on connectivity dynamics in alpine ecosystems caused by the drastic climatic changes during the past ca. 2.6 million years, emphasizing that range fragmentation and allopatric speciation are not the sole factors for accelerated evolution of species richness and endemism in mountains. I here provide a review of the current state of knowledge concerning geological uplift, Quaternary glaciation, and the main phylogeographic patterns ("contraction/recolonization," "platform refugia/local expansion," and "microrefugia") of seed plant species in the THR. In addition, I make specific suggestions as to which factors future avenues of phylogeographic research should take into account based on the fundamentals presented by the MGH and FCS, and associated complementary paradigm shifts.

Spatio-temporal evolution of Allium L. in the Qinghai-Tibet-Plateau region: Immigration and in situ radiation.

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 role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas.

Biodiversity is unevenly distributed on Earth and hotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history (i.e. tens of millions of years). Understanding the underlying processes that have driven the accumulation of species in some areas and not in others may help guide prioritization in conservation and may facilitate forecasts on ecosystem services under future climate conditions. Consequently, the study of the origin and evolution of biodiversity in mountain systems has motivated growing scientific interest. Despite an increasing number of studies, the origin and evolution of diversity hotspots associated with the Qinghai-Tibetan Plateau (QTP) remains poorly understood. We review literature related to the diversification of organisms linked to the uplift of the QTP. To promote hypothesis-based research, we provide a geological and palaeoclimatic scenario for the region of the QTP and argue that further studies would benefit from providing a complete set of complementary analyses (molecular dating, biogeographic, and diversification rates analyses) to test for a link between organismic diversification and past geological and climatic changes in this region. In general, we found that the contribution of biological interchange between the QTP and other hotspots of biodiversity has not been sufficiently studied to date. Finally, we suggest that the biological consequences of the uplift of the QTP would be best understood using a meta-analysis approach, encompassing studies on a variety of organisms (plants and animals) from diverse habitats (forests, meadows, rivers), and thermal belts (montane, subalpine, alpine, nival). Since the species diversity in the QTP region is better documented for some organismic groups than for others, we suggest that baseline taxonomic work should be promoted.