Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Floral evolution by simplification in Monanthotaxis (Annonaceae) and hypotheses for pollination system shifts
Hoekstra, Paul H. ; Wieringa, Jan J. ; Smets, Erik ; Chatrou, Lars W. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
Simplification by reduction has occurred many times independently in the floral evolution of
angiosperms. These reductions have often been attributed to changes in reproductive biology. In the
angiosperm plant family Annonaceae, most species have flowers with six petals, and many stamens and
carpels. In the genus Monanthotaxis several deviations from this pattern have been observed, including
flowers that contain three petals and three stamens only. New DNA sequences were generated for
42 specimens of Monanthotaxis. Five chloroplast markers and two nuclear markers for 72 out of 94
species of Monanthotaxis were used to reconstruct a phylogeny of the genus, which revealed several
well-supported, morphologically distinct clades. The evolution of four quantitative and two qualitative
floral characters was mapped onto this phylogeny, demonstrating a reduction in flower size and number
of flower parts in Monanthotaxis. A large variation in stamen forms and numbers, strong correlations
between petal size, stamen and carpel number, combined with a non-gradual mode of evolution and
the sympatric co-occurrence of Monanthotaxis species from different clades suggest that the high
diversity in the African rainforest of this genus is caused by switches in pollination systems.
Bomen planten op landbouwgrond, wat mag ik? : Handleiding voor agrarisch ondernemers die bomen willen planten op hun bedrijf
Selin Norén, Isabella ; Cuperus, Fogelina ; Kistenkas, F.H. ; Bruil, Willem ; Wieringa, H. ; Schoutsen, M.A. ; Vijn, M.P. ; Sukkel, W. - \ 2018
Wageningen : Wageningen University & Research - 8 p.
What determines plant species diversity in Central Africa?
Proosdij, Andreas S.J. van - \ 2017
University. Promotor(en): Marc Sosef, co-promotor(en): Jan Wieringa. - Wageningen : Wageningen University - ISBN 9789463436618 - 161
plants - biodiversity - species diversity - species - distribution - biogeography - central africa - biosystematics - tropical rain forests - modeling - planten - biodiversiteit - soortendiversiteit - soorten - distributie - biogeografie - centraal-afrika - biosystematiek - tropische regenbossen - modelleren

Planet Earth hosts an incredible biological diversity. Estimated numbers of species occurring on Earth range from 5 to 11 million eukaryotic species including 400,000-450,000 species of plants. Much of this biodiversity remains poorly known and many species have not yet been named or even been discovered. This is not surprising, as the majority of species is known to be rare and ecosystems are generally dominated by a limited number of common species.

Tropical rainforests are the most species-rich terrestrial ecosystems on Earth. The general higher level of species richness is often explained by higher levels of energy near the Equator (latitudinal diversity gradient). However, when comparing tropical rainforest biomes, African rainforests host fewer plant species than either South American or Asian ones. The Central African country of Gabon is situated in the Lower Guinean phytochorical region. It is largely covered by what is considered to be the most species-rich lowland rainforest in Africa while the government supports an active conservation program. As such, Gabon is a perfect study area to address that enigmatic question that has triggered many researchers before: “What determines botanical species richness?”.

In the past 2.5 million years, tropical rainforests have experienced 21 cycles of global glaciations. They responded to this by contracting during drier and cooler glacials into larger montane and smaller riverine forest refugia and expanding again during warmer and wetter interglacials. The current rapid global climate change coupled with change of land use poses new threats to the survival of many rainforest species. The limited availability of resources for conservation forces governments and NGOs to set priorities. Unfortunately, for many plant species, lack of data on their distribution hampers well-informed decision making in conservation.

Species distribution models (SDMs) offer opportunities to bridge at least partly this knowledge gap. SDMs are correlative models that infer the spatial distribution of species using only a limited set of known species occurrence records coupled with high resolution environmental data. SDMs are widely applied to study the past, present and future distribution of species, assess the risk of invasive species, infer patterns of species richness and identify hotspots, as well as to assess the impact of climate change. The currently available methods form a pipeline, with which data are selected and cleaned, models selected, parameterized, evaluated and projected to other areas and climatic scenarios, and biodiversity patterns are computed from these SDMs. In this thesis, SDMs of all Gabonese plant species were generated and patterns of species richness and of weighted endemism were computed (chapter 4 & 5).

Although this pipeline enables the rapid generation of SDMs and inferring of biodiversity patterns, its effective use is limited by several matters of which three are specifically addressed in this thesis. Not knowing the true distribution limits the opportunities to assess the accuracy of models and assess the impact of assumptions and limitations of SDMs. The use of simulated species has been advocated as a method to systematically assess the impact of specific matters of SDMs (virtual ecologist). Following this approach, in chapter 2, I present a novel method to simulate large numbers of species that each have their own unique niche.

One matter of SDMs that is usually ignored but has been shown to be of great impact on model accuracy is the number of species occurrence records used to train a model. In chapter 2, I quantify the effect of sample size on model accuracy for species of different range size classes. The results show that the minimum number of records required to generate accurate SDMs is not uniform for species of every range size class and that larger sample sizes are required for more widespread species. By applying a uniform minimum number of records, SDMs of narrow-ranged species are incorrectly rejected and SDMs of widespread species are incorrectly accepted. Instead, I recommend to identify and apply the unique minimum numbers of required records for each individual species. The method presented here to identify the minimum number of records for species of particular range size classes is applicable to any species group and study area.

The range size or prevalence is an important plant feature that is used in IUCN Red List classifications. It is commonly computed as the Extent Of Occurrence (EOO) and Area Of Occupancy (AOO). Currently, these metrics are computed using methods based on the spatial distribution of the known species occurrences. In chapter 3, using simulated species again, I show that methods based on the distribution of species occurrences in environmental parameter space clearly outperform those based on spatial data. In this chapter, I present a novel method that estimates the range size of a species as the fraction of raster cells within the minimum convex hull of the species occurrences, when all cells from the study area are plotted in environmental parameter space. This novel method outperforms all ten other assessed methods. Therefore, the current use of EOO and AOO based on spatial data alone for the purpose of IUCN Red List classification should be reconsidered. I recommend to use the novel method presented here to estimate the AOO and to estimate the EOO from the predicted distribution based on a thresholded SDM.

In chapter 4, I apply the currently best possible methods to generate accurate SDMs and estimate the range size of species to the large dataset of Gabonese plant species records. All significant SDMs are used here to assess the unique contribution of narrow-ranged, widespread, and randomly selected species to patterns of species richness and weighted endemism. When range sizes of species are defined based on their full range in tropical Africa, random subsets of species best represent the pattern of species richness, followed by narrow-ranged species. Narrow-ranged species best represent the weighted endemism pattern. Moreover, the results show that the applied criterion of widespread and narrow-ranged is crucial. Too often, range sizes of species are computed on their distribution within a study area defined by political borders. I recommend to use the full range size of species instead. Secondly, the use of widespread species, of which often more data are available, as an indicator of diversity patterns should be reconsidered.

The effect of global climate change on the distribution patterns of Gabonese plant species is assed in chapter 5 using SDMs projected to the year 2085 for two climate change scenarios assuming either full or no dispersal. In Gabon, predicted loss of plant species ranges from 5% assuming full dispersal to 10% assuming no dispersal. However, these numbers are likely to be substantially higher, as for many rare, narrow-ranged species no significant SDMs could be generated. Predicted species turnover is as high as 75% and species-rich areas are predicted to loose many species. The explanatory power of individual future climate anomalies to predicted future species richness patterns is quantified. Species loss is best explained by increased precipitation in the dry season. Species gain and species turnover are correlated with a shift from extreme to average values of annual temperature range.

In the final chapter, the results are placed in a wider scientific context. First, the results on the methodological aspects of SDMs and their implications of the SDM pipeline are discussed. The method presented in this thesis to simulate large numbers of species offers opportunities to systematically investigate other matters of the pipeline, some of which are discussed here. Secondly, the factors that shape the current and predicted future patterns of plant species richness in Gabon are discussed including the location of centres of species richness and of weighted endemism in relation to the hypothesized location of glacial forest refugia. Factors that may contribute to the lower species richness of African rainforests compared with South American and Asian forests are discussed. I conclude by reflecting on the conservation of the Gabonese rainforest and its plant species as well as on the opportunities SDMs offer for this in the wider socio-economic context of a changing world with growing demand for food and other ecosystem services.

Naturalized alien flora of the world : Species diversity, taxonomic and phylogenetic patterns, geographic distribution and global hotspots of plant invasion
Pyšek, Petr ; Pergl, Jan ; Essl, Franz ; Lenzner, Bernd ; Dawson, Wayne ; Kreft, Holger ; Weigelt, Patrick ; Winter, Marten ; Kartesz, John ; Nishino, Misako ; Antonova, Liubov A. ; Barcelona, Julie F. ; Cabezas, Francisco J. ; Cárdenas, Dairon ; Cárdenas-Toro, Juliana ; Castaño, Nicolás ; Chacón, Eduardo ; Chatelain, Cyrille ; Dullinger, Stefan ; Ebel, Aleksandr L. ; Figueiredo, Estrela ; Fuentes, Nicol ; Genovesi, Piero ; Groom, Quentin J. ; Henderson, Lesley ; Inderjit, ; Kupriyanov, Andrey ; Masciadri, Silvana ; Maurel, Noëlie ; Meerman, Jan ; Morozova, Olga ; Moser, Dietmar ; Nickrent, Daniel L. ; Nowak, Pauline M. ; Pagad, Shyama ; Patzelt, Annette ; Pelser, Pieter B. ; Seebens, Hanno ; Shu, Wen Sheng ; Thomas, Jacob ; Velayos, Mauricio ; Weber, Ewald ; Wieringa, Jan J. ; Baptiste, María P. ; Kleunen, Mark Van - \ 2017
Preslia 89 (2017)3. - ISSN 0032-7786 - p. 203 - 274.
Alien species - Distribution - Global Naturalized Alien Flora (GloNAF) database - Invasive species - Islands - Life history - Mainland - Naturalized species - Phylogeny - Plant invasion - Regional floras - Species richness - Taxonomy - Zonobiome
Using the recently built Global Naturalized Alien Flora (GloNAF) database, containing data on the distribution of naturalized alien plants in 483 mainland and 361 island regions of the world, we describe patterns in diversity and geographic distribution of naturalized and invasive plant species, taxonomic, phylogenetic and life-history structure of the global naturalized flora as well as levels of naturalization and their determinants. The mainland regions with the highest numbers of naturalized aliens are some Australian states (with New South Wales being the richest on this continent) and several North American regions (of which California with 1753 naturalized plant species represents the world's richest region in terms of naturalized alien vascular plants). England, Japan, New Zealand and the Hawaiian archipelago harbour most naturalized plants among islands or island groups. These regions also form the main hotspots of the regional levels of naturalization, measured as the percentage of naturalized aliens in the total flora of the region. Such hotspots of relative naturalized species richness appear on both the western and eastern coasts of North America, in north-western Europe, South Africa, south-eastern Australia, New Zealand, and India. High levels of island invasions by naturalized plants are concentrated in the Pacific, but also occur on individual islands across all oceans. The numbers of naturalized species are closely correlated with those of native species, with a stronger correlation and steeper increase for islands than mainland regions, indicating a greater vulnerability of islands to invasion by species that become successfully naturalized. South Africa, India, California, Cuba, Florida, Queensland and Japan have the highest numbers of invasive species. Regions in temperate and tropical zonobiomes harbour in total 9036 and 6774 naturalized species, respectively, followed by 3280 species naturalized in the Mediterranean zonobiome, 3057 in the subtropical zonobiome and 321 in the Arctic. The New World is richer in naturalized alien plants, with 9905 species compared to 7923 recorded in the Old World. While isolation is the key factor driving the level of naturalization on islands, zonobiomes differing in climatic regimes, and socioeconomy represented by per capita GDP, are central for mainland regions. The 11 most widely distributed species each occur in regions covering about one third of the globe or more in terms of the number of regions where they are naturalized and at least 35% of the Earth's land surface in terms of those regions' areas, with the most widely distributed species Sonchus oleraceus occuring in 48% of the regions that cover 42% of the world area. Other widely distributed species are Ricinus communis, Oxalis corniculata, Portulaca oleracea, Eleusine indica, Chenopodium album, Capsella bursa-pastoris, Stellaria media, Bidens pilosa, Datura stramonium and Echinochloa crus-galli. Using the occurrence as invasive rather than only naturalized yields a different ranking, with Lantana camara (120 regions out of 349 for which data on invasive status are known), Calotropis procera (118), Eichhornia crassipes (113), Sonchus oleraceus (108) and Leucaena leucocephala (103) on top. As to the life-history spectra, islands harbour more naturalized woody species (34.4%) thanmainland regions (29.5%), and fewer annual herbs (18.7% compared to 22.3%). Ranking families by their absolute numbers of naturalized species reveals that Compositae (1343 species), Poaceae (1267) and Leguminosae (1189) contribute most to the global naturalized alien flora. Some families are disproportionally represented by naturalized aliens on islands (Arecaceae, Araceae, Acanthaceae, Amaryllidaceae, Asparagaceae, Convolvulaceae, Rubiaceae, Malvaceae), and much fewer so on mainland (e.g. Brassicaceae, Caryophyllaceae, Boraginaceae). Relating the numbers of naturalized species in a family to its total global richness shows that some of the large species-rich families are over-represented among naturalized aliens (e.g. Poaceae, Leguminosae, Rosaceae, Amaranthaceae, Pinaceae), some under-represented (e.g. Euphorbiaceae, Rubiaceae), whereas the one richest in naturalized species, Compositae, reaches a value expected from its global species richness. Significant phylogenetic signal indicates that families with an increased potential of their species to naturalize are not distributed randomly on the evolutionary tree. Solanum (112 species), Euphorbia (108) and Carex (106) are the genera richest in terms of naturalized species; over-represented on islands are Cotoneaster, Juncus, Eucalyptus, Salix, Hypericum, Geranium and Persicaria, while those relatively richer in naturalized species on the mainland are Atriplex, Opuntia, Oenothera, Artemisia, Vicia, Galium and Rosa. The data presented in this paper also point to where information is lacking and set priorities for future data collection. The GloNAF database has potential for designing concerted action to fill such data gaps, and provide a basis for allocating resources most efficiently towards better understanding and management of plant invasions worldwide.
Correlated evolutionary rates across genomic compartments in Annonaceae
Hoekstra, Paul H. ; Wieringa, Jan J. ; Smets, Erik ; Brandão, Rita D. ; de Carvalho Lopes, Jenifer ; Erkens, Roy H.J. ; Chatrou, Lars W. - \ 2017
Molecular Phylogenetics and Evolution 114 (2017). - ISSN 1055-7903 - p. 63 - 72.
Annonoideae - Malmeoideae - Nuclear ribosomal DNA - Phylogenetics - Plastid genome - Substitution rates

The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684 bp to 201,723 for Annonoideae and minimal 152,357 to 170,985 bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (dN/dS)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods.

Data from: Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns
Proosdij, A.S.J. van; Raes, N. ; Wieringa, J.J. ; Sosef, M.S.M. - \ 2017
Species Distribution Models, centres of endemism - Species Distribution Models - centres of endemism - biodiversity hotspots - widespread - narrow-ranged - weighted endemism - species richness
In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are overrepresented in species-rich areas. Based on distribution models of Gabonese plant species, we defined sequential subsets from narrow-ranged-to-widespread, widespread-to-narrow-ranged, and 100 randomly arranged species sequences using the range sizes of species in tropical Africa and within Gabon. Along these sequences, correlations between subsets and the total species richness and total weighted endemism patterns were computed. Random species subsets best represent the total species richness pattern, whereas subsets of narrow-ranged species best represent the total weighted endemism pattern. For species ordered according to their range sizes in tropical Africa, subsets of narrow-ranged species represented the total species richness pattern better than widespread species subsets did. However, the opposite was true when range sizes were truncated by the Gabonese national country borders. Correcting for the information content of the subset results in a skew of the sequential correlations, its direction depending on the range-size frequency distribution. Finally, we find a strong, positive, non-linear relation between weighted endemism and total species richness. Observed differences in the contribution of narrow-ranged, widespread and randomly selected species to species richness and weighted endemism patterns can be explained by the range-size frequency distribution and the use of different definitions of widespread or narrow-ranged. We call for a reconsideration of the use of widespread species as an indicator of diversity patterns, and advocate using the full ranges of species when assessing diversity patterns.
Exploring the floristic diversity of tropical Africa
Sosef, Marc S.M. ; Dauby, Gilles ; Blach-Overgaard, Anne ; Burgt, Xander van der; Catarino, Luís ; Damen, Theo ; Deblauwe, Vincent ; Dessein, Steven ; Dransfield, John ; Droissart, Vincent ; Duarte, Maria Cristina ; Engledow, Henry ; Fadeur, Geoffrey ; Figueira, Rui ; Gereau, Roy E. ; Hardy, Olivier J. ; Harris, David J. ; Heij, Janneke de; Janssens, Steven ; Klomberg, Yannick ; Ley, Alexandra C. ; Mackinder, Barbara A. ; Meerts, Pierre ; Poel, Jeike L. van de; Sonké, Bonaventure ; Stévart, Tariq ; Stoffelen, Piet ; Svenning, Jens Christian ; Sepulchre, Pierre ; Zaiss, Rainer ; Wieringa, Jan J. ; Couvreur, Thomas L.P. - \ 2017
BMC Biology 15 (2017)1. - ISSN 1741-7007
Botanical exploration - Digitization - Floristic patterns - Herbarium specimens - Plant growth form - Species richness - Tropical forests
Background: Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa. Results: The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic. Conclusions: The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.
Cutting up the climbers : Evidence for extensive polyphyly in Friesodielsia (annonaceae) necessitates generic realignment across the tribe uvarieae
Guo, Xing ; Hoekstra, Paul H. ; Tang, Chin Cheung ; Thomas, Daniel C. ; Wieringa, Jan J. ; Chatrou, Lars W. ; Saunders, Richard M.K. - \ 2017
Taxon 66 (2017)1. - ISSN 0040-0262 - p. 3 - 19.
Annonaceae - Friesodielsia - Monanthotaxis - Nomenclature - Polyphyly - Taxonomy

Friesodielsia and the closely related genera Dasymaschalon, Desmos, Exellia, Gilbertiella and Monanthotaxis (Annonaceae subfamily Annonoideae tribe Uvarieae) are taxonomically problematic, with obscure generic delimitations and poorly known phylogenetic relationships. The present study addresses the polyphyletic status of Friesodielsia, using two nuclear and five chloroplast DNA regions to resolve this taxonomic confusion by circumscribing strictly monophyletic genera across the tribe. Bayesian, maximum likelihood and maximum parsimony analyses using a broad taxon sampling (101 taxa) reveal that Friesodielsia species form five robust and morphologically distinct clades. In order to ensure strict monophyly of genera, we restrict the generic name Friesodielsia to an exclusively Asian clade, and the African species that were formerly included in the genus are transferred to Afroguatteria, Monanthotaxis and Sphaerocoryne, necessitating ten new nomenclatural combinations. Schefferomitra, a monospecific genus from New Guinea, is shown to be congeneric with Asian Friesodielsia, and the nomenclatural implications of this are discussed. Two monospecific genera, Exellia and Gilbertiella, are furthermore synonymised with Monanthotaxis, necessitating two additional nomenclatural changes. New generic descriptions are provided for Dasymaschalon (ca. 27 species), Desmos (ca. 22 species), Friesodielsia (ca. 38 species) and Monanthotaxis (ca. 94 species) to reflect these revised circumscriptions.

Comparative analysis of spatial genetic structure in an ant-plant symbiosis reveals a tension zone and highlights speciation processes in tropical Africa
Blatrix, Rumsaïs ; Peccoud, Jean ; Born, Céline ; Piatscheck, Finn ; Benoit, Laure ; Sauve, Mathieu ; Djiéto-Lordon, Champlain ; Atteke, Christiane ; Wieringa, Jan J. ; Harris, David J. ; Mckey, Doyle - \ 2017
Journal of Biogeography 44 (2017)8. - ISSN 0305-0270 - p. 1856 - 1868.
Africa - Barteria - Climatic oscillations - Guinea-Congolian rainforest - Incipient speciation - Phylogeography - Pleistocene - Symbiosis - Tension zone - Tetraponera

Aim: Pleistocene climatic oscillations induced range fluctuations in African rain forest organisms and may have shaped species diversification through allopatric speciation events. We compared the spatial genetic structure of two forest species that live in obligate symbiosis and thus must have experienced the same range fluctuations, as a means to discriminate incipient speciation from transient differentiation simply resulting from past divergence. Location: Western central Africa. Methods: We genotyped 765 individuals of the tree Barteria fistulosa and 605 colonies of its symbiotic ant Tetraponera aethiops at 12 and 13 microsatellite loci, respectively. We compared the spatial genetic structure of the two symbionts by using Bayesian clustering algorithms, isolation-by-distance analyses and clines of synthetic alleles. We used species niche modelling (climatic and soil variables) to investigate ecological variables associated with genetic discontinuities in tree populations. Results: The trees and the ants showed congruent patterns of spatial genetic structure. However, the trees showed a very steep genetic discontinuity between groups north and south of latitude 1° N, which was much weaker in the ants. There was no evidence for effective gene flow between the two tree lineages in contact at the transition zone, despite the presence of a few hybrids. Niche modelling did not predict the occurrence of northern trees south of this genetic transition, and vice versa. Main conclusions: The genetic discontinuity near latitude 1° N is inferred to be a tension zone resulting from reproductive incompatibilities between previously allopatric tree lineages. This tension zone may have stabilized at a climatic transition (between boreal and austral seasonal regimes), and matches patterns of genetic structure previously observed in other forest plant species. Our results illustrate independent speciation between two species that live in specific and obligate symbiosis and suggest that a tension zone may separate lineages of several central African forest plants near the thermal equator.

Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns
Proosdij, A.S.J. van; Raes, N. ; Wieringa, J.J. ; Sosef, Marc - \ 2016
PLoS One 11 (2016)2. - ISSN 1932-6203 - 15 p.
In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are overrepresented in species-rich areas. Based on distribution models of Gabonese plant species, we defined sequential subsets from narrow-ranged-to-widespread, widespread-to-narrow-ranged, and 100 randomly arranged species sequences using the range sizes of species in tropical Africa and within Gabon. Along these sequences, correlations between subsets and the total species richness and total weighted endemism patterns were computed. Random species subsets best represent the total species richness pattern, whereas subsets of narrow-ranged species best represent the total weighted endemism pattern. For species ordered according to their range sizes in tropical Africa, subsets of narrow-ranged species represented the total species richness pattern better than widespread species subsets did. However, the opposite was true when range sizes were truncated by the Gabonese national country borders. Correcting for the information content of the subset results in a skew of the sequential correlations, its direction depending on the range-size frequency distribution. Finally, we find a strong, positive, non-linear relation between weighted endemism and total species richness. Observed differences in the contribution of narrow-ranged, widespread and randomly selected species to species richness and weighted endemism patterns can be explained by the range-size frequency distribution and the use of different definitions of widespread or narrow-ranged. We call for a reconsideration of the use of widespread species as an indicator of diversity patterns, and advocate using the full ranges of species when assessing diversity patterns.
A nonet of novel species of Monanthotaxis (Annonaceae) from around Africa
Hoekstra, P.H. ; Wieringa, J.J. ; Chatrou, L.W. - \ 2016
Phytokeys 69 (2016). - ISSN 1314-2011 - p. 71 - 103.
As part of an ongoing revision of the genus Monanthotaxis Baill. (Annonaceae), nine new species are described and one variety is reinstated to species rank. Two new species from West Africa (Monanthotaxis aquila P.H.Hoekstra, sp. nov. and Monanthotaxis atewensis P.H.Hoekstra, sp. nov.), four new species from Central Africa (Monanthotaxis couvreurii P.H.Hoekstra, sp. nov., Monanthotaxis latistamina P.H.Hoekstra, sp. nov., Monanthotaxis tripetala P.H.Hoekstra, sp. nov. and Monanthotaxis zenkeri P.H.Hoekstra, sp. nov.), one new species from Tanzania (Monanthotaxis filipes P.H.Hoekstra, sp. nov.), one new species from the area around Maputo (Monanthotaxis maputensis P.H.Hoekstra, sp. nov.), one new species from the Comoro Islands (Monanthotaxis komorensis P.H.Hoekstra, sp. nov.) and Monanthotaxis klainei (Engl.) Verdc. var. angustifolia (Boutique) Verdc. is raised to species level leading to the replacement name Monanthotaxis atopostema P.H.Hoekstra, nom. nov. (not Monanthotaxis angustifolia (Exell) Verdc.). Complete descriptions, comparisons with related species, ecological information and IUCN conservation assessments are given for the new species. Five species were classified as critical endangered, two species as endangered, one as vulnerable and one as least concern, warranting the need of further collecting and studying those species.
RAINBIO : A mega-database of tropical African vascular plants distributions
Dauby, Gilles ; Zaiss, Rainer ; Blach-Overgaard, Anne ; Catarino, Luís ; Damen, T.H.J. ; Deblauwe, Vincent ; Dessein, Steven ; Dransfield, John ; Droissart, Vincent ; Duarte, Maria Cristina ; Engledow, Henry ; Fadeur, Geoffrey ; Figueira, Rui ; Gereau, Roy E. ; Hardy, Olivier J. ; Harris, David J. ; Heij, Janneke De; Janssens, Steven ; Klomberg, Yannick ; Ley, Alexandra C. ; Mackinder, Barbara A. ; Meerts, Pierre ; Poel, Jeike van de; Sonké, Bonaventure ; Sosef, M.S.M. ; Stévart, Tariq ; Stoffelen, Piet ; Svenning, Jens Christian ; Sepulchre, Pierre ; Burgt, Xander Van Der; Wieringa, J.J. ; Couvreur, T.L.P. - \ 2016
Herbarium specimens - tropical forests - georeferencing - taxonomic backbone - habit - digitization - native species - cultivated species - biodiversity assessment
The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.
RAINBIO : A mega-database of tropical African vascular plants distributions
Dauby, Gilles ; Zaiss, Rainer ; Blach-Overgaard, Anne ; Catarino, Luís ; Damen, Theo ; Deblauwe, Vincent ; Dessein, Steven ; Dransfield, John ; Droissart, Vincent ; Duarte, Maria Cristina ; Engledow, Henry ; Fadeur, Geoffrey ; Figueira, Rui ; Gereau, Roy E. ; Hardy, Olivier J. ; Harris, David J. ; Heij, Janneke de; Janssens, Steven ; Klomberg, Yannick ; Ley, Alexandra C. ; Mackinder, Barbara A. ; Meerts, Pierre ; Poel, Jeike L. van de; Sonké, Bonaventure ; Sosef, Marc S.M. ; Stévart, Tariq ; Stoffelen, Piet ; Svenning, Jens Christian ; Sepulchre, Pierre ; Burgt, Xander van der; Wieringa, Jan J. ; Couvreur, Thomas L.P. - \ 2016
Phytokeys 74 (2016). - ISSN 1314-2011 - p. 1 - 18.
Biodiversity assessment - Cultivated species - Digitization - Georeferencing - Habit - Herbarium specimens - Native species - Taxonomic backbone - Tropical forests

The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

Cognitive performance and iron status are negatively associated with hookworm infection in Cambodian schoolchildren
Kuong, Khov ; Fiorentino, Marion ; Perignon, Marlene ; Chamnan, Chhoun ; Berger, Jacques ; Sinuon, Muth ; Molyden, Vann ; Burja, Kurt ; Parker, Megan ; Ly, Sou Chheng ; Friis, Henrik ; Roos, Nanna ; Wieringa, Frank T. - \ 2016
American Journal of Tropical Medicine and Hygiene 95 (2016)4. - ISSN 0002-9637 - p. 856 - 863.

Soil-transmitted helminth (STH) infection has been associated with lower cognitive performance of schoolchildren. To identify pathways through which STH infection might affect school performance, baseline data from a large rice-fortification trial in Cambodian schoolchildren were used to investigate associations between STH infection, micronutrient status, anemia, and cognitive performance. Complete data on anthropometry, cognitive performance, and micronutrient status were available for 1,760 schoolchildren, 6-16 years of age. STH infection was identified using Kato-Katz, whereas cognitive performance was assessed using Raven's Colored Progressive Matrices (RCPM), block design, and picture completion. STH infection was found in 18% of the children; almost exclusively hookwork infection. After adjusting for age and gender, raw cognitive test scores were significantly lower in hookworminfected children (-0.65; -0.78; -2.03 points for picture completion, RCPM, and block design, respectively; P <0.05 for all). Hookworm infection was associated with iron status (total body iron), but not with vitamin A and zinc status, nor with inflammation or anthropometry. Body iron was negatively associated with increased intensity of hookworm infection (R = 0.22, P <0.001). Hookworm infection in Cambodian schoolchildren was associated with lower cognitive performance, an effect most likely mediated through lower body iron. Interventions that are more effective against hookworm infection are needed to contribute to better health and improvement of cognitive performance.

Large Eddy Simulations of Stably Stratified Turbulence : toward a One-Dimensional Turbulent Potential and Kinetic Energy Parameterization
Rodier, Quentin ; Masson, V. ; Paci, A. ; Steeneveld, G.J. ; Marquet, P. ; Canut, G. - \ 2016
Stably stratified turbulence is observed in stable boundary layer and in the free atmosphere. An appropriate representation of the atmospheric turbulence in stably stratified regime is then crucial to accurately forecast daily weather conditions during night-time and winter. It is also important to better represent momentum transfer in the free tropical troposphere and in highly stably stratified polar boundary layer in climate models. However most numerical weather prediction models currently encounter issues to simulate turbulence at relatively high Richardson number : beyond a critical Richardson number Ric ≈ 0.25, the flow regime turns into a very weak turbulent regime which is not represented by NWP models.
Large eddy simulations of a free atmosphere layer are carried out using the non-hydrostatic mesoscale model Meso-NH developed by the CNRM (Météo-France and CNRS) and the Laboratoire d'Aérologie. For each LES, the free atmosphere layer is initialized by a constant vertical potential temperature gradient and a wind shear. A set of LES is realized with different Ri varying from 0 to 2. An initial potential temperature perturbation is applied. It leads to a stationary stably stratified turbulent regime from which an analysis of the TKE budget and the turbulent structure with respect to the Richardson number is conducted. Convergence issues for extremely stably stratified simulated flow are also discussed.

Starting from the LES, we estimate typical mixing length scales with respect to the static stability using correlation functions of potential temperature and wind variances. These LES and mixing length scales are then used as a reference for the development of a one-dimensional turbulence parameterization using the Energy and Flux Budget (EFB) model described by Zilitinkevich et al. 2013. A preliminary evaluation of a version of the EFB coded in Meso-NH is conducted using nocturnal boundary layer vertical profiles observed with the instrumented Cabauw mast (Van Ulden and Wieringa. 1996)

Further evaluation of the parameterization to the stable boundary layer over complex non-flat terrain will be realized and evaluated using data from the Passy-2015 field campaign conducted in the Northern Alps during the winter of 2014-2015.
Minimum required number of specimen records to develop accurate species distribution models
Proosdij, A.S.J. van; Sosef, M.S.M. ; Wieringa, J.J. ; Raes, N. - \ 2016
Ecography 39 (2016)6. - ISSN 0906-7590 - p. 542 - 552.
Species distribution models (SDMs) are widely used to predict the occurrence of species. Because SDMs generally use presence-only data, validation of the predicted distribution and assessing model accuracy is challenging. Model performance depends on both sample size and species’ prevalence, being the fraction of the study area occupied by the species. Here, we present a novel method using simulated species to identify the minimum number of records required to generate accurate SDMs for taxa of different pre-defined prevalence classes. We quantified model performance as a function of sample size and prevalence and found model performance to increase with increasing sample size under constant prevalence, and to decrease with increasing prevalence under constant sample size. The area under the curve (AUC) is commonly used as a measure of model performance. However, when applied to presence-only data it is prevalence-dependent and hence not an accurate performance index. Testing the AUC of an SDM for significant deviation from random performance provides a good alternative. We assessed the minimum number of records required to obtain good model performance for species of different prevalence classes in a virtual study area and in a real African study area. The lower limit depends on the species’ prevalence with absolute minimum sample sizes as low as 3 for narrow-ranged and 13 for widespread species for our virtual study area which represents an ideal, balanced, orthogonal world. The lower limit of 3, however, is flawed by statistical artefacts related to modelling species with a prevalence below 0.1. In our African study area lower limits are higher, ranging from 14 for narrow-ranged to 25 for widespread species. We advocate identifying the minimum sample size for any species distribution modelling by applying the novel method presented here, which is applicable to any taxonomic clade or group, study area or climate scenario.
Minimum required number of specimen records to develop accurate species distribution models
Proosdij, A.S.J. van; Sosef, M.S.M. ; Wieringa, Jan ; Raes, N. - \ 2015
simulated species - prevalence - AUC - minimum number of records - model performance - null model - species distribution model
Species Distribution Models (SDMs) are widely used to predict the occurrence of species. Because SDMs generally use presence-only data, validation of the predicted distribution and assessing model accuracy is challenging. Model performance depends on both sample size and species’ prevalence, being the fraction of the study area occupied by the species. Here, we present a novel method using simulated species to identify the minimum number of records required to generate accurate SDMs for taxa of different pre-defined prevalence classes. We quantified model performance as a function of sample size and prevalence and found model performance to increase with increasing sample size under constant prevalence, and to decrease with increasing prevalence under constant sample size. The Area Under the Curve (AUC) is commonly used as a measure of model performance. However, when applied to presence-only data it is prevalence-dependent and hence not an accurate performance index. Testing the AUC of an SDM for significant deviation from random performance provides a good alternative. We assessed the minimum number of records required to obtain good model performance for species of different prevalence classes in a virtual study area and in a real African study area. The lower limit depends on the species’ prevalence with absolute minimum sample sizes as low as 3 for narrow-ranged and 13 for widespread species for our virtual study area which represents an ideal, balanced, orthogonal world. The lower limit of 3, however, is flawed by statistical artefacts related to modelling species with a prevalence below 0.1. In our African study area lower limits are higher, ranging from 14 for narrow-ranged to 25 for widespread species. We advocate identifying the minimum sample size for any species distribution modelling by applying the novel method presented here, which is applicable to any taxonomic clade or group, study area or climate scenario.
Global exchange and accumulation of non-native plants
Kleunen, Mark Van; Dawson, Wayne ; Essl, Franz ; Pergl, Jan ; Winter, Marten ; Weber, Ewald ; Kreft, Holger ; Weigelt, Patrick ; Kartesz, John ; Nishino, Misako ; Antonova, Liubov A. ; Barcelona, Julie F. ; Cabezas, Francisco J. ; Cárdenas, Dairon ; Cárdenas-Toro, Juliana ; Castaño, Nicolás ; Chacón, Eduardo ; Chatelain, Cyrille ; Ebel, Aleksandr L. ; Figueiredo, Estrela ; Fuentes, Nicol ; Groom, Quentin J. ; Henderson, Lesley ; Inderjit, ; Kupriyanov, Andrey ; Masciadri, Silvana ; Meerman, Jan ; Morozova, Olga ; Moser, Dietmar ; Nickrent, Daniel L. ; Patzelt, Annette ; Pelser, Pieter B. ; Baptiste, María P. ; Poopath, Manop ; Schulze, Maria ; Seebens, Hanno ; Shu, Wen Sheng ; Thomas, Jacob ; Velayos, Mauricio ; Wieringa, Jan J. ; Pyšek, Petr - \ 2015
Nature 525 (2015)7567. - ISSN 0028-0836 - p. 100 - 103.

All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage. So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.

The Gilbertiodendron ogoouense species complex (Leguminosae : Caesalpinioideae), Central Africa
Burgt, X.M. van der; Mackinder, B.A. ; Wieringa, J.J. ; Estrella, Manuel de la - \ 2015
Kew Bulletin 70 (2015)2. - ISSN 0075-5974
Conservation - Macrolobium - new species - taxonomy

The Gilbertiodendron ogoouense species complex consists of 14 tree species. Eight species are here newly described and one is here reinstated: G. bambolense Burgt; G. breteleri Burgt; G. ebo Burgt & Mackinder; G. ecoukense (Pellegr.) Burgt; G. maximum Burgt & Wieringa; G. minkebense Burgt & Estrella; G. quinquejugum Burgt; G. scutatum Wieringa & Estrella and G. sulfureum Burgt. Five species in the complex were already recognised as accepted: G. brachystegioides (Harms) J. Léonard; G. klainei (Pierre ex Pellegr.) J. Léonard; G. newberyi Burgt; G. ngouniense (Pellegr.) J. Léonard and G. ogoouense (Pellegr.) J. Léonard. All 14 species are medium-sized or large trees of evergreen rain forest on well-drained or periodically inundated soil, at 0 – 900 m altitude. Each of the 14 species is distributed in one or more of the following Central African countries: Cameroon, Equatorial Guinea, Gabon, Congo (Brazzaville), Angola (Cabinda) and Congo (Kinshasa). Included are a key, a table comparing the main morphological characters, illustrations drawn to the same scale and distribution maps of all species. The conservation status of all species is assessed according to IUCN categories and criteria: G. maximum is classified as Critically Endangered, G. ebo and G. newberyi as Endangered, G. breteleri, G. klainei, G. minkebense, G. ngouniense and G. scutatum as Vulnerable, and the remaining six species as Least Concern.

Slimme Winkelwagens: Hoe Realtime Bestedingsfeedback het Winkelgedrag Beinvloedt
Ittersum, K. van; Wansink, B. ; Pennings, J.M.E. ; Sheeman, D. - \ 2015
In: Jaarboek MarktOnderzoekAssociatie : Ontwikkelingen in het Marktonderzoek / Bronner, A.E., Dekker, P., de Leeuw, E., Paas, L.J., de Ruyter, K., Smidts, A., Wieringa, J.E., - p. 95 - 107.
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