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

  • Horvitz N, Wang R, Wan F, Nathan R (2017)

    Pervasive human-mediated large-scale invasion: analysis of spread patterns and their underlying mechanisms in 17 of China's worst invasive plants

    Journal of Ecology 105(1) 85-94.

    Biological invasions constitute a major component of human-induced environmental change and have become a world-wide problem threatening global biodiversity and incurring massive economic costs. Consequently, research on biological invasions proliferates, placing a major emphasis on species traits and habitat characteristics associated with successful invasion. Yet, the mechanisms underlying rapid spread and the resulting patterns remain largely unexplored. Using data collected since 1980 and earlier at the county level all over China, we studied the contribution of potential dispersal vectors – railroads, rail stations, roads, general human activity, rivers and winds – to the spread of 17 of China's worst invasive plant species. Focusing on long-distance dispersal events, we calculated the minimal arrival speed for the first record of each species in each county. We also developed and applied a new method to account for observation bias due to the proximity to roads, using observational data of 776 native (non-invasive) plant species throughout China. We found that human-related vectors are accountable for the vast spread of all 17 invasive plant species we examined. Spread patterns were characterized by long jumps of tens to hundreds of kilometres and extremely fast average spread rates of roughly 2–4 km per year, and a very broad range (0·1–128·2 km per year) with high variability between years. These rates are much higher than those expected from classic dispersal vectors such as water, wind or animals. Commonly used fat-tailed dispersal kernels did not fit the observed distribution of long jumps for any species. Synthesis. We found pervasive empirical evidence for the overriding role of humans in the large-scale spread of invasive plants from multiple taxa. The observed spread patterns differ significantly from those portrayed in the literature, emphasizing the need to develop new frameworks to explore large-scale spread in general and invasive spread in particular. With public data sets of invasive species observations becoming increasingly more available, the time is ripe to go beyond exploration of species traits and habitat suitability and to examine the actual patterns and the mechanisms of large-scale invasive spread, even at a scale of thousands of kilometres over land.

    Keywords: Introduction, dispersal vectors, invasion ecology, invasive species, invasive spread, jump dispersal, long-distance dispersal, minimal arrival speed, plant dispersal, spread pattern

  • 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

  • Ma H, Ge D, Shenbrot G, Pisano J, Yang Q, Zhang Z (2016)

    Hypsodonty of Dipodidae (Rodentia) in Correlation with Diet Preferences and Habitats

    Journal of Mammalian Evolution 1-10.

    The evolution of molar teeth from low-crowned (brachyodont) to high-crowned (hypsodont) has traditionally been recognized as a response to increasing tooth wear due to endogenous (e.g., fiber, silica) and/ or exogenous (e.g., dust, grit) properties of ingested food. Recent work indicates that the mean hypsodonty level of large herbivorous land mammalian communities is a strong predictor of precipitation in their habitats. For small mammals, however, the research is still in an early stage. This study performed comparative studies of hypsodonty on 26 extant dipodid species with and without consideration of phylogeny. The results confirm the role of diet in shaping the cheek tooth crown height in Dipodidae. The significant relationship of investigated environmental variables with hypsodonty may be partly due to phylogenetic effects. Nonetheless, the mean hypsodonty of dipodid communities has significant relationship with regional climatic variables. Hence, the hypsodonty of dipodids also has great potential to be a regional climate proxy.

    Keywords: Climate, DietHabitat, Dipodidae, Hypsodonty, Phylogeny

  • 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

  • Tassia M, Cannon J, Konikoff C, Shenkar N, Halanych K, Swalla B et al. (2016)

    The Global Diversity of Hemichordata

    PLOS ONE 11(10) e0162564.

    Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates. Despite this previous lack of coverage, interest in hemichordates has piqued in the past couple of decades, as they are critical to understanding the evolution of chordates–as acorn worms likely resemble the deuterostome ancestor more closely than any other extant animal. This review provides an overview of our current knowledge of hemichordates, focusing specifically on their global biodiversity, geographic distribution, and taxonomy. Using information available in the World Register of Marine Species and published literature, we assembled a list of 130 described, extant species. The majority (83%) of these species are enteropneusts, and more taxonomic descriptions are forthcoming. Ptychoderidae contained the greatest number of species (41 species), closely followed by Harrimaniidae (40 species), of the recognized hemichordate families. Hemichordates are found throughout the world’s oceans, with the highest reported numbers by regions with marine labs and diligent taxonomic efforts (e.g. North Pacific and North Atlantic). Pterobranchs are abundant in Antarctica, but have also been found at lower latitudes. We consider this a baseline report and expect new species of Hemichordata will continue to be discovered and described as new marine habitats are characterized and explored.

    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

  • Volis S, Tu T, Deng T, Zaretsky M, Fogel K S (2015)

    Phylogeographic study of Mandragora L. reveals a case of ancient human assisted migration

    Israel Journal of Plant Sciences 62(3).

    In reconstructing taxon evolution, historical biogeography is concerned with two kinds of speciation events, both resulting in a fragmented taxon distribution – vicariance and dispersal. We used PCR-RFLP of plastid DNA and a ribosomal internal transcribed spacer, sequencing of the rps16-trnK chloroplast region, flow cytometry (florescence-activated cell sorter; FACS), and ecological niche modeling to understand the role of these two processes in a disjunct distribution of genus Mandragora. The observed phylogeographic structure only partly coincided with currently recognized species. Commonly used recognition of a single species in the whole Mediterranean is not supported, given that a single haplotype observed from Morocco and Spain to Turkey is strikingly different from the haplotypes found in Israel. In the Sino-Himalayan area, the previously recognized M. chinghaiensis is nested within the M. caulescens clade indicating a very recent diversification within this lineage. And, most importantly, the obtained minimum spanning tree, observed haplotype distribution, and results of FACS call into question the existence of M. turkomanica as a species, and even as a lower taxonomic unit. Rather, the mandrake from Central Asia is nested within those from Israel, suggesting their closely related evolutionary history and ancient human assisted migration from Israel to Persia in historic times. Our study suggests that human assisted migration can explain the cases of disjunct species distribution for which vicariance was previously considered as the only plausible explanation.

    Keywords: disjunct distribution, long distance dispe

  • 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