Habitat is more important than climate and animal richness at shaping latitudinal variation in plant diversity in China

Species data from 249 National Nature Reserves in China were used to identify potential underlying drivers of latitudinal gradients in plant diversity. We used generalized linear models to assess correlations between predictor and plant species richness. Variance partitioning was then used to decompose the variation in plant richness into different taxonomic levels among the three groups of predictors (i.e., climate, habitat and animal). We found that species richness showed significant latitudinal trends in richness (p?<?0.001). This remained true when examining gymnosperms, angiosperms and ferns individually. Climate and habitat variables explained more variation in richness across different plant groups than did animal richness. Annual precipitation was the best climate variable across different taxonomic plants groups, and soil pH and elevation range were the best habitat variables across different taxonomic plant groups. The independent effects of habitat variables were higher than that of climate and animal variables across different taxonomic plant groups. Finally, climate, habitat heterogeneity, and animal richness explain 48.8% of the variation in total species richness, 28.2% in gymnosperm richness, 44.2% in angiosperm richness, and 38.9% in fern richness.     

Filling in the GAPS: evaluating completeness and coverage of open‐access biodiversity databases in the United States

Primary biodiversity data constitute observations of particular species at given points in time and space. Open‐access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open‐access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records from the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). We aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well‐surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well‐surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well‐surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. This comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.     

Patterns in the distribution of leaf-miners on British trees

Abstract. 1. A multiple regression analysis of the leaf miners on British native angiosperm tree genera was performed using measures of plant range, maximum height, taxonomic isolation and species per genus as independent variables.
2. 69% of the variation was explained by regression.
3. Taxonomic isolation was the most important variable with species per genus also having a significant effect. Plant range had no demonstrable effect.
4. The analysis was repeated with component taxonomic groups of leaf miners. Up to 85% of the variation was explained.     

Predicting invasive alien plant distributions: how geographical bias in occurrence records influences model performance

Aim To investigate the impact of geographical bias on the performance of ecological niche models for invasive plant species. Location South Africa and Australia. Methods We selected 10 Australian plants invasive in South Africa and nine South African plants invasive in Australia. Geographical bias was simulated in occurrence records obtained from the native range of a species to represent two scenarios. For the first scenario (A, worst‐case) a proportion of records were excluded from a specific region of a species’ range and for the second scenario (B, less extreme) only some records were excluded from that specific region of the range. Introduced range predictions were produced with the Maxent modelling algorithm where models were calibrated with datasets from these biased occurrence records and 19 bioclimatic variables. Models were evaluated with independent test data obtained from the introduced range of the species. Geographical bias was quantified as the proportional difference between the occurrence records from a control and a biased dataset, and environmental bias was expressed as either the difference in marginality or tolerance between these datasets. Model performance [assessed using the conventional and modified AUC (area under the curve of receiver‐operating characteristic plots) and the maximum true skill statistic] was compared between models calibrated with occurrence records from a biased dataset and a control dataset. Results We found considerable variation in the relationship between geographical and environmental bias. Environmental bias, expressed as the difference in marginality, differed significantly across treatments. Model performance did not differ significantly among treatments. Regions predicted as suitable for most of the species were very similar when compared between a biased and control dataset, with only a few exceptions. Main conclusions The geographical bias simulated in this study was sufficient to result in significant environmental bias across treatments, but despite this we did not find a significant effect on model performance. Differences in the environmental spaces occupied by the species in their native and invaded ranges may explain why we did not find a significant effect on model performance.     

Spatial and taxonomic biases in bat records: Drivers and conservation implications in a megadiverse country

Biases in data availability have serious consequences on scientific inferences that can be derived. The potential consequences of these biases could be more detrimental in the less‐studied megadiverse regions, often characterized by high biodiversity and serious risks of human threats, as conservation and management actions could be misdirected. Here, focusing on 134 bat species in Mexico, we analyze spatial and taxonomic biases and their drivers in occurrence data; and identify priority areas for further data collection which are currently under‐sampled or at future environmental risk. We collated a comprehensive database of 26,192 presence‐only bat records in Mexico to characterize taxonomic and spatial biases and relate them to species' characteristics (range size and foraging behavior). Next, we examined variables related to accessibility, species richness and security to explain the spatial patterns in occurrence records. Finally, we compared the spatial distributions of existing data and future threats to these species to highlight those regions that are likely to experience an increased level of threats but are currently under‐surveyed. We found taxonomic biases, where species with wider geographical ranges and narrow‐space foragers (species easily captured with traditional methods), had more occurrence data. There was a significant oversampling toward tropical regions, and the presence and number of records was positively associated with areas of high topographic heterogeneity, road density, urban, and protected areas, and negatively associated with areas which were predicted to have future increases in temperature and precipitation. Sampling efforts for Mexican bats appear to have focused disproportionately on easily captured species, tropical regions, areas of high species richness and security; leading to under‐sampling in areas of high future threats. These biases could substantially influence the assessment of current status of, and future anthropogenic impacts on, this diverse species group in a tropical megadiverse country.     

Integrating the Rabinowitz rarity framework with a National Plant Inventory in South Korea

Increasingly large presence‐only survey datasets are becoming available for use in conservation assessments. Potentially, these records could be used to determine spatial patterns of plant species rarity and endemism. We test the integration of a large South Korean species record database with Rabinowitz rarity classes. Rabinowitz proposed seven classes of species rarity using three variables: geographic range, habitat specificity, and local population size. We estimated the range size and local abundance of 2,215 plant species from species occurrence records and habitat specificity as the number of landcover types each species’ records were found in. We classified each species into a rarity class or as common, compared species composition by class to national lists, and mapped the spatial pattern of species richness for each rarity class. Species were classed to narrow or wide geographic ranges using 315 km, the average from a range size index of all species (D_max), based on maximum distance between observations. There were four classes each within the narrow and wide range groups, sorted using cutoffs of local abundance and habitat specificity. Nationally listed endangered species only appeared in the narrow‐range classes, while nationally listed endemic species appeared in almost all classes. Species richness in most rarity classes was high in northeastern South Korea especially for species with narrow ranges. Policy implications. Large presence‐only surveys may be able to estimate some classes of rarity better than others, but modification to include estimates of local abundance and habitat types, could greatly increase their utility. Application of the Rabinowitz rarity framework to such surveys can extend their utility beyond species distribution models and can identify areas that need further surveys and for conservation priority. Future studies should be aware of the subjectivity of the rarity classification and that regional scale implementations of the framework may differ.     

Mixed messages from multiple information sources on invasive species: a case of too much of a good thing?

Aim The increasing number and availability of online databases of alien species beg a question of their comparability given most do not adopt standard criteria in the definition of species status or taxonomic treatment and vary in their comprehensiveness. In this study, we compare the consistency of two major European databases for the regions they have in common. We assess whether they use consistent terminology to classify species status, provide similar taxonomic classification and coverage, deliver comparable estimates of alien richness per country and identify comparable correlates of alien richness. Location Northern Europe. Methods Data on the total number of alien species as well as the number of established alien species were extracted from the online databases DAISIE and NOBANIS for 13 European countries and classified into comparable taxonomic groups. Analyses across countries examined trends in alien species richness, correlations among taxonomic groups and the explanatory power of population density, country area and per capita GDP on alien species richness. Results Alien species richness, intertaxon correlations and the significance of individual drivers of invasion were all strongly database dependent. Differences were more marked for total numbers of aliens than established aliens. Over all taxonomic groups, DAISIE had lower species richness and fewer significant intertaxon correlations but presented a greater number of significant explanatory models of alien species richness. Trends in species richness were not generally correlated between the two databases with human population density being a more important driver in DAISIE while country area had greater explanatory power in NOBANIS. Main conclusions Considerable caution should be applied when collating data from different databases because often their underlying structure and content may differ markedly. For Europe, the analysis indicates that having two contrasting databases is not an ideal basis for implementing invasive species policy and moves should be made soon to establish a central pan‐European database.     

Evolution of plant senescence

Background  

Senescence is integral to the flowering plant life-cycle. Senescence-like processes occur also in non-angiosperm land plants, algae and photosynthetic prokaryotes. Increasing numbers of genes have been assigned functions in the regulation and execution of angiosperm senescence. At the same time there has been a large expansion in the number and taxonomic spread of plant sequences in the genome databases. The present paper uses these resources to make a study of the evolutionary origins of angiosperm senescence based on a survey of the distribution, across plant and microbial taxa, and expression of senescence-related genes.     

Relative importance of habitat area, connectivity, management and local factors for vascular plants: spring ephemerals in boreal semi-natural grasslands

Using species and environmental data from an extensive grassland area in south-western Finland, we investigated the effect of patch area and connectivity, management and local habitat variables on the occurrence of spring-flowering vascular plants and their richness in boreal agricultural landscapes. Generalized linear models (GLM) and variation partitioning were used to study the explanatory power of the three groups of variables and their combined contributions on the richness and occurrence of six spring-flowering plant species. Generalized additive models (GAMs) and associated cross-validation tests were used to evaluate the predictability of the species occurrence and richness patterns. Present-day grassland patch area and connectivity were important predictors for occurrence and richness of the studied plant species. In addition, local habitat factors, especially radiation, accounted for major fractions of occurrence patterns of the studied species. Hybrid models including variables from all three variable groups had higher explanatory power and predictive capability than partial models. However, performance of the separate single-species models varied considerably between the six study species. Exclusion of radiation or connectivity from the hybrid models decreased their predictive performance, suggesting that these factors are of particular importance for grassland plant species at their northern range margins. When developing conservation and management planning for grassland plant species in Northern Europe, attention should be paid to well-connected networks of grassland patches including large, steeply-sloped patches with a favorable microclimate.     

Sexing pollen reveals female bias in a dioecious plant

* Information on angiosperm sex ratios has largely been restricted to surveys of flowering individuals. These often deviate from equality, with male bias more commonly reported. Female-biased sex ratios are concentrated in a few taxa and have been linked to the possession of heteromorphic sex chromosomes and bias introduced during the gametophytic stage of the life cycle. It has been proposed that differences in gamete quantity and quality could give rise to female bias, although there is no direct evidence with which to evaluate this possibility. * Here, we use flow cytometry to investigate microgametophytic 'sex ratios' in a flowering plant. We demonstrate that differences in DNA content between the sexes in Rumex nivalis, a species with heteromorphic sex chromosomes, make it possible to distinguish female- vs male-determining pollen nuclei. * We found a small but significant female bias in microgametophytes produced by males (mean 0.515) with significant variation among family means (range 0.463-0.586), and 18 of 22 families averaging > 0.50. * The observed female bias at the gametophytic stage of the life cycle is consistent with the direction of bias previously reported for seeds and vegetative and reproductive plants in wild populations of R. nivalis, but is insufficient to fully explain the degree of bias.     

Evolutionary patterns in the geographic range size of Atlantic Forest plants

Species’ geographic range size is arguably the single most important predictor of vulnerability to extinction and a key metric in ecology. Despite this, patterns of specific variation in range size and their underlying reasons are still poorly understood. For example, hypotheses on how evolutionary history affects range size have scarcely been tested. To address these questions, we focused on Brazil's Atlantic Forest flora, one of the most species-rich in the world, relatively well-known and highly threatened. We investigated whether and how lineages’ diversification rate, number of species and age are associated with species’ geographic range size. We estimated the extent of occurrence and area of occupancy of each of 13 283 plant species native to the Atlantic Forest region based on over 500 000 unique records. We used phylogenetic least squares and logistic regressions to analyze how the predictors affect the geographic range size. On average, the higher the diversification rate and number of species in the lineage, the smaller the species range size and the higher the proportion of species with vulnerably small range size. Lineage age showed no clear effect on average range size. The results support our expectations that dynamics of diversification and taxonomic richness considerably affect the species range size. Finally, this work reveals poorly known patterns of range size variation and some of the mechanisms driving variation in range size and vulnerability to extinction.     

Contrasting patterns in the invasions of European terrestrial and freshwater habitats by alien plants,insects and vertebrates

Aim To provide the first comparative overview on the current numbers of alien species that invade representative European terrestrial and freshwater habitats for a range of taxonomic groups. Location Europe. Methods Numbers of naturalized alien species of plants, insects, herptiles, birds and mammals occurring in 10 habitats defined according to the European Nature Information System (EUNIS) were obtained from 115 regional data sets. Only species introduced after ad 1500 were considered. Data were analysed by ANCOVA and regression trees to assess whether differences exist among taxonomic groups in terms of their habitat affinity, and whether the pattern of occurrence of alien species in European habitats interacts with macroecological factors such as insularity, latitude or area. Results The highest numbers of alien plant and insect species were found in human‐made, urban or cultivated habitats; if controlled for habitat area in the region, wetland and riparian habitats appeared to support relatively high numbers of alien plant species too. Invasions by vertebrates were more evenly distributed among habitats, with aquatic and riparian, woodland and cultivated land most invaded. Mires, bogs and fens, grassland, heathland and scrub were generally less invaded. Habitat and taxonomic group explained most variation in the proportions of alien species occurring in individual habitats related to the total number of alien species in a region, and the basic pattern determined by these factors was fine‐tuned by geographical variables, namely by the mainland–island contrast and latitude, and differed among taxonomic groups. Main conclusions There are two ecologically distinct groups of alien species (plants and insects versus vertebrates) with strikingly different habitat affinities. Invasions by these two contrasting groups are complementary in terms of habitat use, which makes an overall assessment of habitat invasions in Europe possible. Since numbers of naturalized species in habitats are correlated among taxa within these two groups, the data collected for one group of vertebrates, for example, could be used to estimate the habitat‐specific numbers of alien species for other vertebrate groups with reasonable precision, and the same holds true for insects and plants.     

Spatial and environmental determinants of vascular plant species richness distribution in the Iberian Peninsula and Balearic Islands

Using an exhaustive data compilation, Iberian vascular plant species richness in 50 times 50 UTM grid cells was regressed against 24 explanatory variables (spatial, geographical, topographical, geological, climatic, land use and environmental diversity variables) using Generalized Linear Models and partial regression analysis in order to ascertain the relative contribution of primary, heterogeneous and spatially structured variables. The species richness variation accounted for by these variables is reasonably high (65% of total deviance). Little less than half of this variation is accounted for spatially structured variables. A purely spatial component of variation is hardly significant. The most significant variables are those related to altitude, and particularly maximum altitude, whose cubic response reflects the occurrence of the maximum number of species at the highest altitudes. This result highlighted the importance of Iberian mountains as hotspots of diversity and the relevance of large and small scale historical factors in contemporary plant distribution patterns. Climatic or energy-related variables contributed little, whereas geological (calcareous and acid rocks) and, to a lesser extent, environmental heterogeneity variables (land use diversity and altitude range) seem to be more important.     

Multidimensional biases,gaps and uncertainties in global plant occurrence information

Plants are a hyperdiverse clade that plays a key role in maintaining ecological and evolutionary processes as well as human livelihoods. Biases, gaps and uncertainties in plant occurrence information remain a central problem in ecology and conservation, but these limitations remain largely unassessed globally. In this synthesis, we propose a conceptual framework for analysing gaps in information coverage, information uncertainties and biases in these metrics along taxonomic, geographical and temporal dimensions, and apply it to all c. 370 000 species of land plants. To this end, we integrated 120 million point‐occurrence records with independent databases on plant taxonomy, distributions and conservation status. We find that different data limitations are prevalent in each dimension. Different metrics of information coverage and uncertainty are largely uncorrelated, and reducing taxonomic, spatial or temporal uncertainty by filtering out records would usually come at great costs to coverage. In light of these multidimensional data limitations, we discuss prospects for global plant ecological and biogeographical research, monitoring and conservation and outline critical next steps towards more effective information usage and mobilisation. Our study provides an empirical baseline for evaluating and improving global floristic knowledge, along with a conceptual framework that can be applied to study other hyperdiverse clades.     

Modelling spatial patterns in harbour porpoise satellite telemetry data using maximum entropy

The distribution of harbour porpoises in EU waters is poorly understood, and modelled predictions of their distributions could inform the strategic spatial planning of future exploitation of the marine environment to avoid potential conflicts. We analysed satellite telemetry data from 39 harbour porpoises Phocoena phocoena in inner Danish waters using a modelling tool rooted in maximum entropy: Maxent. Maxent does not require absence data and has been shown to be effective for data characterised by small sample size, sampling bias and locational errors. For each season we used an iterative bootstrapping procedure to randomly select among the most precise records from each of the 39 tagged individuals, and ran Maxent on pooled records based on explanatory environmental variables hypothesised to serve as good proxies for harbour porpoise prey abundance. Among our environmental variables, distance to coast and bottom salinity had the most explanatory power, and their response shapes were relatively consistent across most seasons. The predictive power of the models (assessed by ROC‐AUC) ranged from 0.70 to 0.86 within seasons. The southern Kattegat, the Belt Seas, most western part of the Baltic Sea and the Sound were predicted to have relatively high probabilities of occurrence across seasons. In contrast, the central part of Kattegat and the Baltic Sea south and east of Limhamn and Darss Ridge consistently showed low probabilities of occurrence. Areas with the lowest probabilities of occurrence were generally characterised by high predictive uncertainty. Our methods have implications for the analyses of satellite tagged animals in terrestrial and marine environments. By coupling a bootstrapping procedure with Maxent we circumvented some of the statistical challenges presented by satellite telemetry data to generate spatial predictions within the inner Danish waters.     

Richness and composition of herbaceous species in restored shrubland and grassland ecosystems in the northern Loess Plateau of China

Restored grasslands and shrublands are integral parts of the semi-natural landscape and are of major importance for biodiversity in the northern Loess Plateau. Determining the underlying factors that control the richness and composition of herbaceous species in restored grasslands and shrublands is urgently needed. Thus, the specific objective of this study was to evaluate the relative importance of soil, plant, and topographic explanatory variables affecting the richness and composition of herbaceous species in restored shrubland and grassland ecosystems in a typical watershed within the northern Loess Plateau. In this study, 27 restored grassland sites and 16 restored shrubland sites were sampled during September 2009. Using variation partitioning (partial canonical correspondence analysis), we determined the individual and shared effects of these three sets of explanatory variables on herbaceous biodiversity in the two restored habitats. Most of the explained variation in plant diversity was related to the pure effect of soil, plant, and topographic variables. Restored shrublands had significantly more species than grasslands, and abandoned dam farmlands had significantly more species than other grassland sites. Moreover, botanical diversity responded differently to the explanatory variables in different plant communities. The pure effects of soil properties, soil moisture in particular, accounted for the largest fractions of explained variation in species diversity in restored grasslands. Both plant and topographic variables had balancing pure effects on species diversity in restored shrublands, in particular the shrub density and slope angle. We conclude that the maintenance of a moderate density of shrubs (less than 3600 shrubs per ha), construction of check-dams, and grazing at a low stocking rate, taking conditions of soil and topographic site into account, may help to conserve biodiversity in the northern Loess Plateau.     

Patterns of species richness for vascular plants in China's nature reserves

Explaining the heterogeneous distribution of biodiversity across the Earth has long been a challenge to ecologists and biogeographers. Here, we document the patterns of plant species richness for different taxonomic groups in China's nature reserves, and discuss their possible explanations at national and regional scales, using vascular plant richness data coupled with information on climate and topographical variables. We found that water deficit, energy and elevation range (a surrogate of habitat heterogeneity) represent the primary explanations for variation in plant species richness of the nature reserves across China. There are consistent relationships between species richness and climate and habitat heterogeneity for different taxonomic vascular plant groups at the national scale. Habitat heterogeneity is strongly associated with plant richness in all regions, whereas climatic constraints to plant diversity vary regionally. In the regions where energy is abundant or water is scarce, plant richness patterns were determined by water and habitat heterogeneity, whereas in the region with low energy inputs, water interacting with energy, and habitat heterogeneity determined its species richness pattern. Our results also suggest that energy variables alone do not represent the primary predictor of plant richness.     

A review of Quaternary range shifts in European aquatic Coleoptera

Aim To undertake a quantitative review of the Quaternary fossil record of European water beetles to evaluate their geographical and temporal coverage, and to characterize the extent and typology of the shifts in their geographical ranges. Location Europe. Methods We compiled Quaternary water beetle records from public databases and published references. We included in the analyses species of 10 families of aquatic Coleoptera, and recorded range shifts through the comparison of the location of fossil remains with the current distribution of the species. We explored the ecological representativeness of the fossil record, as well as the relationship between range shifts and the habitat type of the species. Results Our final data set included over 9000 records for 259 water beetle species. Fossil remains of aquatic beetles have been documented exclusively north of 42° N, with most of the records from the British Isles and virtually none from southern Europe or the Mediterranean Basin. Over 80% of the records were from the Late Glacial and the Holocene periods (the last 15 kyr), and overall approximately 20% of the species have been recorded outside their present range (23% excluding Holocene records). Most range shifts were southern or western extensions of currently widespread, northern species, with 10 species displaying major range shifts through the Palaearctic. Lentic species were significantly more likely to have experienced major range shifts, even accounting for the general ecological bias of the fossil record towards lentic habitats. Main conclusions Our results show that the Quaternary record of aquatic Coleoptera is geographically, temporally and ecologically skewed, necessitating caution when extrapolating general conclusions about range changes and ecological stability to other areas or periods on the basis of such scattered evidence. Most central and northern European species for which there are fossil records seem to have conserved their ranges through the Late Pleistocene, with geographical shifts mostly restricted to species with current widespread north Palaearctic or Holarctic distributions. Major range shifts through the Palaearctic are taxonomically uneven, suggesting either an idiosyncratic behaviour of taxa depending on ecological or phylogenetic factors, or a sampling artefact produced by the limited availability of taxonomic expertise.