Uses of GBIF in scientific research

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

List of publications

  • Stropp J, Ladle R, M. Malhado A, Hortal J, Gaffuri J, H. Temperley W et al. (2016)

    Mapping ignorance: 300 years of collecting flowering plants in Africa

    Global Ecology and Biogeography.

    Aim Spatial and temporal biases in species-occurrence data can compromise broad-scale biogeographical research and conservation planning. Although spatial biases have been frequently scrutinized, temporal biases and the overall quality of species-occurrence data have received far less attention. This study aims to answer three questions: (1) How reliable are species-occurrence data for flowering plants in Africa? (2) Where and when did botanical sampling occur in the past 300 years? (3) How complete are plant inventories for Africa? Location Africa. Methods By filtering a publicly available dataset containing 3.5 million records of flowering plants, we obtained 934,676 herbarium specimens with complete information regarding species name, date and location of collection. Based on these specimens, we estimated inventory completeness for sampling units (SUs) of 25 km × 25 km. We then tested whether the spatial distribution of well-sampled SUs was correlated with temporal parameters of botanical sampling. Finally, we determined whether inventory completeness in individual countries was related to old or recently collected specimens. Results Thirty-one per cent of SUs contained at least one specimen, whereas only 2.4% of SUs contained a sufficient number of specimens to reliably estimate inventory completeness. We found that the location of poorly sampled areas remained almost unchanged for half a century. Moreover, there was pronounced temporal bias towards old specimens in South Africa, the country that holds half of the available data for the continent. There, high inventory completeness stems from specimens collected several decades ago. Main conclusions Despite the increasing availability of species occurrence data for Africa, broad-scale biogeographical research is still compromised by the uncertain quality and spatial and temporal biases of such data. To avoid erroneous inferences, the quality and biases in species-occurrence data should be critically evaluated and quantified prior to use. To this end, we propose a quantification method based on inventory completeness using easily accessible species-occurrence data.

    Keywords: Africa, GBIF, data quality, flowering plants, inventory completeness, spatial and temporal biases, species-occurrence data

  • Ertz D, Diederich P (2015)

    Dismantling Melaspileaceae: a first phylogenetic study of Buelliella, Hemigrapha, Karschia, Labrocarpon and Melaspilea

    Fungal Diversity.

    Melaspileaceae is a heterogeneous group of Ascomycota including lichenized, lichenicolous and saprobic fungi. A first phylogenetic study of Melaspileaceae is presented and is based on mtSSU and nuLSU sequence data. We obtained 49 new sequences for 28 specimens representing 15 species. The genera Buelliella, Hemigrapha, Karschia, Labrocarpon and Melaspilea s. str. are included in a molecular phylogeny for the first time. Melaspileaceae is recovered as polyphyletic, with members placed in two main lineages of Dothideomycetes. Melaspilea s. str. is included in Eremithallales. Eremithallaceae is placed in synonymy with Melaspileaceae. The genus Encephalographa is placed in Melaspileaceae. The genera Buelliella, Karschia, Labrocarpon and several members of Melaspilea are demonstrated to belong to Asterinales, while Hemigrapha is confirmed in this order. The genera Melaspileella, Melaspileopsis, Stictographa are reinstated for former Melaspilea species now placed in Asterinales. Karschia cezannei is described as new, and the new combinations Melaspilea costaricensis, M. enteroleuca, M. urceolata, Melaspileella proximella and Melaspileopsis diplasiospora are made. Melaspileaceae as newly defined includes lichenized and saprobic species. The lichenicolous and saprobic life styles form different intermixed lineages in Asterinales that do not include lichenized taxa. The phylogenetic data provide a first framework for dismantling further the genus Melaspilea for which most of the species are expected to belong to Asterinales.

    Keywords: Asterinales, Eremithallales, Lichenicolous fungi, Phylogeny, Taxonomy

  • Vilaça S, Biosa D, Zachos F, Iacolina L, Kirschning J, Alves P et al. (2014)

    Mitochondrial phylogeography of the European wild boar: the effect of climate on genetic diversity and spatial lineage sorting across Europe

    Journal of Biogeography 41(5) 987-998.

    Aim: Climate changes in the past had a deep impact on the evolutionary history of many species and left genetic signatures that are often still detectable today. We investigated the geographical pattern of mitochondrial DNA divesity in the European wild boar (Sus scrofa). Our final aims were to clarify the influence of present and past climatic conditions, infer the geographical posi- tion of glacial refugia, and suggest post-glacial spatial dynamics. Location: Europe. Methods: D-loop sequences were obtained for 763 individuals from Portugal to western Russia. Phylogenetic, multivariate and interpolation methods were used to describe the genetic and geographical patterns. Climatic suitability during the Last Glacial Maximum (LGM) was predicted using MaxEnt. The effect of present and past suitability on the observed patterns of diversity was evaluated by multiple linear regression. Results: We confirmed the existence of a ubiquitous mitochondrial clade in Europe (E1), an endemic clade in Italy (E2) and a few East Asian haplotypes (A), presumably introgressed from domestic pigs. No Near Eastern haplotypes were detected. Genetic divergence was not simply related to geographical distance. A clear south–north decreasing gradient of diversity was observed, with maximum levels in putative glacial refugia. Latitudinal variation in climatic conditions during the LGM was shown to be a good predictor of current genetic diversity. Moreover, an unexpected similarity between Iberia and east- ern Europe was observed, while central European populations showed a higher affinity to the Italian gene pool. Main conclusions: The current distribution of mitochondrial genetic diversity was highly influenced by past climatic events, especially those related to the LGM, and is consistent with a major contribution of the Italian peninsula and the Balkans to the post-glacial recolonization of northern areas. More recent processes, such as restocking and extensive hunting, probably acted at rather local scales, without great impact on the global pattern of mitochondrial diversity.

    Keywords: Climate change, Last Glacial Maximum, Sus scrofa, genetic differentiation, glacial refugia, mtDNA, phylogeography

  • Gassert F, Schulte U, Husemann M, Ulrich W, Rödder D, Hochkirch A et al. (2013)

    From southern refugia to the northern range margin: genetic population structure of the common wall lizard, Podarcis muralis

    Journal of Biogeography 40(8) 1475-1489.

    Aim Thermophilic species persisted in southern refugia during the cold phases of the Pleistocene, and expanded northwards during warming. These processes caused genetic imprints, such as a differentiation of genetic lineages and a loss of genetic diversity in the wake of (re)colonization. We used molecular markers and species distribution models (SDMs) to study the impact of range dynamics on the common wall lizard, Podarcis muralis, from southern refugia to the northern range margin. Location Parts of the Western Palaearctic. Methods We genotyped 10 polymorphic microsatellites in 282 individuals of P. muralis and sequenced the mitochondrial DNA (mtDNA) cytochrome b gene to study the genetic structure, divergence times and ancestral distribu- tions. Furthermore, we generated SDMs for climate scenarios for 6 and 21 ka derived from two different global circulation models. Results We detected two major mtDNA lineages – a western France clade (Pyrenees to Brittany), and an eastern France clade (southern France to Germany, Belgium and Luxembourg). This split was dated to c. 1.23 Ma. The latter clade was divided into two subclades, which diverged c. 0.38 Ma. Genetic diversity of microsatellites within each clade was nested and showed a significant loss of genetic diversity from south to north, a strong pattern of allele surfing across nearly all loci, and an increase in genetic differentiation towards the northern range margin. Results from SDMs suggest that southward range retraction during the late glacial period split the distribution into geographically distinct refugia. Main conclusions The strong genetic differentiation mirrors the effects of long-term isolation of P. muralis in multiple refugia. Post-glacial recolonization of Northern Europe has taken place from two distinct refugia, most probably along river systems (Rh^ one, Rhine, Moselle) and along the Atlantic coastline, with subsequent nested elimination of genetic diversity and increasing genetic differentiation at the northern range margin.

    Keywords: Climatic oscillations, Europe, genetic structure, leading edge, lizard phylogeography, microsatellites, post-glacial pathways, rear edge, refugia, species distribution models

  • Habel J, Husemann M, Schmitt T, Dapporto L, Rödder D, Vandewoestijne S (2013)

    A forest butterfly in sahara desert oases: isolation does not matter

    The Journal of Heredity 104(2) 234-47.

    Numerous studies addressing the impact of habitat fragmentation on genetic diversity have been performed. In this study, we analyze the effects of a seemingly nonpermeable matrix on the population structure of the forest-dwelling butterfly Pararge aegeria in geographically isolated oases at the northern margin of the Sahara desert using microsatellites, morphological characters, and species distribution modeling. Results from all analyses are mostly congruent and reveal 1) a split between European and North African populations, 2) rather low divergence between populations from the eastern and western part of North Africa (Morocco vs. Tunisia), 3) a lack of differentiation between the oasis and Atlas Mountain populations, 4) as well as among the oasis populations, and 5) no reduction of genetic variability in oasis populations. However, one exception to this general trend resulted from the analyses of wing shape; wings of butterflies from oases are more elongated compared with those from the other habitats. This pattern of phenotypic divergence may suggest a recent colonization of the oasis habitats by individuals, which might be accompanied by a rather dispersive behavior. Species distribution modeling suggests a fairly recent reexpansion of the species' climatic niche starting in the Holocene at about 6000 before present. The combined results indicate a rather recent colonization of the oases by highly mobile individuals from genetically diverse founder populations. The colonization was likely followed by the expansion and persistence of these founder populations under relatively stable environmental conditions. This, together with low rates of gene flow, likely prevented differentiation of populations via drift and led to the maintenance of high genetic diversity.

    Keywords: Pararge aegeria, differentiation, genetic diversity, genitalia, geometric morphometrics, habitat isolation, microsatellites, species distribution modeling, wing morphology

  • Habel J, Engler J, Rödder D, Schmitt T (2011)

    Landscape genetics of a recent population extirpation in a burnet moth species

    Conservation Genetics.

    The intensification of agricultural land use over wide parts of Europe has led to the decline of semi-natural habitats, such as extensively used meadows, with those that remain often being small and isolated. These rapid changes in land use during recent decades have strongly affected populations inhabiting these ecosystems. Increasing habitat deterioration and declining permeability of the surrounding landscape matrix disrupt the gene flow within metapopulations. The burnet moth species Zygaena loti has suffered strongly from recent habitat fragmentation, as reflected by its declining abundance. We have studied its population genetic structure and found a high level of genetic diversity in some of the populations analysed, while others display low genetic diversity and a lack of heterozygosity. Zygaena loti was formerly highly abundant in meadows and along the skirts of forests. However, the species is currently restricted to isolated habitat remnants, which is reflected by the high genetic divergence among populations (F ST: 0.136). Species distribution modelling as well as the spatial examination of panmictic clusters within the study area strongly support a scattered population structure for this species. We suggest that populations with a high level of genetic diversity still represent the former genetic structure of interconnected populations, while populations with low numbers of alleles, high F IS values, and a lack of heterozygosity display the negative effects of reduced interconnectivity. A continuous exchange of individuals is necessary to maintain high genetic variability. Based on these results, we draw the general conclusion that more common taxa with originally large population networks and high genetic diversity suffer stronger from sudden habitat fragmentation than highly specialised species with lower genetic diversity which have persisted in isolated patches for long periods of time.

    Keywords: Allozyme electrophoresis, Habitat fragmentation, Land-use change, Population bottleneck, Species Distribution Modelling, Zygaena loti

  • Habel J, Lens L, Rödder D, Schmitt T (2011)

    From Africa to Europe and back: refugia and range shifts cause high genetic differentiation in the Marbled White butterfly Melanargia galathea

    BMC Evolutionary Biology 11(1) 215.

    BACKGROUND: The glacial-interglacial oscillations caused severe range modifications of biota. Thermophilic species became extinct in the North and survived in southern retreats, e.g. the Mediterranean Basin. These repeated extinction and (re)colonisation events led to long-term isolation and intermixing of populations and thus resulted in strong genetic imprints in many European species therefore being composed of several genetic lineages. To better understand these cycles of repeated expansion and retraction, we selected the Marbled White butterfly Melanargia galathea. Fourty-one populations scattered over Europe and the Maghreb and one population of the sibling taxon M. lachesis were analysed using allozyme electrophoresis. RESULTS: We obtained seven distinct lineages applying neighbour joining and STRUCTURE analyses: (i) Morocco, (ii) Tunisia, (iii) Sicily, (iv) Italy and southern France, (v) eastern Balkans extending to Central Europe, (vi) western Balkans with western Carpathian Basin as well as (vii) south-western Alps. The hierarchy of these splits is well matching the chronology of glacial and interglacial cycles since the Gunz ice age starting with an initial split between the galathea group in North Africa and the lachesis group in Iberia. These genetic structures were compared with past distribution patterns during the last glacial stage calculated with distribution models. CONCLUSIONS: Both methods suggest climatically suitable areas in the Maghreb and the southern European peninsulas with distinct refugia during the last glacial period and underpin strong range expansions to the North during the Postglacial. However, the allozyme patterns reveal biogeographical structures not detected by distribution modelling as two distinct refugia in the Maghreb, two or more distinct refugia at the Balkans and a close link between the eastern Maghreb and Sicily. Furthermore, the genetically highly diverse western Maghreb might have acted as source or speciation centre of this taxon, while the eastern, genetically impoverished Maghreb population might result from a relatively recent recolonisation from Europe via Sicily.

    Keywords: Melanargia galathea, Melanargia lachesis, allozyme electrophoresis, barriers, climate envelope modelling, climatic oscillations, phylogeography

  • Habel J, Rödder D, Stefano S, Meyer M, Schmitt T (2010)

    Strong genetic cohesiveness between Italy and North Africa in four butterfly species

    Biological Journal of the Linnean Society 99 818-830.

    The sea acts as an effective dispersal barrier for most terrestrial animal species. Narrow sea straits, therefore, often represent areas where species are able to disperse from one land mass to another. In the Mediterranean Sea, the narrowest connecting points between North Africa and Europe are the Strait of Gibraltar and the Strait of Sicily. In the past, climatic oscillations caused changing sea levels and thus influenced the permeability of these sea straits. We analysed the genetic structure of four butterfly species that all occur on both sides of the Strait of Sicily. In all four species, we observed a lack of genetic differentiation between the populations of North Africa and those of Italy. Species distribution models support the strong cohesiveness in that they show a largely continuous glacial distribution over Italy and North Africa. The data obtained reveal that there was a large exchange of individuals between Italy and the eastern Maghreb during the last ice age. This might not only be the case for the species under investigation in the present study, but also might represent a more general pattern for mobile thermophilic western Palearctic species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 818–830.

    Keywords: Lycaena phlaeas, Maniola jurtina, Polyommatus icarus, Pyronia cecilia, allozyme electrophoresis, gene flow, genetic differentiation, isolation, species distribution modelling

  • Habel J, Schmitt T, Meyer M, Finger A, Rödder D, Assmann T et al. (2010)

    Biogeography meets conservation: the genetic structure of the endangered lycaenid butterfly Lycaena helle (Denis & Schiffermüller, 1775)

    Biological Journal of the Linnean Society 101(1) 155-168.

    Cold-adapted species are thought to have had their largest distribution ranges in central Europe during the glacial periods. Postglacial warming caused severe range shifts of such taxa into higher latitudes and altitudes. We selected the boreomontane butterfly Lycaena helle (Denis & Schiffermüller, 1775) as an example to demonstrate the genetic effects of range changes, and to document the recent status of highly fragmented remnant populations. We analysed five polymorphic microsatellite loci in 1059 individuals sampled at 50 different localities scattered over the European distribution area of the species. Genetic differentiation was strong among the mountain ranges of western Europe, but we did not detect similarly distinct genetic groups following a geographical pattern in the more eastern areas. The Fennoscandian populations form a separate genetic group, and provide evidence for a colonization from southern Finland via northern Scandinavia to south-central Sweden. Species distribution modelling suggests a large extension of the spatial distribution during the last glacial maximum, but highlights strong retractions to a few mountain areas under current conditions. These findings, combined with our genetic data, suggest a more or less continuous distribution of L. helle throughout central Europe at the end of the last ice age. As a consequence of postglacial warming, the species retreated northwards to Fennoscandia and escaped increasing temperatures through altitudinal shifts. Therefore, the species is today restricted to population remnants located at the mountain tops of western Europe, genetically isolated from each other, and evolved into genetically unique entities. Rising temperatures and advancing habitat destruction threaten this wealth of biodiversity. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 155–168.

    Keywords: Lepidoptera, climate change, fragmentation, microsatellites, mountains, postglacial relict, range shift, species distribution modelling