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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Continental-scale macrofungal assemblage patterns correlate with climate, soil carbon and nitrogen deposition
Andrew, Carrie ; Halvorsen, Rune ; Heegaard, Einar ; Kuijper, Thomas W. ; Heilmann-Clausen, Jacob ; Krisai-Greilhuber, Irmgard ; Bässler, Claus ; Egli, Simon ; Gange, Alan C. ; Høiland, Klaus ; Kirk, Paul M. ; Senn-Irlet, Beatrice ; Boddy, Lynne ; Büntgen, Ulf ; Kauserud, Håvard - \ 2018
Journal of Biogeography 45 (2018)8. - ISSN 0305-0270 - p. 1942 - 1953.
assemblage - biogeography - climate - ectomycorrhizal - Europe - fungi - macroecology - saprotrophic - temporal change

Aim: Macroecological scales of species compositional trends are well documented for a variety of plant and animal groups, but remain sparse for fungi, despite their ecological importance in carbon and nutrient cycling. It is, thus, essential to understand the composition of fungal assemblages across broad geographical scales and the underlying drivers. Our overall aim was to describe these patterns for fungi across two nutritional modes (saprotrophic and ectomycorrhizal). Furthermore, we aimed to elucidate the temporal component of fruiting patterns and to relate these to soil carbon and nitrogen deposition. Location: Central and Northern Europe. Methods: A total of 4.9 million fungal fruit body observations throughout Europe, collected between 1970 and 2010, were analysed to determine the two main environmental and geographical gradients structuring fungal assemblages for two main nutritional modes, saprotrophic and ectomycorrhizal fungi. Results: Two main gradients explaining the geography of compositional patterns were identified, for each nutritional mode. Mean annual temperature (and related collinear, seasonal measures) correlated most strongly with the first gradient for both nutritional modes. Soil organic carbon was the highest correlate of the second compositional gradient for ectomycorrhizal fungi, suspected as an indicator of vegetation- and pH-related covariates. In contrast, nitrogen deposition constituted a second gradient for saprotrophic fungi, likely a proxy for anthropogenic pollution. Compositional gradients and environmental conditions correlated similarly when the data were divided into two time intervals of 1970–1990 and 1991–2010. Evidence of compositional temporal change was highest with increasing elevation and latitude. Main conclusions: Fungal assemblage patterns demonstrate clear biogeographical patterns that relate the nutritional modes to their main environmental correlates of temperature, soil organic carbon and nitrogen deposition. With respect to global change impacts, the highest rates of compositional change by time suggest targeting higher latitudes and elevations for a better understanding of fungal dynamics. We, finally, suggest further examination of the ranges and dispersal abilities of fungi to better assess responses to global change.

Data from: Trait-dependent distributional shifts in fruiting of common British fungi
Gange, A.C. ; Heegaard, E. ; Boddy, L. ; Kirk, P.M. ; Halvorsen, R. ; Kuijper, T.W.M. ; Bässler, C. ; Diez, J. ; Heilman-Clausen, J. ; Høiland, K. ; Büntgen, U. ; Kauserud, H. - \ 2017
fungal ecology - global change biology - community ecology - biogeography - fungi - Agaricomycetes
Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species-specific fungal fruit body abundances have shifted across latitudes over time, using the UK national database of fruiting records. The data employed were recorded over 45 years (1970 – 2014), and include 853,278 records of Agaricales, Boletales and Russulales, though we focus only on the most common species (with more than 3,000 records each). The georeferenced observations were analysed by a Bayesian inference as a Gaussian Additive Model with a specification following a joint species distribution model. We used an offset, random contributions and fixed effects to isolate different potential biases from the trait-specific interactions with latitude/climate and time. Our main aim was assessed by examination of the three-way-interaction of trait, predictor (latitude or climate) and time. The results show a strong trait-specific shift in latitudinal abundance through time, as ECM species have become more abundant relative to saprotrophic species in the north. Along precipitation gradients, phenology was important, in that species with shorter fruiting seasons have declined markedly in abundance in oceanic regions, whereas species with longer seasons have become relatively more common overall. These changes in fruit body distributions are correlated with temperature and rainfall, which act directly on both saprotrophic and ECM fungi, and also indirectly on ECM fungi, through altered photosynthate allocation from their hosts. If these distributional changes reflect fungal activity, there will be important consequences for the responses of forest ecosystems to changing climate, through effects on primary production and nutrient cycling.
What determines plant species diversity in Central Africa?
Proosdij, Andreas S.J. van - \ 2017
Wageningen University. Promotor(en): Marc Sosef, co-promotor(en): N. Raes; 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.

Concealed diversity : taxonomical, phytogeographical and phytosociological notes on brambles (Rubus L. subgen. Rubus) in north-west Europe
Haveman, Rense - \ 2017
Wageningen University. Promotor(en): Joop Schaminee, co-promotor(en): Rienk Jan Bijlsma. - Wageningen : Wageningen University - ISBN 9789463431019 - 200
rubus - diversity - taxonomy - phytogeography - geographical distribution - biogeography - apomixis - northwestern europe - diversiteit - taxonomie - plantengeografie - geografische verdeling - biogeografie - noordwest-europa

Rubus subgen. Rubus (bramble) is one of the large plant genera in Europe, consisting of only a few sexual biological species and at least 700 apomictic lineages. In this thesis, it is argued that the stabilised apomict lineages should best be regarded species, even if their distribution area doesn’t meet the requirements of a regional species as defined in several publications by Weber. Included is a checklist of Dutch bramble species, comprising 191 species belonging to Rubus subgen. Rubus. In the Netherlands, 97 of the 191 species are classified as regional species, with a distribution area diameter under 500 km. On the basis of distribution data of bramble species in Ireland, the UK, Denmark, Germany, and the Netherlands, 12 phytogeographical bramble-regions are distinguished. Although ecological factors play a role in the realisation of these regions, it is argued that the found patterns are primarily the result of evolutionary processes. The density and species composition of Rubus scrubs in the Netherlands is studied using landscape transects. At landscape scale, the bramble species in the scrubs are not randomly distributed, causing a spatial clustering of floristically similar bramble scrubs. It was concluded that only a part of the diversity of Rubus scrubs was accounted for in the Dutch national vegetation classification, and a new scrub type (the Rubetum taxandriae) was described on the basis of these findings. Rubus scrubs are an important biotope for rare shrub species and endemic Rubus species. Additionally, scrubs rich in bramble species are important because they provide foraging and nesting habitats for numerous vertebrates and invertebrates. It is recommended to include the apomict Rubus species in biodiversity accounts, for instance in the national standard list of plant species, as well as the Red List.

Data from: Molecular biogeography of prickly lettuce (Lactuca serriola L.) shows traces of recent range expansion
Andrea, L. D'; Meirmans, Patrick ; Wiel, C.C.M. van de; Guadagnuolo, Roberto ; Treuren, R. van; Kozlowski, Gregor ; Nijs, Hans den; Felber, F. - \ 2016
biogeography - microsatellites - chloroplast PCR-RFLP - population genetics - global change - population structure - phylogeography
Microsatellite data in GenePop format for Lactuca serriola in Europe
The “Umbrella Effect” of the Natura 2000 network : an assessment of species inside and outside the European Natura 2000 protected area network : executive summary
Jones-Walters, L.M. ; Gillings, Simon ; Groen, T.A. ; Hennekens, S.M. ; Noble, David ; Huskens, K. ; Santini, L. ; Sierdsema, H. ; Kleunen, A. van; Swaay, C. van; Sluis, T. van der - \ 2016
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 273A) - 11 p.
biodiversity - natura 2000 - birds directive - habitats directive - biogeography - biodiversiteit - vogelrichtlijn - habitatrichtlijn - biogeografie
BioScore 2 - Plants & Mammals : background and pre-processing of distribution data
Hennekens, S.M. ; Hendriks, J.M. ; Ozinga, W.A. ; Schaminee, J.H.J. ; Santini, L. - \ 2015
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOt-technical report 50) - 221 p.
plants - mammals - biogeography - regression analysis - models - biodiversity - data collection - habitats - planten - zoogdieren - biogeografie - regressieanalyse - modellen - biodiversiteit - gegevens verzamelen
This report highlights the background and pre-processing of the distribution of plant species, habitats and mammal species. For plants a selection of about 900 taxa has been made, based on 45 Annex I habitat types, which represent a substantial part of European natural and semi-natural vegetation. For animals all species existing in Europe have been taken into account. The data covers more or less all EU28 countries and is pre-processed in three steps to feed the BioScore 2 model. In the first step for each species or habitat type a climate/soil model has been created by using Boosted Regression Models (GBM). On the basis of these models presence/absence maps are derived to define the distribution range of the species/habitat types. In the second step additional knowledge was brought in to further specify the potential habitat within the distribution range, by laying an explicit mask over it, selecting only those land use types (land cover classes) suitable for the occurrence of the habitat type or species. In the third step the effect of human-induced pressures on habitat quality and species occurrence/abundance within the suitable habitats in the calculated distribution ranges was taken into account. The dose-effect relations were calculated on the basis of Generalized Linear Models (GLM). All outcomes of the three steps have been further used by the Netherlands Environmental Assessment Agency (PBL) to set up the BioScore 2 model.
Rhyme and reason: plankton changes in the North Sea ecosystem
Alvarez Fernandez, S. - \ 2015
Wageningen University. Promotor(en): Han Lindeboom, co-promotor(en): Erik Meesters. - Wageningen : Wageningen University - ISBN 9789462573321 - 175
plankton - aquatische ecologie - aquatische ecosystemen - zoöplankton - vissen - biogeografie - noordzee - aquatic ecology - aquatic ecosystems - zooplankton - fishes - biogeography - north sea


The North Sea planktonic system is one of the most studied cases of sudden community changes in the marine environment. Continuous Plankton Recorder (CPR) data provided insight into the long-term trends and seasonal patterns of both phytoplankton and zooplankton and their relationships with hydrographical factors as well as climatological events during the last 50 years. A cold episodic event in the late 1970s and a shift towards a warmer community in the late 1980s have been thoroughly described in the literature. Both events have been related to different environmental factors, such as changes in sea surface temperature and Atlantic water inflow through the northern North Sea. This thesis was aimed to achieve a deeper understanding of long term plankton trends in the North Sea, detect more recent changes in the plankton community, and the environmental drivers behind them. The approach taken throughout this research consisted ofanalyzing extensive long term monitoring data in the open North Sea, the Dutch coastal area and the whole north-eastern North Atlantic.

Here we described for the first time a change in the plankton community of the North Sea at the end of the 1990s. This change particularly affected the abundance and seasonal patterns of dinoflgellates and the dominant zooplankton group, the shelf-sea copepods (i.e. Temora longicornis, Pseudocalanus elongatus, Paracalanus sp.). Temperature changes and different water mass composition of the North Sea are suggested as main drivers behind this change.

While looking more in detailed to the plankton trends in the Dutch North Sea waters, we identified an overall C:Chla increase. In coastal waters physiological adaptation to higher light and lower nutrient levels may have enhanced the C:Chlorophyll a, while different processes act in offshore waters. These findings not only indicate the rapidly changing environment in the Dutch coastal zone, but also about the validity of Chlorophyll a as an indicator of phytoplankton biomass trends.

The detected changes in the planktonic system are not the only pelagic changes in the North Sea. We related the changes in plankton abundance and distribution with reported changes in recruitment of North Sea herring, particularly through the predator-prey relationship of some plankton species with pre-metamorphosis larvae. Even though spawning stock biomass has been high during the last decade, recruitment of North Sea herring has decreased since 2002. There were already indications that the early larval stage could be the critical point of development, with reduced survival and growth rates during the 2000s. The analyses presented here showed the abundance of Pseudocalanus sp. during winter to have a strong relationship with larval distribution and abundance later in herring life cycle, suggesting that predator-prey processes, and potentially starvation of first-feeding larvae, are behind the low recruitment in recent years.

These changes in the North Sea pelagic ecosystem are not self-contained, but part of an even larger scale process taking place all across the northeastern Atlantic region. In thisthesis we showed how the changes detected in the North Sea, occurred synchronously in different Atlantic regions. This synchronicity suggests common global trends affecting marine ecosystems. We suggest that rising temperature and changes in oceanic circulation are behind this synchronicity, and that local circumstances, or atmospheric patterns with more local influences, such as North Atlantic Oscillation in the North Sea, modulate the responses of marine ecosystems. In the synthesis the main conclusions of each chapter are put in context together and the importance of zooplankton as a link between primary productivity and higher trophic level consumers is discussed. Furthermore, the importance of monitoring and the correct selection of biological and environmental indicators is also discussed.

The knowledge provided by this doctoral thesis increase our understanding of the processes regulating the plankton community composition in the North Sea (Chapter 1 & 2) and the northeastern Atlantic region (Chapter 4), the potential relationship of plankton community with fish early-stage larvae (Chapter 3) and how environmental changes might affect the relevance of the indicators used to assess the state of the biological system (Chapter 2).

The historical origins of palaeotropical intercontinental disjunctions in the pantropical flowering plant family Annonaceae
Thomas, D.C. ; Chatrou, L.W. ; Stull, G.W. ; Johnson, D.M. ; Harris, D.J. ; Thongpairoj, U. ; Saunders, R.M.K. - \ 2015
Perspectives in plant ecology, evolution and systematics 17 (2015)1. - ISSN 1433-8319 - p. 1 - 16.
long-distance dispersal - out-of-africa - molecular phylogenetics - southeast-asia - northern-hemisphere - vicariance analysis - tropical africa - dna-sequences - biogeography - miocene
Geographic isolation of sister taxa in the African and Asian tropics (palaeotropical intercontinental disjunction; PID) is a major biogeographic pattern explained by four competing hypotheses: rafting on the Indian tectonic plate (‘Gondwanan vicariance hypothesis’); migration facilitated by a northern mid-latitude corridor of frost-free climates during the Eocene (‘boreotropical migration hypothesis’); overland dispersal across Arabia associated with the Miocene Climatic Optimum; and transoceanic dispersal. The explanatory challenges posed by PIDs are addressed here using the pantropical flowering plant family Annonaceae as a study system. Molecular dating and ancestral area reconstructions were undertaken using plastid DNA sequence data (ca. 6 kb) derived from an extensive taxon sampling, incorporating ca. 75% of all genera, with phylogenetically informed sampling of species within genera that are distributed across the African and Asian tropics. Statistical dispersal-vicariance analysis and likelihood reconstructions indicated 12 intercontinental dispersal events between Africa and Asia. All but one of these dispersals were from Africa to Asia. Between 10 and 12 vicariance events were inferred, ranging from the late Palaeocene to the late Miocene, with mean divergence times of seven events in the Miocene. Although migration through the Eocene boreotropics has previously been highlighted as the predominant process underlying intercontinental disjunctions in Annonaceae, our results indicate that post-boreotropical processes have also had a major impact on shaping PIDs. Palaeogeographic reconstructions and the fossil record from the Arabian Peninsula support the plausibility of a hypothesized window of overland dispersal opportunity for lowland tropical forest taxa prior to climate deterioration commencing in the late Middle Miocene, providing an alternative to transoceanic dispersal. The patterns observed underscore the hypothesis that intercontinental floristic exchange, facilitated by both the Eocene boreotropics and the erosion of oceanic and climatic biogeographic barriers between Africa and Asia in the Miocene, had a substantial impact on the assembly of palaeotropical forest floras.
Systematics, evolution and historical biogeography of the family Ochnaceae with emphasis on the genus Campylospermum
Bissiengou, P. - \ 2014
Wageningen University. Promotor(en): Marc Sosef, co-promotor(en): Lars Chatrou; L. Ngok Banak. - Wageningen : Wageningen University - ISBN 9789462572225 - 357
ochnaceae - biosystematiek - taxonomie - evolutie - biogeografie - plantengeografie - fylogenie - taxonomische revisies - fylogenetica - biosystematics - taxonomy - evolution - biogeography - phytogeography - phylogeny - taxonomic revisions - phylogenetics


Ochnaceae s.l. is a family of trees, shrubs or rarely herbs widely distributed in tropical and subtropical forests and savannas of the Old and New World, and has about 500 species in 32 genera. The family is divided into three subfamilies: Medusagynoideae, Quiinoideae and Ochnoideae. We have provided, for the first time, a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogeny backbone of the family using five DNA regions. Based on this, dating analyses were performed using a secondary calibration, and relaxed molecular clock models. The historical biogeography of Ochnaceae s.l. was reconstructed using Dispersal-Vicariance Analysis and Bayesian Binary MCMC. The Neotropics were inferred as being the geographical origin of the family and the Old World was most likely colonized via the North Atlantic Land Bridge during a period when climatic conditions allowed establishment of a boreotropical flora. A full taxonomic revision of the continental African species of the genus Campylospermum has been prepared and additional historical biogeographic analyses were performed with a focus on the genus Campylospermum.

Tracking butterflies for effective conservation
Swaay, C.A.M. van - \ 2014
Wageningen University. Promotor(en): Michiel Wallis de Vries; Marcel Dicke. - Wageningen : Wageningen University - ISBN 9789461739988 - 218
lepidoptera - zoögeografie - biogeografie - populatiedynamica - natuurbescherming - monitoring - nederland - europa - zoogeography - biogeography - population dynamics - nature conservation - netherlands - europe
Dit proefschrift bestaat uit drie delen: het volgen van veranderingen in de verspreiding van vlinders, het volgen van veranderingen in de populatiegrootte van vlinders en hoe deze kennis te gebruiken voor hun bescherming.
Distributional congruence of mammalian herbivores in the Trans-Himalayan Mountains
Namgail, T. ; Wieren, S.E. van; Prins, H.H.T. - \ 2013
Current Zoology 59 (2013)1. - ISSN 1674-5507 - p. 116 - 124.
cross-taxon congruence - species richness - environmental gradients - distribution patterns - iberian peninsula - blue sheep - conservation - ladakh - similarity - biogeography
Large-scale distribution and diversity patterns of mammalian herbivores, especially less charismatic species in alpine environments remain little understood. We studied distributional congruence of mammalian herbivores in the Trans-Himalayan region of Ladakh to see if the distributions of less prominent and smaller herbivores can be determined from those of larger and more prominent herbivores like ungulates. Using a similarity index, we assessed shared distributions of species in 20x20 km2 grid-cells in an area of about 80,000 km2. We used the Unweighted Pair-Group Method with Arithmetic Average (UPGMA) to classify mammalian herbivores into groups with similar distributions. We then used the G-test of independence to look for statistical significance of the groups obtained. We identified six groups of mammalian herbivores with distributions more similar than expected at random. The largest group was composed of nine species whereas the other large group comprised six species. Canonical Correspondence Analysis (CCA), used to relate the groups with environmental features, showed that the largest group occurred in higher and flatter areas, while the other large group occurred in lower and steeper areas. Large herbivores like ungulates can be used as surrogate for less prominent small herbivores while identifying areas for latter’s protection in the inaccessible mountainous regions of the Trans-Himalaya
Community patterns of soil bacteria and nematodes in relation to geographic distance
Monroy, F. ; Putten, W.H. van der; Yergeau, E. ; Duyts, H. ; Mortimer, S.R. ; Bezemer, T.M. - \ 2012
Soil Biology and Biochemistry 45 (2012). - ISSN 0038-0717 - p. 1 - 7.
cooccurrence patterns - microbial communities - global diversity - chalk grassland - spatial scales - biogeography - ecology - microorganisms - biodiversity - gradient
Ecosystems consist of aboveground and belowground subsystems and the structure of their communities is known to change with distance. However, most of this knowledge originates from visible, aboveground components, whereas relatively little is known about how soil community structure varies with distance and if this variability depends on the group of organisms considered. In the present study, we analyzed 30 grasslands from three neighboring chalk hill ridges in southern UK to determine the effect of geographic distance (1–198 km) on the similarity of bacterial communities and of nematode communities in the soil. We found that for both groups, community similarity decayed with distance and that this spatial pattern was not related to changes either in plant community composition or soil chemistry. Site history may have contributed to the observed pattern in the case of nematodes, since the distance effect depended on the presence of different nematode taxa at one of the hill ridges. On the other hand, site-related differences in bacterial community composition alone could not explain the spatial turnover, suggesting that other factors, such as biotic gradients and local dispersal processes that we did not include in our analysis, may be involved in the observed pattern. We conclude that, independently of the variety of causal factors that may be involved, the decay in similarity with geographic distance is a characteristic feature of both communities of soil bacteria and nematodes.
Age structure in neutral theory resolves inconsistencies related to reproductive size threshold
Rosindell, J. ; Jansen, P.A. ; Etienne, R.S. - \ 2012
Journal of Plant Ecology 5 (2012)1. - ISSN 1752-9921 - p. 64 - 71.
species-area relationships - biodiversity - speciation - model - biogeography - limitation - dispersal - diversity - abundance - forests
Neutral theory consists of a suite of models that assume ecological equivalence among individual organisms. They have been most commonly applied to tropical forest tree communities either as null models or as approximations. Neutral models typically only include reproductive adults; therefore, fitting to empirical tree community data requires defining a reproductive-size threshold, which for trees is usually set arbitrarily to a diameter at breast height (DBH) of 100 mm. The inevitable exclusion of some reproductive adults and inclusion of some saplings cause a non-random sampling bias in neutral model fits. Here, we investigate this problem and resolve it by introducing simple age structure into a neutral model.
Testing gradual and speciational models of evolution in extant taxa: the example of ratites
Laurin, M. ; Gussekloo, S.W.S. ; Marjanovic, D. ; Legendre, L. ; Cubo, J. - \ 2012
Journal of Evolutionary Biology 25 (2012)2. - ISSN 1010-061X - p. 293 - 303.
dna genome sequences - fossil record - morphological evidence - divergence times - calibration age - modern birds - aves - biogeography - phylogenies - origin
Ever since Eldredge and Gould proposed their model of punctuated equilibria, evolutionary biologists have debated how often this model is the best description of nature and how important it is compared to the more gradual models of evolution expected from natural selection and the neo-Darwinian paradigm. Recently, Cubo proposed a method to test whether morphological data in extant ratites are more compatible with a gradual or with a speciational model (close to the punctuated equilibrium model). As shown by our simulations, a new method to test the mode of evolution of characters (involving regression of standardized contrasts on their expected standard deviation) is easier to implement and more powerful than the previously proposed method, but the Mesquite module comet (aimed at investigating evolutionary models using comparative data) performs better still. Uncertainties in branch length estimates are probably the largest source of potential error. Cubo hypothesized that heterochronic mechanisms may underlie morphological changes in bone shape during the evolution of ratites. He predicted that the outcome of these changes may be consistent with a speciational model of character evolution because heterochronic changes can be instantaneous in terms of geological time. Analysis of a more extensive data set confirms his prediction despite branch length uncertainties: evolution in ratites has been mostly speciational for shape-related characters. However, it has been mostly gradual for size-related ones.
Modelling concepts in biogeomorphology, results from presentations and discussions sessions of the workshop of 15 February
Riksen, M.J.P.M. ; Groot, A.V. de; Keijsers, J.G.S. ; Poortinga, A. ; Voogt, I.H.A. - \ 2011
Wageningen :
geomorfologie - oeverecosystemen - biogeografie - geomorphology - riparian ecosystems - biogeography
Interactions between vegetation and landscape evolution are a growing field of interest within earth sciences. With processes acting at different spatial and temporal scales, the system’s interactions are often complex. In order to simulate complex process interactions, choices on the approach of model development have to be made
Biodiversity change after climate-induced ice-shelf collapse in the Antarctic
Gutt, J. ; Barratt, I. ; Domack, E. ; Scheidat, M. - \ 2011
Deep-Sea Research. Part II, tropical studies in oceanography 58 (2011)1-2. - ISSN 0967-0645 - p. 74 - 83.
western weddell sea - deep-sea - species-diversity - southern-ocean - 1st insights - ross sea - peninsula - impact - aggregations - biogeography
The marine ecosystem on the eastern shelf of the Antarctic Peninsula was surveyed 5 and 12 years after the climate-induced collapse of the Larsen A and B ice shelves. An impoverished benthic fauna was discovered, that included deep-sea species presumed to be remnants from ice-covered conditions. The current structure of various ecosystem components appears to result from extremely different response rates to the change from an oligotrophic sub-ice-shelf ecosystem to a productive shelf ecosystem. Meiobenthic communities remained impoverished only inside the embayments. On local scales, macro- and mega-epibenthic diversity was generally low, with pioneer species and typical Antarctic megabenthic shelf species interspersed. Antarctic Minke whales and seals utilised the Larsen A/B area to feed on presumably newly established krill and pelagic fish biomass. Ecosystem impacts also extended well beyond the zone of ice-shelf collapse, with areas of high benthic disturbance resulting from scour by icebergs discharged from the Larsen embayments
Biodiversity hotspots on the Dutch Continental Shelf: a marine strategy framework directive perspective
Bos, O.G. ; Witbaard, R. ; Lavaleye, M.S.S. ; Moorsel, G.W.N.M. ; Teal, L.R. ; Hal, R. van; Hammen, T. van der; Hofstede, R. ter; Bemmelen, R.S.A. van; Witte, R.H. ; Geelhoed, S.C.V. ; Dijkman, E.M. - \ 2011
IJmuiden : IMARES (Report / IMARES Wageningen UR C071/11) - 145
biodiversiteit - inventarisaties - bescherming - cartografie - biogeografie - benthos - vis - vogels - zeezoogdieren - habitats - nederland - biodiversity - inventories - protection - mapping - biogeography - fish - birds - marine mammals - netherlands
This report presenst hotspots of biodiversity for benthos, fish, birds, marine mammals and habitats on the Dutch Continental Shelf. These hotspots are based on a spatial application of biodiversity metrics developed in this study for the GES(Good Environmental Status)-descriptor 1 ‘Biological diversity is maintained’ of the Marine Strategy Framework Directive (MSFD) (EU 2008). The choice of the biodiversity metrics is based on the proposed indicators of biodiversity in the Commission Decision (EU 2010). The purpose of this study is to provide insight in possibilities for spatial protection measures in the framework of the MSFD. This report feeds information and ideas into further work for the MSFD in the Netherlands. IMARES has compiled this report for the Dutch Ministry of Economic Affairs, Agriculture and Innovation (Ministry of EL&I) and the Ministry of Infrastructure and the Environment (I&M).
Equilibrium and non-equilibrium concepts in forest genetic modelling: population- and individually-based approaches
Kramer, K. ; Werf, D.C. van der - \ 2010
Forest Systems 19 (2010). - ISSN 2171-5068 - p. 100 - 112.
ecological paradigms - european beech - diversity - dynamics - climate - differentiation - subpopulations - biogeography - management - impact
The environment is changing and so are forests, in their functioning, in species composition, and in the species’ genetic composition. Many empirical and process-based models exist to support forest management. However, most of these models do not consider the impact of environmental changes and forest management on genetic diversity nor on the rate of adaptation of critical plant processes. How genetic diversity and rates of adaptation depend on management actions is a crucial next step in model development. Modelling approaches of genetic and demographic processes that operate in forests are categorized here in two classes. One approach assumes equilibrium conditions in phenotype and tree density, and analyses the characteristics of the demography and the genetic system of the species that determine the rate at which that equilibrium is attained. The other modelling approach does not assume equilibrium conditions and describes both the ecological —and genetic processes to analyse how environmental changes result in selection pressures on functional traits of trees and the consequences of that selection for tree— and ecosystem functioning. The equilibrium approach allows analysing the recovery rate after a perturbation in stable environments, i.e. towards the same pre-perturbation stable state. The nonequilibrium approach allows, in addition to the equilibrium approach, analysing consequences of ongoing environmental changes and forest management, i.e. non-stationary environments, on tree functioning, species composition, and genetic composition of the trees in forest ecosystem. In this paper we describe these two modelling approaches and discuss advantages and disadvantages of them and current knowledge gaps.
Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils
Yergeau, E. ; Bezemer, T.M. ; Hedlund, K. ; Mortimer, S.R. ; Kowalchuk, G.A. ; Putten, W.H. van der - \ 2010
Environmental Microbiology 12 (2010)8. - ISSN 1462-2912 - p. 2096 - 2106.
fatty-acid analysis - bacterial diversity - neighbor matrices - global patterns - ecological data - rhizosphere - protozoa - microorganisms - biogeography - gradient
Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities.
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