94 Works

Eighty-four per cent of all Amazonian arboreal plant individuals are useful to humans

Sara D. Coelho, Carolina Levis, Fabrício B. Baccaro, Fernando O. G. Figueiredo, André Pinassi Antunes, Hans Ter Steege, Marielos Peña-Claros, Juliana Schietti & Charles R. Clement
Plants have been used in Amazonian forests for millennia and some of these plants are disproportionally abundant (hyperdominant). At local scales, people generally use the most abundant plants, which may be abundant as the result of management of indigenous peoples and local communities. However, it is unknown whether plant use is also associated with abundance at larger scales. We used the population sizes of 4,454 arboreal species (trees and palms) estimated from 1946 forest plots...

Dated tree of 24,000 Angiosperms species incl Canary Island colonisation events

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...

Bayesian tip-dated phylogenetics in paleontology: topological effects and stratigraphic fit

Benedict King
The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate, but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several datasets with multiple phylogenetic methods, that topologies produced by tip dating are outliers when compared to...

Data from: The origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the Cretaceous-Paleogene (K-Pg) mass extinction event

Erik Koenen, Dario Ojeda, Freek Bakker, Jan Wieringa, Catherine Kidner, Olivier Hardy, Toby Pennington, Patrick Herendeen, Anne Bruneau & Colin Hughes
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine...

Drivers of amphibian population dynamics and asynchrony at local and regional scales

Hugo Cayuela, Richard A. Griffiths, Nurul Zakaria, Jan W. Arntzen, Pauline Priol, Jean-Paul Léna, Aurélien Besnard & Pierre Joly
Identifying the drivers of population fluctuations in spatially distinct populations remains a significant challenge for ecologists. Whereas regional climatic factors may generate population synchrony (i.e., the Moran effect), local factors including the level of density-dependence may reduce the level of synchrony. Although divergences in the scaling of population synchrony and spatial environmental variation have been observed, the regulatory factors that underlie such mismatches are poorly understood. Few previous studies have investigated how density-dependent processes and...

A genomic footprint of a moving hybrid zone in marbled newts

Jan W. Arntzen, Julia López-Delgado, Isolde Van Riemsdijk & Ben Wielstra
We developed a panel of 44 nuclear genetic markers and applied this to two species of marbled newts in the north (Triturus marmoratus) and the south (T. pygmaeus) of the Iberian Peninsula, to document pattern and process of interspecific gene flow. The northernmost occurrence of T. pygmaeus genetic material was in a T. marmoratus population north of the Vouga river estuary. This suggested the past presence of a hybrid zone, possibly coinciding with a natural...

Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks

Linda Frey, Michael I. Coates, Kristen Tietjen, Martin Rücklin & Christian Klug
We describe the small chondrichthyan Ferromirum oukherbouchi n.gen. et sp. from the Famennian (Late Devonian) of the Maïder region in Morocco. This chondrichthyan is exceptionally well preserved and displays not only mineralized soft tissues but also undeformed cartilages of the head, gills, and shoulder girdle. A reconstruction of the head using 3D-prints revealed a previously unknown kind of jaw articulation. Here, we make the original cropped image stack and PLY-files of the single cartilaginous elements...

Data from: Is the Danube crested newt Triturus dobrogicus polytypic? A review and new nuclear DNA data

Ben Wielstra, Judit Vörös & Jan W. Arntzen
The Danube crested newt Triturus dobrogicus has been proposed to comprise two subspecies: T. d. dobrogicus and T. d. macrosoma. Uncertainty exists in the literature over their distribution and diagnosability. We conduct a multilocus phylogeographical survey and review published data to determine whether a two taxon treatment is warranted. Newly produced and published nuclear DNA data suggest intraspecific variation in the Pannonian Plain part of the range, but with extensive genetic admixture, whereas mitochondrial DNA...

Data from: Scaling up effects of measures mitigating pollinator loss from local- to landscape-level population responses

David Kleijn, Theo E. W. Linders, Anthonie Stip, Jacobus C. Biesmeijer, Felix L. Wäckers & Tibor Bukovinszky
1. Declining pollinator populations have caused concern about consequences for food production, and have initiated an increasing number of initiatives that aim to mitigate pollinator loss through enhancement of floral resources. Studies evaluating effects of mitigation measures generally demonstrate positive responses of pollinators to floral resource enhancement. However, it remains unclear whether this represents landscape-level population effects or results from a spatial redistribution of individuals from otherwise unaffected populations. 2. Here we present a method...

Data from: Minimum required number of specimen records to develop accurate species distribution models

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

Diversification in evolutionary arenas – assessment and synthesis

Nicolai M. Nürk, H. Peter Linder, Renske E. Onstein, Matthew J. Larcombe, Colin E. Hughes, Laura Piñeiro Fernández, Philipp M. Schlüter, Luis Valente, Carl Beierkuhnlein, Vanessa Cutts, Michael J. Donoghue, Erika J. Edwards, Richard Field, Suzette G.A. Flantua, Steven I. Higgins, Anke Jentsch, Sigrid Liede-Schumann & Michael D. Pirie
Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology, ecology and biogeography. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a...

Data from: Genetic pollution of a threatened native crested newt species through hybridization with an invasive congener in the Netherlands

Willem R. M. Meilink, Jan W. Arntzen, Jeroen J. C. W. Van Delft & Ben Wielstra
Genetic pollution of a native species through hybridization with an invasive species poses an insidious conservation threat. To expose genetic pollution, molecular methods employing multilocus data are required. We present a case study of genetic pollution via hybridization of a native crested newt species, Triturus cristatus, by the invasive T. carnifex on the Veluwe in the Netherlands. We sequenced 50 nuclear markers by next generation sequencing and one mitochondrial marker by Sanger sequencing for four...

Data from: Is dispersal guided by the environment? A comparison of interspecific gene flow estimates among differentiated regions of a newt hybrid zone.

Gonçalo Espregueira Themudo, A. M. Nieman & J. W. Arntzen
How frequently genes pass through a hybrid zone may be influenced by the environment. Accordingly, in long hybrid zones that span more than one environmental setting, different patterns may emerge. We reconstruct the amount and direction of gene flow across such a heterogeneous hybrid zone in two species of marbled newts (Triturus marmoratus and T. pygmaeus), in four widely separated areas of the Iberian Peninsula from one mitochondrial and three nuclear genes. The main environmental...

Data from: Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra

Tatiana A. Semenova, Luis N. Morgado, Jeffrey M. Welker, Marilyn D. Walker, Erik Smets & József Geml
Arctic tundra regions have been responding to global warming with visible changes in plant community composition, including expansion of shrubs and declines in lichens and bryophytes. Even though it is well-known that the majority of arctic plants are associated with their symbiotic fungi, how fungal community composition will be different with climate warming remains largely unknown. In this study, we addressed the effects of long-term (18 years) experimental warming on the community composition and taxonomic...

Data from: Phylogeographic analysis reveals northerly refugia for the riverine amphibian Triturus dobrogicus (Caudata: Salamandridae)

Judit Vörös, Peter Mikulíček, Ágnes Major, Ernesto Recuero & Jan W. Arntzen
We investigated the recent evolutionary history of the Danube crested newt, Triturus dobrogicus through reconstructions of: (1) the number and position of refugia at the last glacial maximum, (2) the role of major central European rivers in pattern of post-glacial dispersal, and (3) the present-day distribution pattern. We analysed sequences of mitochondrial DNA (ND2, 1065 bp) and six microsatellite loci in 363 T. dobrogicus individuals from 58 populations covering the range of the species. Our...

Data from: microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

Alysha M. Heimberg, Richard Cowper-Sal·Lari, Marie Sémon, Philip C. J. Donoghue, Kevin J. Peterson & R. Cowper-Sal{Middle Dot}Lari
Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing...

Data from: Beyond the print - virtual paleontology in science publishing, outreach and education

Stephan Lautenschlager & Martin Rücklin
Virtual paleontology unites a variety of computational techniques and methods for the visualization and analysis of fossils. Due to their great potential and increasing availability, these methods have become immensely popular in the last decade. However, communicating the wealth of digital information and results produced by the various techniques is still exacerbated by traditional methods of publication. Transferring and processing three-dimensional information, such as interactive models or animations, into scientific publications still poses a challenge....

Data from: Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol

Jeremy A. Miller, Kevin K. Beentjes, Peter Van Helsdingen, Steven Ijland & Jeremy Miller
We report initial results from an ongoing effort to build a library of DNA barcode sequences for Dutch spiders and investigate the utility of museum collections as a source of specimens for barcoding spiders. Source material for the library comes from a combination of specimens freshly collected in the field specifically for this project and museum specimens collected in the past. For the museum specimens, we focus on 31 species that have been frequently collected...

DiSSCo Prepare Deliverable D8.1 \"Communication and Dissemination Strategy\"

Ana Casino, Céline Cassarino, Marie-Laure Kamatali, Karsten Gödderz, Eva Alonso, Maria Judite Alves, François DUSOULIER & Hilary Goodson
The Communication and Dissemination (C&D) Strategy for DiSSCo Prepare is a supporting instrument to facilitate efficient communication among project partners, strengthen coherence and enlighten the shared vision for external outreach whilst procures and empowers engagement of third parties. The C&D Strategy collates the tools, channels and mechanisms necessary to develop cross-cutting activities throughout the project’s duration and beyond. This document will aim to ensure the most effective information exchange both internally and externally towards external...

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...

Data from: Encroachment of shrubs into subalpine grasslands in the Pyrenees modifies the structure of soil fungal communities and soil properties.

Oriol Grau, Karita Saravesi, Josep M. Ninot, József Geml, Annamari Markkola, Saija H.K. Ahonen & Josep Peñuelas
The encroachment of shrubs into grasslands is common in terrestrial ecosystems dominated by grass. Land abandonment and favourable climatic trends in recent decades have favoured the expansion of shrubs into subalpine grasslands in many mountainous regions across Europe. The advance of the succession from grassland to shrubland is expected to have a major impact on ecosystem functioning. We used DNA metabarcoding to assess whether the structure of soil fungal communities varied along the succession from...

Data from: Drosophila pachea asymmetric lobes are part of a grasping device and stabilize one-sided mating

Flor T. Rhebergen, Virginie Orgogozo, Julien Dumont, Menno Schilthuizen & Michael Lang
Background: Multiple animal species exhibit morphological asymmetries in male genitalia. In insects, left-right genital asymmetries evolved many times independently and have been proposed to appear in response to changes in mating position. However, little is known about the relationship between mating position and the interaction of male and female genitalia during mating, and functional analyses of asymmetric morphologies in genitalia are virtually non-existent. We investigated the relationship between mating position, asymmetric genital morphology and genital...

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: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

Robin Van Velzen, Rens Holmer, Fengjiao Bu, Luuk Rutten, Arjan Van Zeijl, Wei Liu, Luca Santuari, Qingqin Cao, Trupti Sharma, Defeng Shen, Yuda Roswanjaya, Titis A. K. Wardhani, Maryam Seifi Kalhor, Joelle Jansen, D. Johan Van Den Hoogen, Berivan Güngör, Marijke Hartog, Jan Hontelez, Jan Verver, Wei-Cai Yang, Elio Schijlen, Rimi Repin, Menno Schilthuizen, M. Eric Schranz, Renze Heidstra … & Rene Geurts
Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium....

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...

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