Uses of GBIF in scientific research

Peer-reviewed research citing GBIF as a data source, with at least one author from Israel.
For all researches, please visit our "Peer-reviewed publications" page.

List of publications

  • Davis Rabosky A, Cox C, Rabosky D, Title P, Holmes I, Feldman A et al. (2016)

    Coral snakes predict the evolution of mimicry across New World snakes.

    Nature communications 7 11484.

    Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious species (models), generates striking cases of phenotypic convergence that are classic examples of evolution by natural selection. However, mimicry of venomous coral snakes has remained controversial because of unresolved conflict between the predictions of mimicry theory and empirical patterns in the distribution and abundance of snakes. Here we integrate distributional, phenotypic and phylogenetic data across all New World snake species to demonstrate that shifts to mimetic coloration in nonvenomous snakes are highly correlated with coral snakes in both space and time, providing overwhelming support for Batesian mimicry. We also find that bidirectional transitions between mimetic and cryptic coloration are unexpectedly frequent over both long- and short-time scales, challenging traditional views of mimicry as a stable evolutionary 'end point' and suggesting that insect and snake mimicry may have different evolutionary dynamics.

    Keywords: Biological sciences, Ecology, Evolution, Zoology


  • Gueta T, Carmel Y (2016)

    Quantifying the value of user-level data cleaning for big data: A case study using mammal distribution models

    Ecological Informatics 34 139-145.

    The recent availability of species occurrence data from numerous sources, standardized and connected within a single portal, has the potential to answer fundamental ecological questions. These aggregated big biodiversity databases are prone to numerous data errors and biases. The data-user is responsible for identifying these errors and assessing if the data are suitable for a given purpose. Complex technical skills are increasingly required for handling and cleaning biodiversity data, while biodiversity scientists possessing these skills are rare. Here, we estimate the effect of user-level data cleaning on species distribution model (SDM) performance. We implement several simple and easy-to-execute data cleaning procedures, and evaluate the change in SDM performance. Additionally, we examine if a certain group of species is more sensitive to the use of erroneous or unsuitable data. The cleaning procedures used in this research improved SDM performance significantly, across all scales and for all performance measures. The largest improvement in distribution models following data cleaning was for small mammals (1g–100g). Data cleaning at the user level is crucial when using aggregated occurrence data, and facilitating its implementation is a key factor in order to advance data-intensive biodiversity studies. Adopting a more comprehensive approach for incorporating data cleaning as part of data analysis, will not only improve the quality of biodiversity data, but will also impose a more appropriate usage of such data.

    Keywords: Australian mammals, Big-data, Biodiversity informatics, Data-cleaning, MaxEnt, SDM performance


  • Meiri S (2016)

    Small, rare and trendy: traits and biogeography of lizards described in the 21st century

    Journal of Zoology.

    The pace of new reptile species descriptions, especially of new lizard descriptions, is rapidly increasing. The number of recognized lizard species has increased by more than 30% since the turn of the century. I examined the traits of newly described lizard taxa, and compared them to those of species described earlier, to predict where new species will be found, what traits they have, and whether they are likely to be more extinction-prone than well-known species. I compiled data on the biogeography and ecology of newly described forms and examined the relationship between these traits and the date of description. As expected, new descriptions are generally of small species, predominantly with small geographic ranges. Most species have been described from the Oriental Realm, whereas few new species were described from Africa. New descriptions are disproportionally biased in favor of geckos and of nocturnal species – and, surprisingly, contain few subterranean forms. Newly described lizard species are more likely to be threatened with extinction and may be more susceptible to population decline. Although the rate of new lizard descriptions is still accelerating, this work contributes to predicting what types of species are likely to be found in the future – and where. The small ranges of such species, in regions suffering from severe habitat degradation, suggests that strong mitigation measures are needed to ensure that many of these species will not be lost shortly after being described.

    Keywords: activity times, biome, description date, population decline, range size, species discovery, taxonomy, threat


  • Chocron R, Flather C, Kadmon R (2015)

    Bird diversity and environmental heterogeneity in North America: a test of the area-heterogeneity trade-off

    Global Ecology and Biogeography.

    Aim Deterministic niche theory predicts that increasing environmental heterogeneity increases species richness. In contrast, a recent stochastic model suggests that heterogeneity has a unimodal effect on species richness since high levels of heterogeneity reduce the effective area available per species, thereby increasing the likelihood of stochastic extinction (the ‘area–heterogeneity trade-off’). We tested these contrasting predictions using data on bird distributions in North America. Location North America. Methods The effect of heterogeneity on species richness was tested using simultaneous autoregressive regression models based on two measures of heterogeneity (elevational range and land-cover richness) each quantified at two scales (400 m, 5 km), three measures of species richness (observed, corrected for incomplete detection, and corrected for regional richness) and three variable selection methods [forced entry, Akaike information criterion (AIC)-based and a null-model approach]. Covariates included precipitation, temperature, elevation and latitude. For all variables, both linear and quadratic terms were included in the analyses. Results Overall, heterogeneity had a weak effect on species richness and the contribution of the quadratic term of heterogeneity to the explained variance was very small (< 1%). Nevertheless, in all 36 models, the coefficients of both the linear and quadratic terms of heterogeneity were statistically significant and the estimated inflection point was within the range of the data, as predicted by the area–heterogeneity trade-off. Moreover, in 30 out of the 36 models, support for a unimodal effect of heterogeneity on species richness based on information theoretic criteria was strong (ΔAIC > 10), and in 22 of those 30 models the null hypothesis of a monotonically positive relationship could be rejected at the 0.05% significance level. Main conclusions Patterns of bird richness in North America were predominantly consistent with the predictions of the area–heterogeneity trade-off. Future attempts to understand the mechanisms affecting species diversity should pay more attention to the potential consequences of this fundamental trade-off.

    Keywords: BBS, community ecology, elevational range, habitat diversity, land-cover richness, niche theory, species richness


  • Kozhoridze G, Orlovsky N, Orlovsky L, Blumberg D, Golan-Goldhirsh A (2015)

    Geographic distribution and migration pathways of Pistacia - present, past and future

    Ecography 38 001-014.

    The global distribution of Pistacia is correlated to its adaptability to environmental conditions and mechanisms that had driven the genus to the current unique narrow latitudinal belt in between 10° North and 45° North. The current geostatisitcal distribution maps of the genus are shown and the derived probability maps over a period between 121 Kyr before present and the year 2100 were calculated. The tolerance of Pistacia trees to harsh climate conditions was related to leaf phenology, evergreeness vs deciduousness, which has led to geographic classification of the genus in two correspond- ing sections that corroborate recent molecular genetic studies. The deciduous trees are more tolerant to extreme climate conditions (–26°C to 46°C) than the evergreen species (–8°C to 41°C), except Pistacia lentiscus, which occurs at a max. temperature of 45°C. The close spatial distribution of the later species and the deciduous ones may have been conducive in further evolution of the genus. Based on the long evolution of Pistacia (approx. 84 Ma), we suggested that the genus may have originated in the boreal forest and its migration pathways might have been evoked in relation to climate change, shifting the species distribution to evolving suitable environmental conditions. The fact that most of the genera in the family of Anacardiaceae and the whole genus Pistacia are dioecious raised questions about plausible relationships between the geographic distribution, environmental conditions and evolution of dioecy. The genus Pistacia was shown to be a good candidate for research about the relationships between environmental conditions, adaptation traits and geographic distribution.

    Keywords: BBS, community ecology, elevational range, habitat diversity, land-cover richness, niche theory, species richness


  • Horvitz N, Wang R, Zhu M, Wan F, Nathan R (2014)

    A simple modeling approach to elucidate the main transport processes and predict invasive spread: River-mediated invasion of A geratina adenophora in China

    Water Resources Research 50(12) 9738-9747.

    A constantly increasing number of alien species invade novel environments and cause enormous damage to both biodiversity and economics worldwide. This global problem is calling for better understanding of the different mechanisms driving invasive spread, hence quantification of a range of dispersal vectors. Yet, methods for elucidating the mechanisms underlying large-scale invasive spread from empirical patterns have not yet been developed. Here we propose a new computationally efficient method to quantify the contribution of different dispersal vectors to the spread rate of invasive plants. Using data collected over 30 years regarding the invasive species Ageratina adenophora since its detection at the Sichuan province, we explored its spread by wind and animals, rivers, and roads into 153 subcounties in the Sichuan, Chongqingshi, and Hubei provinces of China. We found that rivers are the most plausible vector for the rapid invasion of this species in the study area. Model explorations revealed robustness to changes in key assumptions and configuration. Future predictions of this ongoing invasion process project that the species will quickly spread along the Yangtze River and colonize large areas within a few years. Further model developments would provide a much needed tool to mechanistically and realistically describe large-scale invasive spread, providing insights into the underlying mechanisms and an ability to predict future spatial invasive dynamics.

    Keywords: Ageratina adenophora, biodiversity, biological invasion, dispersal modeling, invasive alien species, spread rate


  • Kent R, Bar-Massada A, Carmel Y (2014)

    Bird and mammal species composition in distinct geographic regions and their relationships with environmental factors across multiple spatial scales

    Ecology and evolution 4(10) 1963-71.

    Global patters of species distributions and their underlying mechanisms are a major question in ecology, and the need for multi-scale analyses has been recognized. Previous studies recognized climate, topography, habitat heterogeneity and disturbance as important variables affecting such patterns. Here we report on analyses of species composition - environment relationships among different taxonomic groups in two continents, and the components of such relationships, in the contiguous USA and Australia. We used partial Canonical Correspondence Analysis of occurrence records of mammals and breeding birds from the Global Biodiversity Information Facility, to quantify relationships between species composition and environmental variables in remote geographic regions at multiple spatial scales, with extents ranging from 10(5) to 10(7) km(2) and sampling grids from 10 to 10,000 km(2). We evaluated the concept that two elements contribute to the impact of environmental variables on composition: the strength of species' affinity to an environmental variable, and the amount of variance in the variable. To disentangle these two elements, we analyzed correlations between resulting trends and the amount of variance contained in different environmental variables to isolate the mechanisms behind the observed relationships. We found that climate and land use-land cover are responsible for most explained variance in species composition, regardless of scale, taxonomic group and geographic region. However, the amount of variance in species composition attributed to land use / land cover (LULC) was closely related to the amount of intrinsic variability in LULC in the USA, but not in Australia, while the effect of climate on species composition was negatively correlated to the variability found in the climatic variables. The low variance in climate, compared to LULC, suggests that species in both taxonomic groups have strong affinity to climate, thus it has a strong effect on species distribution and community composition, while the opposite is true for LULC.

    Keywords: canonical correspondence analysis, environmental determinants, multiple scales


  • Krasnov B, Pilosof S, Shenbrot G, Khokhlova I (2013)

    Spatial variation in the phylogenetic structure of flea assemblages across geographic ranges of small mammalian hosts in the Palearctic.

    International Journal for Parasitology 43(9) 763-70.

    We investigated spatial variation in the phylogenetic structure (measured as a degree of phylogenetic clustering) of flea assemblages across the geographic ranges of 11 Palearctic species of small mammalian hosts and asked whether the phylogenetic structure of the flea assemblage of a host in a locality is affected by (i) distance of this locality from the centre of the host's geographic range, (ii) geographic position of the locality (distance to the equator) and (iii) phylogenetic structure of the entire flea assemblage of the locality. Our results demonstrated that the key factor underlying spatial variation of the phylogenetic structure of the flea assemblage of a host was the distance from the centre of the host's geographic range. However, the pattern of this spatial variation differed between host species and might be explained by their species-specific immunogenetic and/or distributional patterns. Local flea assemblages may also, to some extent, be shaped by environmental filtering coupled with historical events. In addition, the phylogenetic structure of a local within-host flea assemblage may mirror the phylogenetic structure of the entire across-host flea assemblage in that locality and, thus, be affected by the availability of certain phylogenetic lineages.

    Keywords: Animals, Demography, Ectoparasitic Infestations, Ectoparasitic Infestations: epidemiology, Ectoparasitic Infestations: veterinary, Mammals, Phylogeny, Siphonaptera, Siphonaptera: genetics, Siphonaptera: physiology


  • Kent R, Carmel Y (2011)

    Presence-only versus presence-absence data in species composition determinant analyses

    Diversity and Distributions 17(3) 474-479.

    Aim Studying relationships between species and their physical environment requires species distribution data, ideally based on presence–absence (P–A) data derived from surveys. Such data are limited in their spatial extent. Presence-only (P-O) data are considered inappropriate for such analyses. Our aim was to evaluate whether such data may be used when considering a multitude of species over a large spatial extent, in order to analyse the relationships between environmental factors and species composition. Location The study was conducted in virtual space. However, geographic origin of the data used is the contiguous USA. Methods We created distribution maps for 50 virtual species based on actual environmental conditions in the study. Sampling locations were based on true observations from the Global Biodiversity Information Facility. We produced P–A data by selecting ∼1000 random locations and recorded the presence/absence of all species. We produced two P-O data sets. Full P-O set was produced by sampling the species in locations of true occurrences of species. Partial P-O was a subset of full P-O data set matching the size of the P–A data set. For each data set, we recorded the environmental variables at the same locations. We used CCA to evaluate the amount of variance in species composition explained by each variable. We evaluated the bias in the data set by calculating the deviation of average values of the environmental variables in sampled locations compared to the entire area. Results P–A and P-O data sets were similar in terms of the amount of variance explained by the different environmental variables. We found sizable environmental and spatial bias in the P-O data set, compared to the entire study area. Main conclusions Our results suggest that although P-O data from collections contain bias, the multitude of species, and thus the relatively large amount of information in the data, allow the use of P-O data for analysing environmental determinants of species composition.

    Keywords: biodiversity, canonical correspondence analysis, environmental determinants, gbif, simulations, species composition, virtual species


  • Kent R, Bar-Massada A, Carmel Y (2011)

    Multiscale Analyses of Mammal Species Composition – Environment Relationship in the Contiguous USA

    PLoS ONE 6(9) e25440.

    Relationships between species composition and its environmental determinants are a basic objective of ecology. Such relationships are scale dependent, and predictors of species composition typically include variables such as climate, topographic, historical legacies, land uses, human population levels, and random processes. Our objective was to quantify the effect of environmental determinants on U.S. mammal composition at various spatial scales. We found that climate was the predominant factor affecting species composition, and its relative impact increased in correlation with the increase of the spatial scale. Another factor affecting species composition is land-use–land-cover. Our findings showed that its impact decreased as the spatial scale increased. We provide quantitative indication of highly significant effect of climate and land- use–land-cover variables on mammal composition at multiple scales.

    Keyword: species composition patterns