Database Of Species Occurrences Research Articles

Melaleuca (Myrtaceae): Biogeography of an important genus of trees and shrubs in a changing world

The number of naturalised and invasive woody plant species has increased rapidly in recent decades. Despite the increasing interest in tree and shrub invasions, little is known about the invasion ecology of most species. This paper explores the global movement of species in the genus Melaleuca (Myrtaceae; here including the genus Callistemon). We assess the global introduction history, distribution and biogeographic status of the genus. Various global species occurrence databases, citizen science (iNaturalist), and the literature were used.Seventy-two species [out of 386 Melaleuca species; 19%] have been introduced to at least 125 regions outside their native range. The main regions of global Melaleuca introductions are Southeast Asia, the southern parts of North America, south-eastern South America, southern Africa and Europe. The earliest record of a Melaleuca species outside of the native range of the genus is 1789. First records of Melaleuca species outside their native range were most commonly recorded in the 1960s, with records from all over the world. The main reasons for Melaleuca introductions were for use in the tea tree (pharmaceutical value) and ornamental horticulture industries. Melaleuca introductions, naturalizations and invasions are recent compared to many other woody plant taxa. Experiences in Florida and South Africa highlight the potential of Melaleuca species to spread rapidly and have significant ecological impacts. It is likely that the accumulating invasion debt will result in further naturalization and invasion of Melaleuca species in the future.

Diversity of Platyhelminthes Proseriata in Western Mediterranean sandy beaches: a database of species occurrences and traits

Diversity of Platyhelminthes Proseriata in Western Mediterranean sandy beaches: a database of species occurrences and traits

Lizards (Reptilia: Squamata) from the Caatinga, northeastern Brazil: Detailed and updated overview

AbstractThe Caatinga is the largest seasonal dry tropical forest in South America and it has been historically neglected in terms of its biodiversity. Regarding lizards, different studies led to the current knowledge of diversity and endemism in Caatinga, but detailed syntheses are scarce in the literature. We present the most detailed and up-to-date synthesis of knowledge about Caatinga lizards by providing a detailed (i) list of species; (ii) taxonomic richness patterns; (iii) knowledge gaps and spatial biases; and (iv) detailed distribution maps of all species that contain at least one occurrence record within Caatinga limits. We created a distribution database using occurrences of lizards in Caatinga based on scientific collections, field collection, and literature. We produce up-to-date distribution maps, calculate the Extent of Occurrence and provide the environmental and bioclimatic profile for each species recorded. We draw taxonomic richness and sampling gap maps. Our database has 20,538 records of occurrence of lizards of the Caatinga. We recorded 93 lizard species (13 families), 52.7% of which are endemic. Forthy-four percent of the species present restricted distributions. We identified that 53% of the Caatinga area (or 70% of the municipalities) has no record of occurrence of lizards. The data presented are an important step towards synthesizing in detail the accumulated knowledge about Caatinga lizards and is crucial for accurate strategies for the conservation planning. It directs actions to advance our knowledge on Caatinga lizards: to concentrate inventories in sample void areas; continuous update of the species occurrence database, advance in the generation of autoecology data for species.

Amphibian fauna of Pakistan with notes on future prospects of research and conservation.

Research on amphibians and their conservation have gained worldwide attention, as the group includes the highest number of threatened and Data Deficient species when compared to other vertebrates. However, amphibians have long been neglected in wildlife conservation, management decisions, policy making, and research agendas in Pakistan. In this paper, an annotated checklist of the 21 amphibian species of Pakistan, a key to their identification, and detailed discussions on variation in species, including the genera Minervarya and Sphaerotheca, are provided. We found a statistically significant difference in the morphometric measurements of males but non-significant difference in the females of the two forms (rusty dorsum and dotted dorsum) of S.maskeyi. Some genera, such as Microhyla, Uperodon, Minervarya, Allopaa, Chrysopaa, Euphlyctis, Nanorana, and Sphaerotheca, in Pakistan are in need of additional data for molecular and morphological comparisons with taxa in other South Asian countries. The predicaments of amphibian research in Pakistan are discussed, gaps identified, and suggestions are made. Although the occurrence of chytrid fungus in Pakistan is predicted of low likelihood, a lack of data merits studying the prevalence of the fungus, particularly in the northern regions of the country which exhibit complex and dynamic ecosystems. It is recommended that systematic and coordinated surveys are conducted throughout the country to build a database of species occurrences and distributions. Additionally, the monitoring of wild populations and threat mitigation, as well as appropriate legislation, are suggested as long-term measures. By adopting an inclusive wildlife conservation approach in Pakistan, amphibians could be integrated into wildlife conservation and management efforts.

Taxonomic bias in occurrence information of angiosperm species in China.

Taxonomic bias is a well-known shortcoming of species occurrence databases. Understanding the causes of taxonomic bias facilitates future biological surveys and addresses current knowledge gaps. Here, we investigate the main drivers of taxonomic bias in occurrence data of angiosperm species in China. We used a database including 5,936,768 records for 28,968 angiosperm species derived from herbarium specimens and literature sources. Generalized additive models (GAMs) were applied to investigate explanatory powers of 17 variables on the variation in record numbers of species. Five explanatory variables were selected for a multi-predictor GAM that explained 69% of the variation in record numbers: plant height, range size, elevational range, numbers of scientific publications and web pages. Range size was the most important predictor in the model and positively correlated with number of records. Morphological and phenological traits and social-economic factors including economic values and conservation status had weak explanatory powers on record numbers of plant species, which differs from the findings in animals, suggesting that causes of taxonomic bias in occurrence databases may vary between taxonomic groups. Our results suggest that future floristic surveys in China should more focus on range-restricted and socially or scientifically less "interesting" species.

Increasing accuracy: The advantage of using open access species occurrence database in the Red List assessment

Abstract. Robiansyah I, Wardani W. 2020. Increasing accuracy: The advantage of using open access species occurrence database in the Red List assessment. Biodiversitas 21: 3658-3664. IUCN Red List is the most widely used instrument to assess and advise the extinction risk of a species. One of the criteria used in IUCN Red List is geographical range of the species assessed (criterion B) in the form of extent of occurrence (EOO) and/or area of occupancy (AOO). While this criterion is presumed to be the easiest to be completed as it is based mainly on species occurrence data, there are some assessments that failed to maximize freely available databases. Here, we reassessed the conservation status of Cibotium arachnoideum, a tree fern distributed in Sumatra and Borneo. This species was previously assessed by Praptosuwiryo (2020, Biodiversitas 21 (4): 1379-1384) which classified the species as Endangered (EN) under criteria B2ab(i,ii,iii); C2a(ii). Using additional data from herbarium specimens recorded in the Global Biodiversity Information Facility (GBIF) website and from peer-reviewed scientific papers, in the present paper we show that C. arachnoideum has a larger extent of occurrence (EOO) and area of occupancy (AOO), more locations and different conservation status compared to those in Praptosuwiryo (2020). Our results are supported by the predicted suitable habitat map of C. arachnoideum produced by MaxEnt modelling method. Based on our assessment, we propose the category of Vulnerable (VU) C2a(i) as the global conservation status for C. arachnoideum. Our study implies the advantage of using open access databases to increase the accuracy of extinction risk assessment under the IUCN Red List criteria in regions like Indonesia, where adequate taxonomical information is not always readily available.

Use of openly available occurrence data to generate biodiversity maps within the South African EEZ

Biodiversity maps are an important component of ecosystem-based management and conservation. In the past, biodiversity maps were largely generated using patchy occurrence data from a range of data sources. Currently, substantial species occurrence data are readily available for large parts of the world and are accessible programmatically. Considering both the observed and expected changes in species distributions, and hence biodiversity, in response to present and future climate change, it is important to utilise readily available species occurrence databases to generate temporal and spatial biodiversity maps. In this study biodiversity maps were generated for three generic functional groups within the exclusive economic zone of South Africa: zooplankton, fishes and benthos. This was achieved by stacking individual species-distribution maps. Freely available occurrence data from the Ocean Biogeographic Information System (OBIS) were accessed for this purpose. Ensemble species-distribution modelling, employing five widely used statistical methods, was used to generate species-distribution maps for each functional group. The resulting spatial patterns of biodiversity for the three functional groups were largely in agreement with known patterns. The results of this study highlight the value of open-source occurrence and environmental data to generate biodiversity maps that can potentially be used in future spatial prioritisation or planning for management of marine areas and in environmental-change studies.

DnB, the Database of Nymphalids in Brazil, with a Checklist for Standardized Species Lists

DnB (Database of nymphalids in Brazil) centralizes the state of the art of all Nymphalidae species lists ever reported in Brazil. Butterflies are diverse, ecologically relevant, charismatic, and are effective flagships and bioindicators for conservation. With about 850 described species in Brazil, Nymphalidae is the group with the most stable taxonomy among the three richest Neotropical butterfly families and are frequently used in several biological disciplines as a model system. This study was developed from the need of an up-to-date, curated, and throughout database of species occurrences, the first of its kind in this continental, heterogeneous, and highly diverse country. The data can be used as a starting point for several purposes, such as mapping the distribution of Brazilian nymphalids, producing regional species lists with information of their richness, estimating priority regions (due to species occurrence or lack of sampling) and niche modeling – see DnB tutorials. Using both coarse-grained and exhaustive search strategies, we compiled 489 studies (peer-reviewed or not), from which 357 had species lists and were thus catalogued in a user-friendly software. We provide a separate worksheet with 34 columns of additional information, to filter DnB by e.g. biome, urban sampling, collection method; or to assess the quality of studies. Descriptive analyses revealed, as commonly reported, sampling bias towards large urban centers and proximity to research institutions (Wallacean shortfall), as well as taxonomic (Linnaean) shortfall of biodiversity. Aiming to standardize the publication and peer-review of species lists, we suggest a protocol, or checklist, of all steps required to ensure the comparability and minimum quality of such publications. DnB is available at https://doi.org/10.5281/zenodo.2561408, with a translated version in Portuguese available at http://doi.org/10.5281/zenodo.2561417 and we aim to update and re-publish it every 10 years so we encourage authors to send corrections and new species lists, published in any media, to 2018dnb@gmail.com.

A simple method for assessing the completeness of a geographic range size estimate

Measuring geographic range size is a fundamental part of ecology and conservation. Geographic range size is used as a criterion by the IUCN Red List of Threatened Species in estimating species extinction risk. Yet the geographic distributions of many threatened species are poorly documented, and it is often unclear whether a geographic range size estimate is complete. Here we use a large and near-exhaustive database of species occurrences to (i) estimate extent of occurrence (a measure of geographic range size routinely used in Red List assessments), and (ii) develop a method to assess whether our estimate for each species is complete. We use an extensive database of point locality records for 24 Himalayan Galliformes, a group of highly threatened bird species. We examine the chronological pattern of increase of geographic range size estimates and compare this accumulation curve with a null model generated by performing 1000 iterations for each species using the point locality information in random order. Using Generalised Estimation Equations (GEE) and Generalised Least Square (GLS), we show that estimates of geographic range size for most species has now asymptoted, and that the range size estimates have improved more rapidly over time than expected by chance, suggesting relatively efficient sampling over time. The approach used in this study can be used as a simple method for assessing the completeness of a geographic range size estimates for any taxon.

Zoogeography of a South African Province: A framework for management

AbstractState‐level conservation in South Africa is structured around distinct political entities (i.e. municipalities). This is problematic because an ecological approach that considers species distribution is required to delineate meaningful management units. To do so, vegetation types can be used as management units—however, it is uncertain whether vertebrate communities are associated with vegetation types as defined by the national vegetation map. Here, we investigate mammal diversity patterns within and among biomes (savannah and grassland) and bioregions and test whether different mammal communities were associated with different vegetation types. We used an extensive database of species occurrences in the North West Province. We found that species richness was higher in the savannah than grassland biome. Beta diversity was higher within the savannah than grassland biome, due to greater environmental heterogeneity, though one grassland bioregion was similar to the savannah bioregions. Mammal communities were significantly different among bioregions, but not biomes, suggesting mammal communities are congruent with vegetation type at finer scales (i.e. bioregional), but not at coarser scales (biomes). It thus makes sense to use a bioregional framework to design mammal management strategies. The invasion of grasslands by savannah species should be monitored, specifically given the predicted changes in climate.

Integrating multiple species criteria and species hypotheses in subterranean biology

Decades of debates around the species problem have resulted in the emergence of a unified species concept with multiple criteria to delimit species taxa. Many biologists now agree to consider species as separately evolving segments of metapopulation lineages (i.e. the species concept), and to consider species taxa (i.e. the elementary units used in biodiversity science) as scientific hypotheses of separately evolving entities. In this framework, sets of species hypotheses are generated using different criteria (i.e. morphological distinguishability, genetic isolation) that mirror the properties expressed by species at different times and sequential orders during the extended and heterogeneous process of speciation. This conceptual and methodological advance in taxonomy has several implications for biodiversity science. First, species taxa represent a heterogeneous set of hypotheses whose properties are contingent on the heterogeneous, continuous and extended nature of speciation. Second, species databases need to integrate information on the diverse properties of species by attributing specimens to multiple species hypotheses generated using different delimitation criteria. Third, biodiversity science at large can provide novel insights into biodiversity processes by incorporating multiple species hypotheses into the analysis of biodiversity patterns. Here, we show how these implications have been taken into account by subterranean biologists. First, we briefly review the criteria and methods used to delimit species in subterranean biology and the diverse sets of species hypotheses they generated. Second, we present a new generation of species occurrence databases that integrate different species criteria and hypotheses while fully respecting the scientific rigor of taxonomy. Last, we show how incorporating multiple species hypotheses into macroecological analyses of European groundwater fauna bolsters our under­standing of the factors shaping large-scale patterns of species richness and geographic range size.

Biodiversity hotspots are not congruent with conservation areas in the Gulf of California

As marine systems are threatened by increasing human impacts, mechanisms to maintain biodiversity and ecosystem functions and services are needed. Protecting areas of conservation importance may serve as a proxy for maintaining these functions, while also facilitating efficient use and management of limited resources. Biodiversity hotspots have been used as surrogates for spatial conservation importance; however, as many protected areas have been established opportunistically and under differing criteria, it is unclear how well they actually protect hotspots. We evaluated how well the current protected area network and priority areas selected through previous systematic conservation planning exercises preserve biodiversity hotspots in the Gulf of California, Mexico. We also determined spatial congruence between biodiversity hotspots based on different criteria, which may determine their ability to be used as surrogates for each other. We focus on the Gulf of California because it is a megadiverse system where limited information regarding species diversity and distribution has constrained development of strategies for conservation and management. We developed a species occurrence database and identified biodiversity hotspots using four different criteria: species richness, rarity, endemism, and threatened species. We interpolated species occurrence, while accounting for heterogeneous sampling efforts. We then assessed overlap of hotspots with existing protected areas and priority areas, and between hotspots derived by distinct criteria. We gathered 286,533 occurrence records belonging to 12,105 unique species, including 6388 species identified as rare, 642 as endemic, and 386 as threatened. We found that biodiversity hotspots showed little spatial overlap with areas currently under protection and previously identified priority areas. Our results highlight the importance of distinct spatial areas of biodiversity and suggest that different ecological mechanisms sustain different aspects of diversity and multiple criteria should be used when defining conservation areas.

Geographic distribution modeling of the margay (Leopardus wiedii) and jaguarundi (Puma yagouaroundi): a comparative assessment

The Neotropical region currently harbors 8 recognized species of small cats, including the margay (Leopardus wiedii) and jaguarundi (Puma yagouaroundi). These similar-sized species have broad geographic distributions and commonly occur in sympatry. We constructed species occurrence databases and used the maximum entropy (Maxent) modeling approach to develop models of habitat suitability for each of these species. We identified the environmental predictors with the highest importance for species occurrence and evaluated how they influence habitat suitability for both wild cats. Variables related to temperature and precipitation were good predictors of species occurrence, with both cats responding similarly to them. However, margay showed higher variation in habitat suitability depending on local climatic predictors. The estimated models indicated high niche similarity (> 76%) between these cats, but despite this we identified different areas with the most favorable conditions for each species' occurrence. Approximately 50% and 72% of the entire suitable area were estimated as being moderately to highly suitable for margay and jaguarundi, respectively, with the margay model comprising a higher proportion of forest environments in comparison to that of the jaguarundi. These findings will be relevant in the context of conservation planning when indicating the priority areas for their long-term preservation.

Use of Online Species Occurrence Databases in Published Research since 2010

Use of Online Species Occurrence Databases in Published Research since 2010

Nálezová databáze ochrany přírody – možnosti obohacení výuky, karty druhů a mapy jejich rozšíření

Species Occurrence Database is an ofcial instrument run by Nature Conservation Agency of the Czech Republic to fulfl the duties in species surveillance. Besides that, it has a wide spectrum of uses and applications, including several public sources, which could be useful also for the educational purposes. Among those, Species Map-sites are especially worth mentioning. Tese sites interpret the data of the database into information-rich species grid maps, which are also comparable on the same site with the published sources or paralleled with the time distribution of records as phenological diagrams.

Deconstructing richness patterns by commonness and rarity reveals bioclimatic and spatial effects in black fly metacommunities

Summary Deconstructing biological communities by grouping species according to their commonness or rarity might improve our understanding about the processes driving variation in biological communities. Such an approach considers differences among organisms and emergent ecological patterns. In this study, we addressed the relative role of spatial and large‐scale bioclimatic variables along a commonness and rarity gradient using Simuliidae (Diptera) species richness. A database of species occurrences at 459 locations in Brazil was used to estimate the distribution of 58 simuliid species. Total species richness at each location was estimated first using all occurrences and then by removing one species at a time, following a commonest to rarest gradient (CtR) and vice‐versa (RtC). Partial regression analysis was used to test the influence of sets of bioclimatic (E) and spatial (S) variables for Simuliidae species richness across both CtR and RtC gradients. In the CtR gradient, the pure spatial component alone explained between 40% and 60% of the variation in simuliid richness when the total number of species was greater than ˜35. After removal of the 35th most common species, the model fit decreased sharply reaching nearly zero when only rare species were present. Variation explained by the shared component E + S decreased continuously along the CtR gradient. The relative role of predictor variables on the RtC gradient was similar to CtR gradient. However, removing the rare species first did not change which components best explained species richness. Our gradual deconstructive approach revealed that common species contribute more to species richness variation than rare species, and that the role of predictors in explaining this pattern cannot be untangled by analysing richness of rare and common species in a categorical way.

Towards a more reproducible ecology

Towards a more reproducible ecology

Large-scale evaluation of carnivore road mortality: the effect of landscape and local scale characteristics

Traffic infrastructure is currently one of the main anthropogenic causes affecting carnivore populations, and understanding factors behind spatiotemporal patterns of road mortality is crucial in developing successful conservation measures. Here, we investigated the effect of landscape and local characteristics on road mortality of several carnivore species. Road-kill data from the period 2000–2014 were obtained from a nation-wide volunteer-based survey and Species Occurrence Database of the Czech Republic. From a total of 1020 recorded carnivore road-kills, the most frequently documented was the stone marten (24.2 %) followed by European otter (22.7 %) and red fox (20.2 %). At the landscape scale (1000 m radius), road-kills of habitat generalists (red fox, stone marten, European polecat, least weasel and stoat) were mainly detected in areas with a mixture of arable land and human settlements, while road-kills of habitat specialists (pine marten, Eurasian badger and European otter) and non-native species (raccoon dog and raccoon) were mainly found in areas with a high proportion of forests, grasslands and water bodies. At the local scale (50 m radius), the presence of linear habitats (forest edges, corridors) was positively linked to road-kills of European otter, stone marten, Eurasian badger, stoat, least weasel, European polecat and red fox. The presence of watercourses increased mortality risk in European otter and raccoon dog and oppositely decreased mortality risk in stone marten, least weasel and red fox. We documented a significant effect of road topography only for raccoons, whose road-kills were mostly found in parallel sections of roads relative to buried and raised roads. Based on our results, several mitigation measures that could serve in reducing carnivore mortality in human-dominated landscapes are suggested.

An infrastructure-oriented approach for supporting biodiversity research

During the last years, considerable progresses have been made in developing on-line species occurrence databases. These are crucial in environmental and agricultural challenges, e.g., they are a basic element in the generation of species distribution models. Unfortunately, their exploitation is still difficult and time consuming for many scientists. No database currently exists that can claim to host, and make available in a seamless way, all the species occurrence data needed by the ecology scientific community. Occurrence data are scattered among several databases and information systems. It is not easy to retrieve records from them, because of differences in the adopted protocols, formats and granularity. Once collected, datasets have to be selected, homogenised and pre-processed before being ready-to-use in scientific analysis and modelling. This paper introduces a set of facilities offered by the D4Science Data Infrastructure to support these phases of the scientific process. It also exemplifies how they contribute to reduce the time spent in data quality assessment and curation thus improving the overall performance of the scientific investigation.

Lanternfish (Myctophidae) zoogeography off eastern Australia: a comparison with physicochemical biogeography.

In this first attempt to model the distributions of a mesopelagic fish family at this scale in the eastern Australian region (10°S to 57°S), lanternfish species occurrence data spanning a period from 1928 to 2010 were modelled against environmental covariates. This involved: (1) data collation and taxonomic quality checking, (2) classification of trawls into “horizontal” (presence-absence) and “oblique” (presence-only) types, and classification of vertical migration patterns using existing literature and the species occurrence database, (3) binomial GAMs using presence-absence data for representative temperate, subtropical and tropical species to examine depth interactions with environmental covariates and refine the selection of environmental layers for presence-only MAXENT models, (4) Presence-only MAXENT modelling using data from all trawls and the reduced environmental layers, and (5) Multivariate analysis (area-wise and species-wise) of the resulting matrix of logistic score by geographic pixel. We test the hypothesis that major fronts in the region (Tasman Front, Subtropical Convergence, Subantarctic Front) represent zoogeographic boundaries. A four-region zoogeographic scheme is hypothesised: Coral Sea region, Subtropical Lower Water region, Subtropical Convergence/South Tasman region and Subantarctic region. The Tasman Front, Subtropical Convergence and Subantarctic Front represented zoogeographic boundaries. An additional boundary at ∼25°S (coined the ‘Capricorn’ boundary) was adopted to delineate the Coral Sea from Subtropical Lower Water regions. Lanternfish zoogeographic regions are congruent with some aspects of two prevailing physicochemical biogeographic schema in the region, but neither of these schema alone accurately predicts lanternfish distributions. As lanternfishes integrate vertical ocean processes, the hypothesised lanternfish zoogeography may represent a useful model for a generalised pelagic biogeography that should be tested for other oceanic groups.