Background:For several regions, ecologists and taxonomists have assembled information on phenotypes for almost all species of the megadiverse angiosperms. However, testing hypotheses on regional evolutionary and biogeographic history requires highly resolved and dated phylogenies covering the same taxa, which are often lacking at regional scales. Here, we filled this knowledge gap for one of the best-studied regional floras: the native angiosperms of the Netherlands. New information:We provide a molecular phylogenetic dataset and two time-calibrated trees (based on BEAST and MrBayes approaches) of the native angiosperm flora of the Netherlands, reconstructed from publicly available DNA sequences. The resulting phylogenies include 1178 species from the 2017 species list on SynBioSys NL, a national database that provides a curated checklist of native vascular plant species occurring in the Netherlands (also core to the flora of adjacent countries), and are provided in multiple formats (Newick, Nexus), along with alignments, BEAST and MrBayes input files, and metadata linking taxa to GenBank accession numbers. This dataset offers a phylogenetic framework that is based on molecular data covering more than 95% of the native species included in the checklist, reproducible and extremely well-resolved phylogeny (99.92% of nodes resolved in the maximum clade credibility tree; reflecting the absence of polytomies; 67.9% of nodes with posterior probability above 0.95 and 92.3% above 0.50) for researchers. These data will permit the signal of evolutionary history in patterns of biodiversity across the Netherlands, such as the age structure of habitat species pools or functional groups, where a focus on native species is essential. All resources are openly available via IDiv (https://doi.org/10.25829/idiv.3600-myr3t3) under a CC-BY license.

ABSTRACT Across the planet, angiosperm diversification has been shaped by palaeoclimates and biotic interactions, particularly with pollinators, leaving signatures in the angiosperm age structure. Regional floras represent biased samples of this global diversification shaped by dispersal, extinction and environmental filtering, yet it remains unclear whether floristic age structure reflects pollination strategies or their interaction with palaeoclimates. We constructed a 93% resolved phylogeny of all native 1178 angiosperms in the Netherlands and characterized age structure of eight pollination syndromes by standardized epoch‐specific lineage diversities (stELDs) quantifying the proportional increase in lineages per 10‐Myr interval. Overall, stELDs peaked under the coldest intervals and were lowest for intermediate‐temperature intervals (geological age alone had no effect). This age structure was strongest in wind‐pollinated species. Resolving insect pollination into six syndromes revealed strong heterogeneity: lepidoptera‐pollination was most strongly associated with warmest palaeotemperatures, bumblebee and wasp‐pollination under intermediate temperatures, and fly, lepidoptera and beetle‐pollination under coldest temperatures. Paleotemperature signatures correlated positively with contemporary seasonal flowering temperatures, indicating conserved thermal niches across ecological and macroevolutionary timescales. We suggest that temperate floras reflect both recent cold‐house diversification of wind‐ and certain insect‐pollinated lineages and earlier warm‐house radiations of lineages pollinated by older insect clades. Phylogenetic age structures permit detecting such patterns.

Aim: Species richness of local communities is often considered to be disconnected from the macroevolutionary diversification of lineages operating at much larger spatiotemporal scales. However, local communities occupy patches of habitat types, many of which persist across large spatiotemporal scales. We hypothesise that high local species richness of specific habitat types could result from ongoing local assembly in which both very closely related and very distantly related species can locally co-occur. Alternatively, such local richness of specific habitat types could result from historical assembly in which historical colonisation by many lineages and diversification within habitat-type increased richness of the habitat species-pool and thereby the local communities sampled from it. Location: The Netherlands. Time Period: 1932-2012. Major Taxa Studied: Angiosperms. Methods: We analysed 6851 small-scale local plots (median 54 m2) belonging to all major habitat types in the Netherlands. We quantified mean pairwise phylogenetic distances across all species and between phylogenetically nearest species, standardised for 0-expectations for a given species richness. We quantified these measures for local communities, averaged within habitat types and for the species-pools of the habitat types. Results: Local richness varied 21-fold among habitat types. Local richness increased with mean pairwise distances and decreased with mean nearest-taxon distances of local communities (but not of habitat species-pools). These patterns were independent of the size of the regional habitat species-pool, the presence of exotic species and the environmental conditions. Main Conclusions: Local species richness varies massively among habitat types within a region. We suggest that some habitat types are locally species rich because today they permit the most distantly related and the most closely related species to coexist, likely through stabilising and equalising mechanisms, respectively. These mechanisms should be tested in the future.

The interaction of recent orographic uplift and climate heterogeneity acted as a key role in the East Himalaya-Hengduan Mountains (EHHM) has been reported in many studies. However, how exactly the interaction promotes clade diversification remains poorly understood. In this study, we both used the chloroplast trnT-trnF region and 11 nuclear microsatellite loci to investigate the phylogeographic structure and population dynamics of Hippophae gyantsensis and estimate what role geological barriers or ecological factors play in the spatial genetic structure. The results showed that this species had a strong east-west phylogeographic structure, with several mixed populations identified from microsatellite data in central location. The intraspecies divergence time was estimated to be about 3.59Ma, corresponding well with the recent uplift of the Tibetan Plateau. Between the two lineages, there was significant climatic differentiation without geographic barriers. High consistency between lineage divergence, climatic heterogeneity, and Qingzang Movement demonstrated that climatic heterogeneity but not geographic isolation drives the divergence of H. gyantsensis, and the recent regional uplift of the QTP, as the Himalayas, creates heterogeneous climates by affecting the flow of the Indian monsoon. The east group of H. gyantsensis experienced population expansion c. 0.12Ma, closely associated with the last interglacial interval. Subsequently, a genetic admixture event between east and west groups happened at 26.90ka, a period corresponding to the warm inter-glaciation again. These findings highlight the importance of the Quaternary climatic fluctuations in the recent evolutionary history of H. gyantsensis. Our study will improve the understanding of the history and mechanisms of biodiversity accumulation in the EHHM region.

Summary The functioning of present ecosystems reflects deep evolutionary history of locally cooccurring species if their functional traits show high phylogenetic signal (PS). However, we do not understand what drives local PS. We hypothesize that local PS is high in undisturbed and stressful habitats, either due to ongoing local assembly of species that maintained ancestral traits, or to past evolutionary maintenance of ancestral traits within habitat species‐pools, or to both. We quantified PS and diversity of 10 traits within 6704 local plant communities across 38 Dutch habitat types differing in disturbance or stress. Mean local PS varied 50‐fold among habitat types, often independently of phylogenetic or trait diversity. Mean local PS decreased with disturbance but showed no consistent relationship to stress. Mean local PS exceeded species‐pool PS, reflecting nonrandom subsampling from the pool. Disturbance or stress related more strongly to mean local than to species‐pool PS. Disturbed habitats harbour species with evolutionary divergent trait values, probably driven by ongoing, local assembly of species: environmental fluctuations might maintain different trait values within lineages through an evolutionary storage effect. If functional traits do not reflect phylogeny, ecosystem functioning might not be contingent on the presence of particular lineages, and lineages might establish evolutionarily novel interactions.

• Dispersal has played an important role in the evolutionary history of neotropical Chrysophylloideae. • The Andean uplift or the Pleistocene climatic changes did not cause increases in diversification rates in Chrysophylloideae. • The Central American Seaway and the Andean uplift did not generally prevented migration in Chrysophylloideae.

Understanding how species diversify and evolve in species-rich areas like the lowland rain forest in the Neotropics is critical for conservation in times of unprecedented threats. To determine how the Andean uplift, the formation of the Panama land bridge, and Pleistocene climatic fluctuations affected dispersal and diversification in the Sapotaceae subfamily Chrysophylloideae, we collected 146 Chrysophylloideae accessions in previously under-explored areas, generating one of the most geographically complete data sets for neotropical Sapotaceae. Sapotaceae is a good model to test diversification hypotheses in lowland neotropical rain forests as it predominantly occurs <1000 m altitude, and it is an abundant and species-rich group in this biome. We generated a time calibrated phylogeny of 123 Sapotaceae species based upon the nuclear ribosomal internal transcribed spacer region that suggests migration between lineages to the east and the west Andean Cordilleras occurred before and after periods of major uplift, indicating that the Andes did not represent a significant barrier to dispersal for Sapotaceae, although it may have promoted vicariance in some cases. Dispersal between South and Central America occurred mainly prior to the formation of the Panama land bridge, suggesting that this event did not affect migration patterns in Chrysophylloideae. We inferred diversification rates and detected three shifts in the phylogeny, but they are not congruent with tectonic movements during the middle Miocene and climatic changes during the Pleistocene. Finally, some species with restricted distributions appear to be phylogenetically nested within species with broader ranges, suggesting ancestor descendent relationships and insights into patterns of speciation in rain forest trees.

Present biodiversity comprises the evolutionary heritage of Earth's epochs. Lineages from particular epochs are often found in particular habitats, but whether current habitat decline threatens the heritage from particular epochs is unknown. We hypothesized that within a given region, humans threaten specifically habitats that harbor lineages from a particular geological epoch. We expect so because humans threaten environments that dominated and lineages that diversified during these epochs. We devised a new approach to quantify, per habitat type, diversification of lineages from different epochs. For Netherlands, one of the floristically and ecologically best-studied regions, we quantified the decline of habitat types and species in the past century. We defined habitat types based on vegetation classification and used existing ranking of decline of vegetation classes and species. Currently, most declining habitat types and the group of red-listed species are characterized by increased diversification of lineages dating back to Paleogene, specifically to Paleocene-Eocene and Oligocene. Among vulnerable habitat types with large representation of lineages from these epochs were sublittoral and eulittoral zones of temperate seas and 2 types of nutrient-poor, open habitats. These losses of evolutionary heritage would go unnoticed with classical measures of evolutionary diversity. Loss of heritage from Paleocene-Eocene became unrelated to decline once low competition, shade tolerance, and low proportion of non-Apiaceae were accounted for, suggesting that these variables explain the loss of heritage from Paleocene-Eocene. Losses of heritage from Oligocene were partly explained by decline of habitat types occupied by weak competitors and shade-tolerant species. Our results suggest a so-far unappreciated human threat to evolutionary heritage: habitat decline threatens descendants from particular epochs. If the trends persist into the future uncontrolled, there may be no habitats within the region for many descendants of evolutionary ancient epochs, such as Paleogene.

Gnetum is a genus in the Gnetales that has a unique but ambiguous placement within seed plant phylogeny. Previous studies have shown that Gnetum has lower values of photosynthetic characters than those of other seed plants, but few Gnetum species have been studied, and those that have been studied are restricted to narrow taxonomic and geographic ranges. In addition, the mechanism underlying the lower values of photosynthetic characters in Gnetum remains poorly understood. Here, we investigated the photosynthetic characters of a Chinese lianoid species, i.e., Gnetum parvifolium, and co-occurring woody angiosperms growing in the wild, as well as seedlings of five Chinese Gnetum species cultivated in a greenhouse. The five Gnetum species had considerably lower values for photosynthesis parameters (net photosynthetic rate, transpiration rate, intercellular CO2 concentration, and stomatal conductance) than those of other seed plant representatives. Interrelated analyses revealed that the low photosynthetic capacity may be an intrinsic property of Gnetum, and may be associated with its evolutionary history. Comparison of the chloroplast genomes (cpDNAs) of Gnetum with those of other seed plant representatives revealed that 17 coding genes are absent from the cpDNAs of all species of Gnetum. This lack of multiple functional genes from the cpDNAs probably leads to the low photosynthetic rates of Gnetum. Our results provide a new perspective on the evolutionary history of the Gnetales, and on the ecophysiological and genomic attributes of tropical biomes in general. These results could also be useful for the breeding and cultivation of Gnetum.

Plant species coexisting in direct contact produce patches of mixed litters. Mixing litter sometimes synergistically accelerates and sometimes antagonistically decelerates litter decomposition, but we insufficiently understand why. Here, we hypothesize that antagonism or synergy within a mixed‐litter patch depends on the neighbouring litter matrix. Specifically, phylogenetical or functional dissimilarity within neighbouring litter, or among patch and neighbouring litter, may favour complementarity and thereby within‐patch synergy. From a pool of 20 grassland species, we created 120 mixed‐litter patches of two species, and exposed these patches to neighbourhoods in long‐term grassland mesocosms of different functional and phylogenetic compositions. We found 60% less (antagonism) to 80% more (synergy) decomposition than expected from single‐species litters. Functionally similar, and grass‐dominated, mixed‐litter patches decomposed most synergistically. Synergy was most strongly favoured by phylogenetic distance among neighbours and functional dissimilarity between neighbours and patch. Synthesis . Our results show that the relationship between biodiversity and ecosystem functioning was context‐dependent. We suggest that the coexistence of grasses and the formation of phylogenetically diverse, functionally distinct, patchy vegetation may be reinforced by synergistic nutrient recycling.

Migrations from the Qinghai-Tibetan Plateau (QTP) to other temperate regions represent one of the main biogeographical patterns for the Northern Hemisphere. However, the ages and routes of these migrations are largely not known. We aimed to reconstruct a well-resolved and dated phylogeny of Hippophae L. (Elaeagnaceae) and test hypothesis of a westward migration of this plant out of the QTP across Eurasian mountains in the Miocene. We produced two data matrices of five chloroplast DNA (cpDNA) and five nuclear DNA markers for all distinct taxa of Hippophae. These matrices were used to reconstruct phylogenetic relationships in the genus. In dating analyses, we first estimated the stem node age of Elaeagnaceae using five fossil records evenly distributed across a tree of Rosales. We used this estimate and two fossil records to calibrate the cpDNA and nDNA phylogenies of Hippophae. The same phylogenies were used to reconstruct ancestral areas within the genus. The monophyly of Hippophae, all five species, and most of subspecies was strongly supported by both plastid and nuclear data sets. Diversification of Hippophae likely started in central Himalayas/southern Tibet in the early Miocene and all extant distinct species had probably originated by the middle Miocene. Diversification of Hippophae rhamnoides likely started in the late Miocene east of the QTP from where this species rapidly expanded to central and western Eurasia. Our findings highlight the impact of different stages in uplift of the QTP and Eurasian mountains and climatic changes in the Neogene on diversification and range shifts in the highland flora on the continent. The results provide support to the idea of an immigration route for some European highland plants from their ancestral areas on the QTP across central and western mountain ranges of Eurasia in the late Miocene.

Recent decades have seen a decline of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization – and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates.

We provide an example of habitat use along multiple environmental gradients and its variation among species within each of the angiosperm genera in the Netherlands (from Ozinga et al., 2013). We find that many of these genera exhibit minimal variation of the preferred habitats among their constituent species, while only a few show large variation, even after accounting for the present-day richness and the age of the genera (Fig. S1). This result appears to be true for the fossil record as well. Notes S3 provides an example of both strong and weak variation in habitat use through deep evolutionary time from the fossil record. Overall, clades appear to vary strongly in the degree to which their species occupy similar habitats.

Sea buckthorn (Hippophae L., Elaeagnaceae) has been exploited by humans for thousands of years on the Quinghai-Tibetan Plateau (QTP) and nearby areas. However, the considerable modern economic potential of this plant has started to receive full appreciation only recently. Expanding its traditional use in harsh climatic zones as important source of nutrients, vitamins, and as wood in treeless areas, today this plant is used also on large scales as landscape protection tools against corrosion of soil, and as a source of wide range of products in pharmaceutic, cosmetic, and nutritional supplement industries. This review aims to provide the latest insights from studies on the evolutionary history and biogeography of the genus, structure, and phylogeography of genetic diversity within its species. Understanding the genic and genomic interactions among populations and phylogenetically distant lineages within species of Hippophae should help to improve the efficiency of exploitation of genetic resources in this crop. Research efforts in the past century in breeding, systematics, cytogenetics, biochemistry, and genetics of Hippophae have created a solid background for advances in modern biotechnology of this crop. Recent studies reported application of next-generation sequencing (NGS) technologies and identification of thousands of genes in transcriptomes of sea buckthorn. Analyses of the transcriptomes provided better understanding of gene expression in biochemical pathways of unsaturated fatty acids, some other secondary metabolites, and regulation of gene complexes responsible for adaptation to different categories of abiotic stress. Further studies should focus on the creation of genetic maps of breeding populations; identification of quantitative trait loci, biochemical pathways of synthesis of bioactive secondary metabolites and correspondent genes, molecular mechanisms of tolerance and resistance to abiotic stress, diseases, and pests; and cloning of genes of agricultural importance. Advances in these research areas can lead to genetic engineering of plants with a combination of traits of high horticultural, medicinal, or nutrient value, adapted to specific environments of areas of their cultivation.

Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the "ELDERness surfaces." These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.

AimBiodiversity hot-spots are regions containing evolutionary heritage from ancient or recent geological epochs, i.e. evolutionary museums' or cradles', respectively. We hypothesize that: (1) there are also museums' and cradles' within regions - some species pools of particular habitat types contain angiosperm (flowering plants) lineages from ancient geological epochs, others from recent epochs; (2) habitat-specific abiotic factors control the number of angiosperm lineages from a given epoch contained in a given habitat species pool.LocationThe flora of the Netherlands.MethodsWe studied the world's largest vegetation-plot database and a new, uniquely resolved dated angiosperm phylogeny available for the Netherlands. We characterized species pools of habitat types by a novel concept: epoch-specific lineage diversities.ResultsWe found that species pools of most habitat types were characterized by over- or underrepresentation of lineages from at least one epoch, dating back to the origin of angiosperms. These patterns are not captured by mean lineage ages. Abiotic environments explained on average 56% and up to 75% of the variance in the number of lineages per epoch, but with opposing effects of the same factor for different epochs. Specifically, warm and dry habitats tend to contain lineages dating back to warm and dry epochs. Identifying lineages from sets of random time intervals rather than from a set of geological epochs significantly reduced relationships with the environment.Main conclusionsWithin a region, habitat types differ significantly in the evolutionary heritage they contain from different geological epochs, and these differences are controlled by the environment.

Background: Gnetum parvifolium stems and roots have been used for a long time in traditional Chinese medicines. Stilbenes are bioactive compounds present in G. parvifolium plants, and they possess antioxidative and anticancer properties. However, little is known about the responses of G. parvifolium stilbene biosynthetic pathways to stress conditions. Therefore, we investigated stilbene biosynthesis, including the expression of relevant genes, in G. parvifolium exposed to high-temperature and ultraviolet-C treatments.Results: High temperatures did not influence the accumulation of total stilbenes in stems but decreased stilbene concentrations in roots at 3 h, with a subsequent restoration to control levels. In contrast, ultraviolet irradiation induced the accumulation of total stilbenes in stems but not in roots. We also observed that high temperatures inhibited the production of resveratrol and piceatannol in G. parvifolium stems and roots, whereas ultraviolet treatments initially inhibited their accumulation (up to 6 h) but induced their production at later time points. Analyses of specific genes (i.e., PAL, C4H, 4CL, STS, and CYP) revealed that their expression levels generally increased in stress-treated stems and roots, although there was some variability in the expression profiles during treatments.Conclusions: Our results indicated that high temperatures and ultraviolet irradiation differentially affect the biosynthesis of specific stilbenes in G. parvifolium stems and roots. Therefore, cultivating G. parvifolium seedlings under optimal stress conditions may increase the biosynthesis of specific stilbene compounds. (C) 2016 Pontificia Universidad Catolica de Valparaiso. Production and hosting by Elsevier B.V. All rights reserved.

Summary Global change triggers rapid alterations in the composition and diversity of plant communities which may change ecosystem functioning. Do changes in community diversity also change traits persistently, that is does coexistence with numerous or functionally or phylogenetically distinct species trigger, in a given focal species, trait shifts that persist? We studied the grass Dactylis glomerata. Dactylis was grown in experimental plots with different species compositions for 5 years, sampled, cloned and grown in a common garden. We studied amines, regulators integrating growth responses of organisms to their environment. We found that the mean levels and variances of most amines depended on the diversity of the source community, notably the species richness and the phylogenetic and functional distinctness from Dactylis, unbiased by species identity or biomass shifts. Synthesis. Our results suggest that different levels of ambient diversity can, within a few years, select for different genotypes which have different compositions of growth regulators. Our study also suggests that a plant species can evolve in response to the diversity or distinctness of the surrounding plant community. Evolutionary changes of plant phenotypes might mediate an impact of past biological diversity on present ecosystem functioning.

Phylogenetic distances of coexisting species differ greatly within plant communities, but their consequences for decomposers and decomposition remain unknown. We hypothesized that large phylogenetic distance of leaf litter mixtures increases differences of their litter traits, which may, in turn, result in increased resource complementarity or decreased resource concentration for decomposers and hence increased or decreased chemical transformation and reduction of litter. We conducted a litter mixture experiment including 12 common temperate tree species (evolutionarily separated by up to 106 Myr), and sampled after seven months, at which average mass loss was more than 50%. We found no effect of increased phylogenetic distance on litter mass loss or on abundance and diversity of invertebrate decomposers. However, phylogenetic distance decreased microbial biomass and increased carbon/nitrogen (C/N) ratios of litter mixtures. Consistently, four litter traits showed (marginally) significant phylogenetic signal and in three of these traits increasing trait difference decreased microbial biomass and increased C/N. We suggest that phylogenetic proximity of litter favours microbial decomposers and chemical transformation of litter owing to a resource concentration effect. This leads to a new hypothesis: closely related plant species occurring in the same niche should promote and profit from increased nutrient availability.