Completeness of national freshwater fish species inventories around the world

The aim was to discriminate the countries with relatively comprehensive inventories of freshwater fishes from those with insufficiently prospected inventories. We used a data set of 16,734 freshwater fish species with a total of 1,373,449 occurrence records. Accumulation curves relating the increase in the number of species to the number of records, and completeness values obtained after extrapolating these curves to estimate the total number of predicted species were calculated for each country using the RWizard application KnowBR. Using the final slope values of the accumulation curves, the obtained completeness values, and the ratio between the number of records and the observed species, maps and plots representing the location of good, fair and poor quality inventories at country level were obtained. Inventory completeness ranged from 5.3% (Guinea-Bissau) to 108.4% (United Kingdom), with a pooled mean of 65.9%. We observed that a completeness higher than 90%, a slope lower than 0.02 and a ratio of records/species observed greater than 15 were good thresholds for identifying countries with good quality inventories; only 26 countries met these requirements, mainly located in Europe and North America. However, more than 71% of countries worldwide have inventories that can be categorised as of poor quality. Furthermore, even those countries with relatively accurate national inventories possess a high variability in the completeness of their provincial or regional inventories.     

Environmental DNA reveals a mismatch between diversity facets of Amazonian fishes in response to contrasting geographical,environmental and anthropogenic effects

Freshwater ecosystems are among the most endangered ecosystem in the world. Understanding how human activities affect these ecosystems requires disentangling and quantifying the contribution of the factors driving community assembly. While it has been largely studied in temperate freshwaters, tropical ecosystems remain challenging to study due to the high species richness and the lack of knowledge on species distribution. Here, the use of eDNA-based fish inventories combined to a community-level modelling approach allowed depicting of assembly rules and quantifying the relative contribution of geographic, environmental and anthropic factors to fish assembly. We then used the model predictions to map spatial biodiversity and assess the representativity of sites surveyed in French Guiana within the EU Water Framework Directive (WFD) and highlighted areas that should host unique freshwater fish assemblages. We demonstrated a mismatch between the taxonomic and functional diversity. Taxonomic assemblages between but also within basins were mainly the results of dispersal limitation resulting from basin isolation and natural river barriers. Contrastingly, functional assemblages were ruled by environmental and anthropic factors. The regional mapping of fish diversity indicated that the sites surveyed within the EU WFD had a better representativity of the regional functional diversity than taxonomic diversity. Importantly, we also showed that the assemblages expected to be the most altered by anthropic factors were the most poorly represented in terms of functional diversity in the surveyed sites. The predictions of unique functional and taxonomic assemblages could, therefore, guide the establishment of new survey sites to increase fish diversity representativity and improve this monitoring program.     

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.     

An approach to bioassess pelagic ciliate biodiversity at different taxonomic resolutions in response to various habitats in the Amundsen Sea (Antarctica)

The rapid melting of glaciers and loss of sea ice will result in changes in habitat conditions that may drive substantial changes in biodiversity. In order to bioassess the changing polar ecosystem and evaluate biological conservation, pelagic ciliate communities at different taxonomic resolutions were studied at five habitats in the Amundsen Sea during the austral summer from December 2010 to January 2011. Distinctive spatial patterns were observed in the communities among the five habitats (oceanic areas, transitional areas, polynyas, edges of glaciers, and edges of sea ice) in response to environmental variability (e.g., temperature, salinity, chlorophyll a, and nutrients). The distributions in the numbers of different taxonomic levels and of three biodiversity indices (Shannon-Wiener H′, Pielou’s J′, and Margalef D) also revealed clear spatial variability with the maximum mean species number and indices in the polynya and maximum genus and family numbers in the transitional area. The presence/absence of data at taxonomic resolutions up to the family level provided sufficient information to evaluate the ecological patterns of pelagic ciliate communities and could accurately reflect habitat variations. The k-dominance curves illustrated clearly that maximum diversity was presented in the polynya at the species level and in the transitional area at the genus and family level. We suggest that the diversity at higher taxonomic resolutions should be considered more in future monitoring. Our findings provide basic data and an approach toward answering important questions about biological conservation, especially the biodiversity at various taxonomic resolutions in response to the increasing climate changes in polar ecosystems.     

GBIF information is not enough: national database improves the inventory completeness of Amazonian epiphytes

Distribution data sharing in global databases (e.g. GBIF) allowed the knowledge synthesis in several biodiversity areas. However, their Wallacean shortfalls still reduce our capacity to understand distribution patterns. Including exclusive records from other databases, such as national ones (e.g. SpeciesLink), could mitigate these shortfall problems, but it remains not evaluated. Therefore, we assessed whether (i) the inventory completeness, (ii) taxonomic contribution and (iii) spatial biases could be improved when integrating both global and national biodiversity databases. Using Amazonian epiphytes as a model, we compared the available taxonomic information spatially between GBIF and SpeciesLink databases using a species contribution index. We obtained the inventory completeness from sources using species accumulation curves and assessed their spatial biases by constructing spatial autoregressive models. We found that both databases have a high amount of exclusive records (GBIF: 36.7%; SpeciesLink: 21.7%) and species (17.8%). Amazonia had a small epiphyte inventory completeness, but it was improved when we analyzed both databases together. Individually, both database records were biased to sites with higher altitude, population and herbarium density. Together, river density appeared as a new predictor, probably due to the higher species contribution of SpeciesLink along them. Our findings provide strong evidence that using both global and national databases increase the overall biodiversity knowledge and reduce inventory gaps, but spatial biases may persist. Therefore, we highlight the importance of aggregating more than one database to understand biodiversity patterns, to address conservation decisions and direct shortfalls more efficiently in future studies.

     

Changes in the taxonomic diversity of the reef fish community of San José Island, Gulf of California, Mexico

Although San José Island is considered one of the most important islands in the lower Gulf of California due to its commercial fishing activities, few studies have evaluated their fish taxonomic diversity. The aim of this study was to determine the variation in the taxonomic diversity of the conspicuous fish community in eight locations around San José Island from March 2001 to February 2002. We assessed the changes in the diversity of rocky reef fish based on the taxonomic distances between species, using Fisher’s alpha diversity index, average taxonomic distinctiveness (AvTD Δ+), and taxonomic distinctiveness (Δ*). Visual censuses were conducted in 48 transects consisting of 100?×?5?m quadrants (500?m² sampling area) at an average depth of 5?m, from 09:00 to 16:00. A total of 26,608 fishes belonging to 112 species and 76 genera were found. The index of relative abundance was used to determine the most important species, which were in order of abundance: Abudefduf troschelii, Thalassoma lucasanum, Stegastes rectifraenum, Mulloidichthys dentatus, Chromis atrilobata, Lutjanus argentiventris, and Scarus ghobban. According to Fisher’s alpha diversity index, the highest diversity of species was found in July and the lowest in February. The indices of Δ+ and Δ* indicated significant temporal and spatial differences.     

Survey completeness of a global citizen-science database of bird occurrence

Measuring the completeness of survey inventories created by citizen-science initiatives can identify the strengths and shortfalls in our knowledge of where species occur geographically. Here, we use occurrence information from eBird to measure the survey completeness of the world's birds in this database at three temporal resolutions and four spatial resolutions across the annual cycle during the period 2002 to 2018. Approximately 84% of the earth's terrestrial surface contained bird occurrence information with the greatest concentrations occurring in North America, Europe, India, Australia and New Zealand. The largest regions with low levels of survey completeness were located in central South America, northern and central Africa, and northern Asia. Across spatial and temporal resolutions, survey completeness in regions with occurrence information was 55–74% on average, with the highest values occurring at coarser temporal and coarser spatial resolutions and during spring migration within temperate and boreal regions. Across spatial and temporal resolutions, survey completeness exceeded 90% within ca 4–14% of the earth's terrestrial surface. Survey completeness increased globally from 2002 to 2018 across all months of the year at a rate of ca 3% yr^–1. The slowest gains occurred in Africa and in montane regions, and the most rapid gains occurred in India and in tropical forests after 2012. Thus, occurrence information from a global citizen-science program for a charismatic and well-studied taxon was geographically broad but contained heterogeneous patterns of survey completeness that were strongly influenced by temporal and especially spatial resolution. Our results identify regions where the application of additional effort would address current knowledge shortfalls, and regions where the maintenance of existing effort would benefit long-term monitoring efforts. Our findings highlight the potential of citizen science initiatives to further our knowledge of where species occur across space and time, information whose applications under global change will likely increase.     

Are different facets of plant diversity well protected against climate and land cover changes? A test study in the French Alps

Climate and land cover changes are important drivers of the plant species distributions and diversity patterns in mountainous regions. Although the need for a multifaceted view of diversity based on taxonomic, functional and phylogenetic dimensions is now commonly recognized, there are no complete risk assessments concerning their expected changes. In this paper, we used a range of species distribution models in an ensemble‐forecasting framework together with regional climate and land cover projections by 2080 to analyze the potential threat for more than 2500 plant species at high resolution (2.5 × 2.5 km) in the French Alps. We also decomposed taxonomic, functional and phylogenetic diversity facets into α and β components and analyzed their expected changes by 2080. Overall, plant species threats from climate and land cover changes in the French Alps were expected to vary depending on the species' preferred altitudinal vegetation zone, rarity, and conservation status. Indeed, rare species and species of conservation concern were the ones projected to experience less severe change, and also the ones being the most efficiently preserved by the current network of protected areas. Conversely, the three facets of plant diversity were also projected to experience drastic spatial re‐shuffling by 2080. In general, the mean α‐diversity of the three facets was projected to increase to the detriment of regional β‐diversity, although the latter was projected to remain high at the montane‐alpine transition zones. Our results show that, due to a high‐altitude distribution, the current protection network is efficient for rare species, and species predicted to migrate upward. Although our modeling framework may not capture all possible mechanisms of species range shifts, our work illustrates that a comprehensive risk assessment on an entire floristic region combined with functional and phylogenetic information can help delimitate future scenarios of biodiversity and better design its protection.     

云南被子植物蔷薇分支的进化历史研究

本文以云南被子植物蔷薇分支为研究对象,基于物种间的演化关系,结合其地理分布,从进化历史的角度探讨了物种、特有种、受威胁物种的种类组成及系统发育组成的分布格局,并整合自然保护地的空间分布,对生物多样性的重点保护区域进行识别。结果显示：云南被子植物蔷薇分支的物种密度与系统发育多样性、特有种密度、受威胁物种密度均呈显著正相关,云南南部和西北部是物种丰富度与系统发育多样性最为丰富的区域;就云南整体而言,蔷薇分支的标准化系统发育多样性较低;云南南部、东南部、西北部是蔷薇分支的重点保护区域。     

Hotspots and ecoregions: a test of conservation priorities using taxonomic data

The loss of biodiversity is now recognized as a global problem of significant magnitude [ Science 289: 2279]. Conservation efforts focus on measuring species diversity and distribution, assessing biodiversity threats, and managing habitats to maintain that diversity. The accuracy of measuring species diversity depends on the quality and scale of the data. Recently indirect estimates of diversity based on the skilled opinions of international taxonomic authorities were used to define 25 global conservation hotspots [ Nature 403: 853–858] and 871 ecoregions [ Bioscience 51: 933–938]. These data, originating from first-hand fieldwork and museum study, are readily available, but not necessarily repeatable nor testable. If this type of information prevails for conservation purposes, it is critical that we test the quality of this information with verifiable data at finer scales (e.g., regional inventories, specimen records, and accumulated distribution data). Here we perform such a test for the hotspots and ecoregions found in the Indo-Pacific by comparing the estimates of the expert scientists with authenticated published diversity data on flowering plants. We found a high correlation between our counts of species richness and endemism with the experts' estimates, but surprisingly found less congruity among the seven families examined. A revised list of conservation priority regions based on our plant data is provided.     

Skeletal completeness of the non‐avian theropod dinosaur fossil record

Non‐avian theropods were a highly successful clade of bipedal, predominantly carnivorous, dinosaurs. Their diversity and macroevolutionary patterns have been the subject of many studies. Changes in fossil specimen completeness through time and space can bias our understanding of macroevolution. Here, we quantify the completeness of 455 non‐avian theropod species using the skeletal completeness metric (SCM), which calculates the proportion of a complete skeleton preserved for a specimen. Temporal patterns of theropod skeletal completeness show peaks in the Carnian, Oxfordian–Kimmeridgian and Barremian–Aptian, and lows in the Berriasian and Hauterivian. Lagerstätten primarily drive the peaks in completeness and observed taxonomic diversity in the Oxfordian–Kimmeridgian and the Barremian–Aptian. Theropods have a significantly lower distribution of completeness scores than contemporary sauropodomorph dinosaurs but change in completeness through time for the two groups shows a significant correlation when conservation Lagerstätten are excluded, possibly indicating that both records are primarily driven by geology and sampling availability. Our results reveal relatively weak temporal sampling biases acting on the theropod record but relatively strong spatial and environmental biases. Asia has a significantly more complete record than any other continent, the mid northern latitudes have the highest abundance of finds, and most complete theropod skeletons come from lacustrine and aeolian environments. We suggest that these patterns result from historical research focus, modern climate dynamics, and depositional transportation energy plus association with conservation Lagerstätten, respectively. Furthermore, we find possible ecological biases acting on different theropod subgroups, but body size does not influence theropod completeness on a global scale.     

Effort d’échantillonnage et atlas floristiques – exhaustivité des mailles et caractérisation des lacunes dans la connaissance

Floristic atlases have an important input to flora conservation planning even though their data quality varied greatly across countries. This study aimed to assess survey completeness of cells of floristic atlases. Then, a surveying guide is designed to overcome as efficiently as possible sampling biases. A review and analyses on a wide dataset were carried out to select an estimator of the true species richness of surveyed cells. The Jackknife 1, a non-parametric estimator, appeared as the best compromise for regional floristic atlases. The number of records in each cell was used as an estimator of sampling effort. The ratio between the observed species richness and the estimated species richness measures the completeness of inventories in each surveyed cell. Eighteen variables were selected to describe current inventories and design new surveys. These variables highlight locations, periods and species to be given priority in future studies.     

Assessing the completeness of bryophytes inventories: an oceanic island as a case study (Terceira,Azorean archipelago)

How useful, complete or unbiased are comprehensive databases in order to provide reliable estimations of diversity? Using compiled data from bryophytes in Terceira Island (Azores), we specifically aim (1) to describe the register of species over time, (2) to assess the inventory completeness, i.e., the ratio between the observed and the maximum expected species, and (3) to locate the most promising areas for further surveys. First, each new recorded species was plotted against its collecting year, using the number of database-records as a surrogate of survey effort, to get the accumulation curves. These curves were then extrapolated to obtain the theoretical number of existing species according to Clench and exponential models. Spatial and habitat characteristics of the recorded taxa were also explored. Our results show an increasing trend in the rate of recorded species (c. five species per year), as well as a maximum of around a third of the theoretically “real” number of expected species that could yet remain unknown. Nevertheless, predictions of species richness were highly variable depending on the fitting curve used. Survey effort was similar between liverworts and mosses, as were inventory completeness values, but the rate of new recorded species was higher for mosses. Although bryologists visited preferably native habitats, we show that new species citations may also be found in modified habitats (e.g., exotic forests and semi-natural grasslands). We conclude that the analysis of extensive databases is a useful tool in revealing the recording and taxonomic gaps, further showing that bryophyte inventories could still be incomplete in Terceira Island. A strategy on how to improve species’ collections in remote areas is suggested, hoping to contribute to all-inclusive biodiversity studies in the Azores and elsewhere.     

青弋江鱼类分类群和功能群的α和β多样性纵向梯度格局

确定溪流鱼类多样性的时空分布格局可为鱼类多样性保护与管理提供科学基础。尽管溪流鱼类分类群多样性的纵向梯度格局已有大量报道, 但以鱼类生物学特征为基础的功能多样性研究较少。本文基于2009-2010年4个季度对青弋江1-5级溪流共15个样点的调查数据, 利用形态特征数据和食性构建了鱼类复合功能群, 研究了不同级别溪流间鱼类分类群和功能群组成及多样性的异同, 着重探讨了鱼类分类群和功能群的α和β多样性沿溪流纵向梯度的变化规律。采集到的56种鱼类可分为4个营养功能群和5个运动功能群, 共计14个“营养-运动”复合功能群。双因素交互相似性分析结果显示, 鱼类分类群和功能群组成都随河流级别显著变化, 但季节动态不显著; 双因素方差分析后发现, 鱼类分类群和功能群α、β多样性都随河流级别显著变化, 但受季节影响不显著。经回归分析, 分类群和功能群α多样性与河流级别大小呈显著的线性正相关, 但最大分类群α多样性出现于4级河流, 最大功能群α多样性在4级和5级河流间一致; 分类群和功能群β多样性与河流级别大小呈显著的二项式关系, 呈U型分布。分类群β多样性的空间变化主要取决于物种周转, 而功能群β多样性主要由嵌套所驱动。本研究表明, 沿着“上游-下游”的纵向梯度, 河流鱼类的α和β多样性的空间变化规律不同, 分类群和功能群α多样性的空间格局基本一致, 但分类群(主要是物种周转)和功能群β多样性(主要是功能嵌套)的空间变化过程的驱动机制不同。     

The influence of sampling intensity on the perception of the spatial distribution of tropical diversity and endemism: a case study of ferns from Bolivia

The distribution of tropical plant and animal diversity is still poorly documented, especially at spatial resolutions of practical use for conservation. In the present study, we evaluated the level to which geographical incomplete data availability of species occurrence affects the perception of biodiversity patterns (species richness and endemism) among pteridophytes in Bolivia. We used a data base of Bolivian pteridophytes (27,501 records), divided it into three time periods (1900–70, up to 1990 and up to 2006), and created grid-files at 15'-resolution for species richness and endemism. For each of these biodiversity properties we estimated the species richness (Chao 2) and the index of sampling completeness (C index) per grid, and then all these variables at both species richness and endemism were correlated. Patterns of richness were fairly consistent along all periods; the richest areas were placed along the humid-montane forest, even though they were strongly influenced by collecting intensity. Endemism had a lower degree of correlation with collecting intensity, but varied much more strongly through time than species richness. According to the C index, which gives the ratio between estimated (by Chao 2) and recorded values of species richness and endemism, both biodiversity properties tended to be undersampled in the richest grid cells. Inter-temporal correlations showed sharper differences of correlations for endemism than species richness. Consequently, already in 1970, botanists had a correct idea of the spatial distribution of pteridophyte richness in Bolivia (even though the magnitude was grossly underestimated). In contrast, patterns of endemism, which are of high conservation importance, may not even today be reliably known.     

Species distributions represent intraspecific genetic diversity of freshwater fish in conservation assessments

相似文献   

Taxon size predicts rates of rarity in vascular plants

We surveyed rarity in the vascular plants of the continental U.S.A. and Canada and the vascular plants of Hawaii to test the hypothesis that rates of rarity are independent of taxonomic group size. We demonstrated that taxonomic groups of plants with few species consistently contained fewer than the expected numbers of rare species. This pattern was apparent at the levels of genus, family, order and class. We also found that the pattern remained when we examined rates of rarity by comparing sister taxa that share a common ancestor. This pattern may arise from either differential speciation and extinction patterns or taxonomic bias in species designations (lumping and splitting). The pattern of lineages with few species demonstrating reduced rates of rarity is opposite to that previously observed in mammals and birds. If the protection of representatives from a diversity of lineages is a conservation objective, plant conservation is facilitated by the fact that relatively few species-poor lineages contain rare species.     

What governs the functional diversity patterns of fishes in the headwater streams of the humid forest enclaves: environmental conditions,taxonomic diversity or biotic interactions?

The relationship between functional and taxonomic diversity is a major issue in ecology. Biodiversity in aquatic environments is strongly influenced by environmental gradients that act as dispersion and niche barriers. Environmental conditions act as filters to select functional traits, but biotic interactions also play a role in assemblage structure. In headwater streams, the relationship between functional and taxonomic diversity remains unclear. In this study we investigated how environmental conditions, taxonomic diversity and biotic interactions influence the spatial distribution of traits and functional diversity in stream fish species. Standardized sampling of fish species was carried out in 50 m sections of 16 streams located in rainforest enclaves in a semiarid region of Brazil (Caatinga biome). The functional diversity indices displayed different responses to the predictor variables used. Functional richness was mainly influenced by environmental conditions, while functional evenness was mostly determined by taxonomic diversity. On the other hand, functional dispersion was explained by a combination of environmental conditions and taxonomic diversity. The spatial distribution of fish species with the same functional traits was random, indicating that biotic interactions are not a strong predictor in these ecosystems. Channel width, pH and substrate were the most important variables in the spatial distribution of the functional traits of the fish species. Our results suggest that the functional structure of fish assemblages in headwater streams depends mainly on environmental conditions and taxonomic diversity.     

Evaluating higher taxa as surrogates of harvestmen biodiversity (Arachnida: Opiliones) along a latitudinal gradient in the Atlantic Forest

Habitat loss and fragmentation have highlighted the importance of monitoring remaining habitats. For megadiverse groups such as arthropods, of which many species are still being discovered, the use of higher taxonomic levels as substitutes for diversity may be a useful tool. The aim of this study was to evaluate the use of substitute taxonomic resolutions to assess the richness and composition of Laniatores harvestmen (Arachnida: Opiliones). The five resolutions selected were as follows: genus, family, subfamily, indicator taxa and intermediate resolution (combination of genus and species identification levels). In addition, we evaluated whether the diversity substitutes provide good estimates of latitudinal gradients. Nineteen Atlantic Forest sites located along a latitudinal gradient in northeastern Brazil were sampled. We recorded a total of 88 harvestmen species/morpho-species, distributed in 7 families, 15 subfamilies and 36 genera. Genus and intermediate resolution were excellent substitutes for harvestmen species richness. The efficiency differed according to the substitute resolution used. Four resolutions were adequate to replace the harvestmen composition: genus, intermediate resolution, indicator taxa, and subfamily. The number of harvestmen species recorded was significantly different between Seasonal Semideciduous Forest and Costal Atlantic Rainforest. The same relationship was also observed the same relationship was observed when we consider genus and intermediate resolution. Our results suggest the use of genus as a substitute for richness and composition of harvestmen for reducing monitoring costs and providing evaluation in a shorter time and a more practical way.     

Three reasons to re-evaluate fungal diversity ‘on Earth and in the ocean’

Attempts to assess fungal global species richness are confounded by several problems: uncertainty about the number of described species, incomplete fungal inventories even at a high taxonomic level, high diversity of unknown, often small and elusive taxa, high levels of morphological conservation, and incomplete knowledge of their ecological and biogeographical distributions. The two main bases for estimating total fungal diversity are (1) the number of described species and their taxonomic structure, and (2) extrapolating species-area relationships. We argue that knowledge of fungal taxonomy and environmental sampling of fungi are both too incomplete for either approach to be reliable. However, it is likely that the true number of fungal species on the planet is a seven-digit number, and may even be an order of magnitude higher.