117 Works

Data from: Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence?

Hendrik Breitkopf, Philipp M. Schlüter, Shuqing Xu, Florian P. Schiestl, Salvatore Cozzolino & Giovanni Scopece
Local adaptation to different pollinators is considered one of the possible initial stages of ecological speciation as reproductive isolation is a by-product of the divergence in pollination systems. However, pollinator-mediated divergent selection will not necessarily result in complete reproductive isolation, because incipient speciation is often overcome by gene flow. We investigated the potential of pollinator shift in the sexually deceptive orchids Ophrys sphegodes and Ophrys exaltata and compared the levels of floral isolation vs. genetic...

Data from: Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation

Kathleen R. Stoof-Leichsenring, Laura S. Epp, Martin H. Trauth & Ralph Tiedemann
This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (76-67 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by...

Data from: A question of time: the land snail Murella muralis (Gastropoda: Pulmonata) reveals constrains to past ecological speciation

Viviana Fiorentino, Giuseppe Manganelli, Folco Giusti, Ralph Tiedemann & Valerio Ketmaier
The lively debate about speciation currently focuses on the relative importance of factors driving population differentiation. While many studies are increasingly producing results on the importance of selection, little is known about the interaction between drift and selection. Moreover there is still little knowledge on the spatial-temporal scales at which speciation occurs, i.e. arrangement of habitat patches, abruptness of habitat transitions, climate and habitat changes interacting with selective forces. To investigate these questions, we quantified...

Intraspecific trait variation alters the outcome of competition in freshwater ciliates

Sabine Floeder, Joanne Yong, Toni Klauschies, Ursula Gaedke, Tobias Poprick, Thorsten Brinkhoff & Stefanie Moorthi
Trait variation among heterospecific and conspecific organisms may substantially affect community and food web dynamics. While the relevance of competition and feeding traits have been widely studied for different consumer species, studies on intraspecific differences are more scarce, partly owing to difficulties in distinguishing different clones of the same species. Here, we investigate how intraspecific trait variation affects the competition between the freshwater ciliates Euplotes octocarinatus and Coleps hirtus in a nitrogen-limited chemostat system. The...

Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions

Sandra Kahl, Christian Kappel, Jasmin Joshi & Michael Lenhard
To predict how widely distributed species will perform under future climate change it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the...

3D Neutron Computed Laminography of Maize Plants

Nicole Rudolph-Mohr, Sarah Bereswill, Christian Tötzke, Nikolay Kardjilov & Sascha E. Oswald
Plant root systems induce biogeochemical patterns in the soil by respiration, water uptake and root exudation that can be measured with in-situ imaging techniques. Slab-shaped rhizoboxes represent the optimum design for 2D optical fluorescence imaging of pH and oxygen dynamics in the rhizosphere as well as measurement of soil water content by neutron radiography. However, quality of standard tomographic (3D) imaging of laterally extended samples suffers from insufficient neutron transmission over a significant angular range....

Data from: Spatial and temporal aridity gradients provide poor proxies for plant-plant interactions under climate change: a large-scale experiment

Johannes Metz & Katja Tielbörger
1. Plant-plant interactions may critically modify the impact of climate change on plant communities. However, the magnitude and even direction of potential future interactions remains highly debated, especially for water limited ecosystems. Predictions range from increasing facilitation to increasing competition with future aridification. 2. The different methodologies used for assessing plant-plant interactions under changing environmental conditions may affect the outcome but they are not equally represented in the literature. Mechanistic experimental manipulations are rare compared...

Data from: Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax

Samantha V. Beck, Gary R. Carvalho, Axel Barlow, Lukas Rüber, Heok Hui Tan, Estu Nugroho, Daisy Wowor, Siti Azizah Mohd Nor, Fabian Herder, Zainal A. Muchlisin & Mark De Bruyn
The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have...

Data from: A Western route of prehistoric human migration from Africa into the Iberian Peninsula

Gloria Gonzalez-Fortes, Francesca Tassi, Emiliano Trucchi, Kirstin Henneberger, Johanna L.A. Paijmans, Daviz Diez-Del-Molino, Hannes Schroeder, Cecilio Barroso, Francisco J. Bermudez, Cecilio Barroso-Medina, Ana M.S. Bettencourt, Hugo A. Sampaio, Aurora Grandal-D'Anglade, Antonio Salas, Arturo De Lombera-Hermida, Ramon Fabregas, Manuel Vaquero, Susana Alonso, Maria Lozano, Xavier Rodríguez-Alvarez, Carlos Fernández-Rodríguez, Andrea Manica, Michael Hofreiter & Guido Barbujani
Being at the Western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from...

Data from: Parasitoid gene expression changes after adaptation to symbiont-protected hosts

Alice B. Dennis, Vilas Patel, Kerry M. Oliver & Christoph Vorburger
Reciprocal selection between aphids, their protective endosymbionts, and the parasitoid wasps that prey upon them offers an opportunity to study the basis of their coevolution. We investigated adaptation to symbiont-conferred defense by rearing the parasitoid wasp Lysiphlebus fabarum on aphids (Aphis fabae) possessing different defensive symbiont strains (Hamiltonella defensa). After ten generations of experimental evolution, wasps showed increased abilities to parasitize aphids possessing the H. defensa strain they evolved with, but not aphids possessing the...

Data from: Simulation of the nodal flow of mutant embryos with small number of cilia: comparison of mechanosensing and vesicle transport hypotheses

Toshihiro Omori, Katja Winter, Kyosuke Shinohara, Hiroshi Hamada & Takuji Ishikawa
Left-right (L-R) asymmetry in the body plan is determined by nodal flow in vertebrate embryos. Shinohara et al. used Dpcd and Rfx3 mutant mouse embryos and showed that only a few cilia were sufficient to achieve L-R asymmetry. However, the mechanism underlying the breaking of symmetry by such weak ciliary flow is unclear. The flow-mediated signals related to L-R asymmetry have not been clarified; there are two models for L-R symmetry breaking: vesicle transport and...

Data from: Partial genomic survival of cave bears in living brown bears

Axel Barlow, James A. Cahill, Stefanie Hartmann, Christoph Theunert, Georgios Xenikoudakis, Gloria G. Fortes, Johanna L. A. Paijmans, Gernot Rabeder, Christine Frischauf, Aurora Grandal-D'Anglade, Ana García-Vázquez, Marine Murtskhvaladze, Urmas Saarma, Peeter Anijalg, Tomaž Skrbinšek, Giorgio Bertorelle, Boris Gasparian, Guy Bar-Oz, Ron Pinhasi, Montgomery Slatkin, Love Dalén, Beth Shapiro & Michael Hofreiter
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the...

Data from: Genetic identity and herbivory drive the invasion of a common aquatic microbial invader - phytoplankton and zooplankton abundance

Sarah Bolius, Karoline Morling, Claudia Wiedner & Guntram Weithoff
Despite the increasing number of species invasions, the factors driving invasiveness are still under debate. This is particularly the case for ‘invisible’ invasions by aquatic microbial species. Since in many cases only a few individuals or propagules enter a new habitat, their genetic variation is low and might limit their invasion success, known as the genetic bottleneck. Thus, a key question is, how genetic identity and diversity of invading species influences their invasion success and,...

Fluorescent (C)LSM image sequences of Dictyostelium discoideum (Ax2 - LifeAct mRFP) for cell track and cell contour analysis

Maike Stange, Ted Moldenhawer & Carsten Beta
This data set is designed for cell contour and cell track analysis. Hence image sequences of moving Dictyostelium discoideum cells are recorded. For the purpose to facilitate the detection of the cell contour we take fluorescent images of the cortical protein actin to obtain a high contrast between background and cell body. In each image sequences several cells are recorded. This allows for an analysis of all cells at once or to crop single cell...

Globally, plant-soil feedbacks are weak predictors of plant abundance

Kurt Reinhart, Jonathan Bauer, Sarah McCarthy-Neumann, Andrew MacDougall, José Hierro, Mariana Chiuffo, Scott Mangan, Johannes Heinze, Joana Bergmann, Jasmin Joshi, Richard Duncan, Jeff Diaz, Paul Kardol, Gemma Rutten, Markus Fischer, Wim Van Der Putten, T. Bezemer & John Klironomos
Plant-soil feedbacks (PSFs) have been shown to strongly affect plant performance under controlled conditions, and PSFs are thought to have far reaching consequences for plant population dynamics and the structuring of plant communities. However, thus far the relationship between PSF and plant species abundance in the field is not consistent. Here, we synthesize PSF experiments from tropical forests to semiarid grasslands, and test for a positive relationship between plant abundance in the field and PSFs...

Bee diversity in island-like habitats (kettle holes) to assess connectivity in agricultural landscapes - Part 1 of data collection

Sissi Lozada-Gobilard
During June and July of 2017, wild bees were collected using color traps (blue, yellow and white pans) in small water bodies called kettle holes embedded in agricultural landscapes in the north of Germany. After all wild bees were identified to species level, from a subset of samples we measured the Intertegular distance ITD (distance between the wings) as body size and searched for functional traits regarding sociality (solitary, eusocial, parasitic) nesting type (below- or...

EFFECTS OF MICROPLASTICS AND DROUGHT ON SOIL ECOSYSTEM FUNCTIONS AND MULTIFUNCTIONALITY

Yudi M. Lozano, Carlos A. Aguilar-Trigueros, Gabriela Onandia, Stefanie Maaß, Tingting Zhao & Matthias C. Rillig
Microplastics in soils have become an important threat for terrestrial systems as they may potentially alter the geochemical/biophysical soil environment and can interact with drought. As microplastics may affect soil water content, this could exacerbate the well-known negative effects of drought on ecosystem functionality. Thus, functions including litter decomposition, soil aggregation or those related with nutrient cycling can be altered. Despite this potential interaction, we know relatively little about how microplastics, under different soil water...

DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity

Katrin Kiemel, Guntram Weithoff & Ralph Tiedemann
Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor...

Hayabusa2 Thermal Infrared Imager (TIR) Bundle

Tatsuaki Okada, Satoshi Tanaka, Tetsuya Fukuhara, Takehiko Arai, Takeshi Imamura, Yoshiko Ogawa, Kohei Kitazato, Toru Kouyama, Naoya Sakatani, Yuri Shimaki, Tomohiko Sekiguchi, Hiroki Senshu, Jun Takita, Makoto Taguchi, Hirohide Demura, Ryosuke Nakamura, Sunao Hasegawa, Tsuneo Matsunaga, Takehiko Wada, Jörn Helbert, Thomas G. Müller, Axel Hagermann, Jens Biele, Matthias Grott, Maximilian Hamm … & Marco Delbo
This PDS4 bundle collects all the operational data products produced by the Hayabusa2 TIR instrument.

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Kristýna Eliášová, José Ignacio Lucas Lledó, José Horacio Grau, Miroslava Loudová, Anna A. Bannikova, Katerina I. Zolotareva, Vladimír Beneš, Pavel Hulva & Barbora Černá Bolfíková
Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study...

Data and R code from \"Grazing and ecosystem service delivery in global drylands\"

Fernando T. Maestre, Yoann Le Bagousse-Pinguet, David Eldridge, Hugo Saiz, Enrique Valencia, Miguel Berdugo, juan gaitan, Nicolas GROSS, Beatriz Gozalo, Victoria Ochoa, Miguel García-Gómez, Sergio Asensio, Betty J. Mendoza, César Plaza, Paloma Díaz-Martínez, Ana Rey, HANG-WEI HU, Ji-Zheng He, Anika Lehmann, Matthias C. Rillig, Simone Cesarz, Nico Eisenhauer, Eduardo Moreno Jiménez, Osvaldo E. Sala, Mehdi Abedi … & Biodesert consortium
There are two zip files with the data and R scripts used in the article "Grazing and ecosystem service delivery in global drylands".
The file "Main_Data_code.zip" contains the data and R code used in the main analyses of the paper. These data also include the location and major environmental characteristics of the plots surveyed.
The file "Livestock_data_code.zip" contains the data and R code used in the characterization and validation of grazing pressure levels (see Methods)....

Data from: De novo assembly and characterization of the skeletal muscle and electric organ transcriptomes of the African weakly-electric fish Campylomormyrus compressirostris (Mormyridae, Teleostei)

Francesco Lamanna, Frank Kirschbaum & Ralph Tiedemann
African weakly electric-fishes (Mormyridae) underwent an outstanding adaptive radiation (about 200 species), putatively owing to their ability to communicate through species-specific weak electric signals. The electric organ discharge (EOD) is produced by muscle-derived electrocytes organized in piles to form an electric organ. Despite the importance of this trait as a pre-zygotic isolation mechanism, genomic resources remained limited. We present here a first draft of the skeletal muscle and electric organ transcriptomes from the weakly-electric fish...

Data from: Are gastropods, rather than ants, important dispersers of seeds of myrmecochorous forest herbs?

Manfred Türke, Kerstin Andreas, Martin M. Gossner, Esther Kowalski, Markus Lange, Steffen Boch, Stephanie A. Socher, Jörg Müller, Daniel Prati, Markus Fischer, Rainer Meyhöfer & Wolfgang W. Weisser
Seed dispersal by ants (myrmecochory) is widespread and seed adaptations to myrmecochory are common, especially in the form of fatty appendices (elaiosomes). In a recent study, slugs were identified as seed dispersers of myrmecochores in a Central European beech forest. Here we used 105 beech forest sites to test whether myrmecochore presence and abundance is related to ant or to gastropod abundance and whether experimentally exposed seeds are removed by gastropods. Myrmecochorous plant cover was...

Data from: Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data

Stefanie Hartmann, Conrad Helm, Birgit Nickel, Matthias Meyer, Torsten H. Struck, Ralph Tiedemann, Joachim Selbig & Christoph Bleidorn
BACKGROUND: In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree...

Data from: Seed dispersal by ungulates as an ecological filter: a trait-based meta-analysis

Aurélie Albert, Alistair G. Auffret, Eric Cosyns, Sara A. O. Cousins, Bram D'Hondt, Carsten Eichberg, Amy E. Eycott, Thilo Heinken, Maurice Hoffmann, Bogdan Jaroszewicz, Juan E. Malo, Anders Mårell, Maarten Mouissie, Robin J. Pakeman, Mélanie Picard, Jan Plue, Peter Poschlod, Sam Provoost, Kiowa Alraune Schulze & Christophe Baltzinger
Plant communities are often dispersal-limited and zoochory can be an efficient mechanism for plants to colonize new patches of potentially suitable habitat. We predicted that seed dispersal by ungulates acts as an ecological filter – which differentially affects individuals according to their characteristics and shapes species assemblages – and that the filter varies according to the dispersal mechanism (endozoochory, fur-epizoochory and hoof-epizoochory). We conducted two-step individual participant data meta-analyses of 52 studies on plant dispersal...

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