103 Works

Data from: Rapid, habitat-related evolution of land snail colour morphs on reclaimed land

Menno Schilthuizen
I made use of the known dates of reclamation (and of afforestations) in the IJsselmeerpolders in The Netherlands to assess evolutionary adaptation in Cepaea nemoralis. At 12 localities (three in each polder), I sampled a total of 4390 adult individuals in paired open and shaded habitats, on average 233 m apart, and scored these for genetic shell colour polymorphisms. The results show (highly) significant differentiation at most localities, although the genes involved differed per locality....

Data from: Microsatellite analysis of museum specimens reveals historical differences in genetic diversity between declining and more stable Bombus species

Kevin Maebe, Ivan Meeus, Maarten Ganne, Thibaut De Meulemeester, Koos Biesmeijer & Guy Smagghe
Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make...

Data from: Kicking Triturus arntzeni when it’s down: large-scale nuclear genetic data confirm that newts from the type locality are genetically admixed

B. Wielstra & J. W. Arntzen
We collected nuclear DNA data (52 markers) with next-generation sequencing for nine Triturus newt specimens, including the holotype and two of the paratypes of T. arntzeni, from the type locality at Vrtovać in eastern Serbia. We compare these data to a reference set composed of the four crested newt species distributed in eastern Serbia namely T. cristatus, T. dobrogicus, T. ivanbureschi and T. macedonicus to determine to which of these species the newts from the...

Data from: Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth

Tatiana A. Semenova, Luis N. Morgado, Jeffrey M. Welker, Marilyn D. Walker, Erik Smets & József Geml
Climate warming leads to more intensive evaporation from the Arctic sea resulting in increased precipitation in the low Arctic, e.g., higher snowfall during winter. Deeper snow keeps the arctic soils warmer and alters soil attributes and vegetation, e.g., increase in nitrogen availability, expansion of shrubs and decline in shade-intolerant lichens and bryophytes. Changes in soil properties and vegetation are expected to influence on saprotrophic and plant-symbiotic fungi, but how increased snow depth affects their community...

Data from: Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns

Andre S. J. Van Proosdij, Niels Raes, Jan J. Wieringa & Marc S. M. Sosef
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...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Time-calibrated molecular phylogeny of pteropods

Alice K. Burridge, Christine Hörnlein, Arie W. Janssen, Martin Hughes, Stephanie L. Bush, Ferdinand Marlétaz, Rebeca Gasca, Annelies C. Pierrot-Bults, Ellinor Michel, Jonathan A. Todd, Jeremy R. Young, Karen J. Osborn, Steph B.J. Menken, Katja T.C.A. Peijnenburg, Katja T. C. A. Peijnenburg & Steph B. J. Menken
Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and...

Data from: Evolutionary processes, dispersal limitation and climatic history shape current diversity patterns of European dragonflies

Stefan Pinkert, Klaas-Douwe B. Dijkstra, Dirk Zeuss, Christoph Reudenbach, Roland Brandl & Christian Hof
We investigated the effects of contemporary and historical factors on the spatial variation of European dragonfly diversity. Specifically, we tested to what extent patterns of endemism and phylogenetic diversity of European dragonfly assemblages are structured by (i) phylogenetic conservatism of thermal adaptations and (ii) differences in the ability of post-glacial recolonization by species adapted to running waters (lotic) and still waters (lentic). We investigated patterns of dragonfly diversity using digital distribution maps and a phylogeny...

Data from: A signature of dynamic biogeography: enclaves indicate past species replacement

Ben Wielstra, Terence Burke, Roger K. Butlin & J. W. Arntzen
Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted...

Data from: Testing an hypothesis of hybrid zone movement for toads in France

Isolde Van Riemsdijk, Roger K. Butlin, Ben Wielstra, Jan W. Arntzen & Isolde Riemsdijk
Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in...

Data from: Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

Andrea E. Acurio, Flor T. Rhebergen, Sarah E. Paulus, Virginie Courtier-Orgogozo & Michael Lang
Background: Male genitals have repeatedly evolved left-right asymmetries, and the causes of such evolution remain unclear. The Drosophila nannoptera group contains four species, among which three exhibit left-right asymmetries of distinct genital organs. In the most studied species, Drosophila pachea, males display asymmetric genital lobes and they mate right-sided on top of the female. Copulation position of the other species is unknown. Results: To assess whether the evolution of genital asymmetry could be linked to...

First come, first served: possible role for priority effects in marine populations under different degrees of dispersal potential

Christiaan De Leeuw, Katja Peijnenburg, Rosemary Gillespie, Diede Maas, Naoto Hanzawa, Yosephine Tuti, Abdul Toha, Ludi Aji & Leontine Becking
Aim Studying clearly delineated populations in marine lakes, islands of sea, we investigate the interplay of habitat size, immigration, and priority effects in shaping marine population genetic structure. Location Marine lakes and coastal locations in Indonesia, Palau, Papua New-Guinea and Australia. Taxon Mussels (Mytillidae, Brachidontes spp.) Methods Populations were sampled from four coastal locations and 22 marine lakes of similar age (~8,000 years), yet differing in size (0.04 - 4.7 km2) and degree of connection...

DiSSCo Prepare Deliverable D9.2 \"Data Management Plan\"

Dimitris Koureas & Eva Alonso

Modelling the distribution of Amazonian tree species in response to long-term climate change during the mid-late Holocene

Vitor Gomes, Francis Mayle, William Gosling, Ima Vieira, Rafael Salomão & Hans Ter Steege
Aim: To (a) assess the environmental suitability for rainforest tree species of Moraceae and Urticaceae across Amazonia during the Mid-Late Holocene and (b) determine the extent to which their distributions increased in response to long-term climate change over this period. Location: Amazonia. Methods: We used MaxEnt and inverse distance weighting interpolation to produce environmental suitability and relative abundance models at 0.5-degree resolution for tree species of Moraceae and Urticaceae, based on natural history collections and...

Climate-diversity relationships underlying cross-taxon diversity of the Africa fauna and their implications for conservation

Stefan Pinkert, Dirk Zeuss, Viola Clausnitzer, Jens Kipping, Klaas-Douwe B. Dijkstra, Stefan Brunzel & Roland Brandl
Aim: Many taxa show remarkable similarities in their diversity patterns and these similarities are commonly used to define large-scale conservation priorities. Here, we investigated the relative importance of contemporary climate and climate change since the Last Glacial Maximum for determining the species richness and rarity patterns of four animal taxa. We assessed the extent to which diversity patterns are congruent across taxa because of similar responses to these climatic aspects and we identify regions that...

Dark septate endophytes and arbuscular mycorrhizal fungi (Paris-morphotype) affect the stable isotope composition of ‘classically’ non-mycorrhizal plants

Philipp Giesemann, David Eichenberg, Marcus Stöckel, Lukas Seifert, Sofia Gomes, Vincent Merckx & Gerhard Gebauer
The vast majority of terrestrial plants exchange nutrients with fungal partners forming different mycorrhizal types. The minority of plants considered as non-mycorrhizal, however, are not necessarily free of any fungi, but are frequently colonized by elusive fungal endophytes, such as dark septate endophytes (DSE) or fine root endophytes (FRE). While a functional role of FRE in improvement of nutrient gain was recently elucidated, the function of DSE is still in discussion and was here addressed...

Data from: Developmental influence on evolutionary rates and the origin of placental mammal tooth complexity

Aidan Couzens, Karen Sears & Martin Rücklin
This package includes code and data used to build a 'parameter space' from outputs of a reaction-diffusion model of tooth morphogenesis called ToothMaker and then perform simulations of tooth complexity evolution within that parameter space. The datasets include the output of simulations conducted in ToothMaker (required to build the parameter spaces) as well as classification of tooth complexity and pattern data with the parameter space. In addition to the datasets relevant to ToothMaker, the package...

Temporal and palaeoclimatic context of the evolution of insular woodiness in the Canary Islands: Supplementary tables and figures

Alexander Hooft Van Huysduynen & Frederic Lens
Insular woodiness (IW), referring to the evolutionary transition from herbaceousness towards woodiness on islands, has arisen more than 30 times on the Canary Islands (Atlantic Ocean). One of the IW hypotheses suggests that drought has been a major driver of wood formation, but we do not know in which palaeoclimatic conditions the insular woody lineages originated. Therefore, we provided an updated review on the presence of IW on the Canaries, reconstructed the palaeoclimate, and estimated...

Submerged aquatic vegetation, water quality (pH, salinity, and turbidity) and waterfowl abundance data from 1991-2017 in Back Bay, Virginia

Carly Sibilia, Jesús Aguirre-Gutiérrez, Lauren Mowbray & Yadvinder Malhi
Back Bay, Virginia, has been documented as an important foraging area for waterfowl since at least the mid-1800s. Expansive submerged plant beds historically supported diverse assemblages of non-breeding waterfowl, however coastal development and other anthropogenic influences have since led to fluctuations in submerged aquatic vegetation (SAV) and an associated decline in waterfowl abundance in the bay. To gain insight into the effects of environmental drivers on waterfowl foraging guilds, our study explores the effects of...

Data from: Episodic radiations in the fly tree of life

Brian M. Wiegmann, Michelle D. Trautwein, Isaac S. Winkler, Norman B. Barr, Jung-Wook Kim, Christine Lambkin, Matthew A. Bertone, Brian K. Cassel, Keith M. Bayless, Alysha M. Heimberg, Benjamin M. Wheeler, Kevin J. Peterson, Thomas Pape, Bradley J. Sinclair, Jeffrey H. Skevington, Vladimir Blagoderov, Jason Caravas, Sujatha Narayanan Kutty, Urs Schmidt-Ott, Gail E. Kampmeier, F. Christian Thompson, David A. Grimaldi, Andrew T. Beckenbach, Gregory W. Courtney, Markus Friedrich … & J.-W. Kim
Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms,...

Data from: Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient

József Geml, Nicolás Pastor, Lisandro Fernandez, Silvia Pacheco, Tatiana Semenova, Alejandra G. Becerra, Christian Y. Wicaksono, Eduardo R. Nouhra & Tatiana A. Semenova
The Yungas, a system of tropical and subtropical montane forests on the eastern slopes of the Andes, are extremely diverse and severely threatened by anthropogenic pressure and climate change. Previous mycological works focused on macrofungi (e.g., agarics, polypores) and mycorrhizae in Alnus acuminata forests, while fungal diversity in other parts of the Yungas has remained mostly unexplored. We carried out Ion Torrent sequencing of ITS2 rDNA from soil samples taken at 24 sites along the...

Data from: Global biogeography and evolution of Cuvierina pteropods

Alice K. Burridge, Erica Goetze, Niels Raes, Jef Huisman & Katja T. C. A. Peijnenburg
Background: Shelled pteropods are planktonic gastropods that are potentially good indicators of the effects of ocean acidification. They also have high potential for the study of zooplankton evolution because they are metazoan plankton with a good fossil record. We investigated phenotypic and genetic variation in pteropods belonging to the genus Cuvierina in relation to their biogeographic distribution across the world’s oceans. We aimed to assess species boundaries and to reconstruct their evolutionary history. Results: We...

Data from: Fast adaptive responses in the oral jaw of Lake Victoria cichlids

Jacco C. Van Rijssel, Ellen S. Hoogwater, Mary A. Kishe-Machumu, Elize Van Reenen, Kevin V. Spits, Ronald C. Van Der Stelt, Jan H. Wanink & Frans Witte
Rapid morphological changes in response to fluctuating natural environments are a common phenomenon in species that undergo adaptive radiation. The dramatic ecological changes in Lake Victoria provide a unique opportunity to study environmental effects on cichlid morphology. This study shows how four haplochromine cichlids adapted their premaxilla to a changed diet over the past 30 years. Directly after the diet change toward larger and faster prey in the late 1980s, the premaxilla (upper jaw) changed...

Data from: Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

Ben Wielstra, Jan W. Arntzen, Kristiaan J. Van Der Gaag, Maciej Pabijan & Wieslaw Babik
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns...

Data from: DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep

Abdolbaset Ghorbani, Barbara Gravendeel, Sugirthini Selliah, Shahin Zarré & Hugo De Boer
Tubers of terrestrial orchids are harvested and traded from the eastern Mediterranean to the Caspian Sea for the traditional product Salep. Overexploitation of wild populations and increased middle-class prosperity have escalated prices for Salep, causing overharvesting, depletion of native populations and providing an incentive to expand harvesting to untapped areas in Iran. Limited morphological distinctiveness among traded Salep tubers renders species identification impossible, making it difficult to establish which species are targeted and affected the...

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  • Naturalis Biodiversity Center
  • Leiden University
  • Wageningen University & Research
  • University of Sheffield
  • Meise Botanic Garden
  • Royal Botanic Garden Edinburgh
  • Botanischer Garten und Botanisches Museum Berlin
  • Smithsonian Institution
  • University of Zurich
  • Natural History Museum