105 Works

Data from: Strong and consistent natural selection associated with armour reduction in sticklebacks

Arnaud Le Rouzic, Kjartan Østbye, Tom O. Klepaker, Thomas F. Hansen, Louis Bernatchez, Dolph Schluter & Leif Asbjørn Vøllestad
Measuring the strength of natural selection is tremendously important in evolutionary biology, but remains a challenging task. In this work, we analyse the characteristics of selection for a morphological change (lateral-plate reduction) in the threespine stickleback Gasterosteus aculeatus. Adaptation to freshwater, leading to the reduction or loss of the bony lateral armor, has indeed occurred in parallel on numerous occasions in this species. Completely-plated and low-plated sticklebacks were introduced into a pond, and the phenotypic...

Data from: Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

Sofia A. V. Fortunato, Marcin Adamski, Olivia Mendivil Ramos, Sven Leininger, Jing Liu, David E. K. Ferrier & Maja Adamska
Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors1, 2, 3, 4, including homeobox genes belonging to the Antennapedia (ANTP) class5, 6, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians5. It has...

Data from: Taxonomy, biogeography and DNA barcodes of Geodia species (Porifera, Demospongiae, Tetractinellida) in the Atlantic boreo-arctic region

Paco Cárdenas, Hans Tore Rapp, Anne Birgitte Klitgaard, Megan Best, Mikael Thollesson & Ole Secher Tendal
Geodia species north of 60°N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G. macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G. simplex, Isops phlegraei, I. pallida, I. sphaeroides, Synops pyriformis, G. parva, G. normani, G. atlantica, Sidonops mesotriaena (now called G. hentscheli), and G. simplicissima. In addition to these...

Data from: Evolutionary origin of the Scombridae (tunas and mackerels): members of a Paleogene adaptive radiation with 14 other pelagic fish families

Masaki Miya, Matt Friedman, Takashi P. Satoh, Hirohiko Takeshima, Tetsuya Sado, Wataru Iwasaki, Yusuke Yamanoue, Masanori Nakatani, Kohji Mabuchi, Jun G. Inoue, Jan Yde Poulsen, Tsukasa Fukunaga, Yukuto Sato & Mutsumi Nishida
Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and...

Data from: Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

Eric C. Anderson, Hans J. Skaug & Daniel J. Barshis
We develop a model based on the Dirichlet-compound multinomial distribution (CMD) and Ewens sampling formula to predict the fraction of SNP loci that will appear fixed for alternate alleles between two pooled samples drawn from the same underlying population. We apply this model to next-generation sequencing (NGS) data from Baltic Sea herring recently published by (Corander et al., , Molecular Ecology, 2931–2940), and show that there are many more fixed loci than expected in the...

Data from: Seasonal dynamics of Atlantic herring (Clupea harengus L.) populations spawning in the vicinity of marginal habitats

Florian Eggers, Aril Slotte, Lísa Anne Libungan, Arne Johannessen, Cecilie Kvamme, Even Moland, Esben Moland Olsen & Richard D. M. Nash
Gillnet sampling and analyses of otolith shape, vertebral count and growth indicated the presence of three putative Atlantic herring (Clupea harengus L.) populations mixing together over the spawning season February–June inside and outside an inland brackish water lake (Landvikvannet) in southern Norway. Peak spawning of oceanic Norwegian spring spawners and coastal Skagerrak spring spawners occurred in March–April with small proportions of spawners entering the lake. In comparison, spawning of Landvik herring peaked in May–June with...

Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud, Simon Henriet, Sutada Mungpakdee, Jean-Marc Aury, Corinne Da Silva, Henner Brinkmann, Jana Mikhaleva, Lisbeth C. Olsen, Claire Jubin, Cristian Cañestro, Jean-Marie Bouquet, Gemma Danks, Julie Poulain, Coen Campsteijn, Marcin Adamski, Ismael Cross, Fekadu Yadetie, Matthieu Muffato, Alexandra Louis, Stephen Butcher, Georgia Tsagkogeorga, Anke Konrad, Sarabdeep Singh, Marit F. Jensen, Evelyne Huynh Cong … & Daniel Chourrout
Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on...

Data from: A molecular gut content study of Themisto abyssorum (Amphipoda) from Arctic hydrothermal vent and cold seep systems

Bernt Rydland Olsen, Christofer Troedsson, Kenan Hadziavdic, Hans Tore Rapp & Rolf B. Pedersen
The use of DNA as a marker for prey inside the gut of predators has been instrumental in further understanding of known and unknown interactions. Molecular approaches are in particular useful in unavailable environments like the deep-sea. Trophic interactions in the deep-sea are difficult to observe in situ, correct deep-sea experimental laboratory conditions are difficult to obtain, animals rarely survive the sampling, or the study organisms feed during the sampling due to long hauls. Preliminary...

Data from: Cryptic and pseudo-cryptic diversity in the world’s most common bark beetle – Hypothenemus eruditus

Marius Kambestad, Lawrence R. Kirkendall, Iren L. Knutsen & Bjarte H. Jordal
Hypothenemus eruditus is regarded as the world’s most common bark beetle, collected from numerous host plants on all forested continents. Previous taxonomic treatments remark that the species is morphologically variable and difficult to identify, but to date, no study has analyzed molecular data to investigate possible cryptic or seemingly cryptic (pseudo-cryptic) diversity in this species. We sequenced 216 specimens matching or closely resembling the currently accepted description of H. eruditus for a mitochondrial (COI) and...

Data from: Higher predation risk for insect prey at low latitudes and elevations

Tomas Roslin, Bess Hardwick, Vojtech Novotny, William K. Petry, Nigel R. Andrew, Ashley Asmus, Isabel C. Barrio, Yves Basset, Andrea Larissa Boesing, Timothy C. Bonebrake, Erin K. Cameron, Wesley Dáttilo, David A. Donoso, Pavel Drozd, Claudia L. Gray, David S. Hik, Sarah J. Hill, Tapani Hopkins, Shuyin Huang, Bonny Koane, Benita Laird-Hopkins, Liisa Laukkanen, Owen T. Lewis, Sol Milne, Isaiah Mwesige … & Eleanor M. Slade
Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic...

Data from: High levels of multiple paternity in a spermcast mating freshwater mussel

Sebastian Wacker, Bjørn M. Larsen, Per Jakobsen & Sten Karlsson
Multiple paternity is an important characteristic of the genetic mating system and common across a wide range of taxa. Multiple paternity can increase within-population genotypic diversity, allowing selection to act on a wider spectre of genotypes, and potentially increasing effective population size. While the genetic mating system has been studied in many species with active mating behaviour, little is known about multiple paternity in sessile species releasing gametes into the water. In freshwater mussels, males...

Equilibrium in plant functional trait responses to warming is stronger under higher climate variability during the Holocene

Pierre Gaüzère, Lars Iversen, Alistair Seddon, Cyrille Violle & Ben Blonder
Aim.The functional trait composition of plant communities is thought to be largely determined by climate, but relationships between contemporary trait distributions and climate are often weak. Spatial mismatches between trait and climatic conditions are commonly thought to arise from disequilibrium responses to past environmental changes. We here investigated whether current trait-climate disequilibrium were likely to emerge during plant functional responses to Holocene climate warming. Location.North America Time period.14-0Kya Major taxa studied. Terrestrial plants Methods. We...

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: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming

Eric Meineri, Kari Klanderud, John Guittar, Deborah Goldberg & Vigdis Vandvik
Understanding the degree to which plant communities are open to seedling recruitment is key to predicting how they will be impacted by climate change. We experimentally assessed whether communities assembled under colder climates were inherently more open to recruitment than warmer-climate communities, after controlling for differences in the current climate under which the communities were growing. We then tested whether variation in openness to recruitment could be explained by community biomass or by the plant...

Data from: Reindeer trampling promotes vegetation changes in tundra heathlands: results from a simulation experiment

Dagmar Egelkraut, Hélène Barthelemy & Johan Olofsson
This dataset contains all the raw data belonging to the research article 'Reindeer trampling promotes vegetation changes in tundra heathlands: results from a simulation experiment', by Egelkraut, Barthelemy and Olofsson, published in Journal of Vegetation Science. The experiment experimentally simulated various herbivore activities (Defoliation, Moss removal, Fertilization, Trampling, FDT, FDTM) on lightly grazed tundra heath vegetation, in order to determine in what way each of these activities cntributed to change in vegetation community and structure....

Palm fruit colours are linked to the broad-scale distribution and diversification of primate colour vision systems

Renske Onstein, Daphne Vink, Jorin Veen, Christopher Barratt, Suzette Flantua, Serge Wich & Daniel Kissling
A long-standing hypothesis in ecology and evolution is that trichromatic colour vision (the ability to distinguish red from green) in frugivorous primates has evolved as an adaptation to detect conspicuous (reddish) fruits. This could provide a competitive advantage over dichromatic frugivores which cannot distinguish reddish colours from a background of green foliage. Here, we test whether the origin, distribution and diversity of trichromatic primates is positively associated with the availability of conspicuous palm fruits, i.e....

Data from: Marine ecosystem connectivity mediated by migrant–resident interactions and the concomitant cross-system flux of lipids

Mikael Van Deurs, Anders Persson, Martin Lindegren, Charlotte Jacobsen, Stefan Neuenfeldt, Christian Jørgensen & P. Anders Nilsson
Accumulating research argues that migrants influence the functioning and productivity of local habitats and ecosystems along migration routes and potentially drive cross-system energy fluxes of considerable magnitude, yet empirical documentation of local ecological effects and descriptions of the underlying mechanisms are surprisingly rare. In this study, we discovered migrant–resident interactions and substantial cross-system lipid transportation in the transition zone between the Baltic Sea and the North Sea where a resident cod population (predators) was found...

Data from: Resolution of a global mango and fig pest identity crisis

Andrew J. Johnson, Miloš Knížek, Thomas H. Atkinson, Bjarte H. Jordal, Randy C. Ploetz & Jiri Hulcr
Hypocryphalus Hopkins, 1915 and Cryphalus Erichson, 1836 (Curculionidae: Scolytinae: Cryphalini) are significant pests of fig, mango, and other economically important fruit trees, yet have received little attention from systematists. An integrated approach using molecular and morphological evidence resolved the identities of the species feeding on mango and fig. The following taxonomic changes are proposed: Hypocryphalus mangiferae (Stebbing, 1914), stat. rev.; Hypocryphalus dilutus (Eichhoff, 1878a), stat. rev. (=Cryphalus dilutusEichhoff, 1878b, syn. n.); Hypocryphalus discretus (Eichhoff, 1878a),...

AQUACOSM VIMS-Ehux – Core data

Flora Vincent, Guy Schleyer, Constanze Kuhlisch, Celia Marrasé, Rafel Simó, Jorun Egge, Assaf Vardi & Daniella Schatz
The cosmopolitan coccolithophore Emiliania huxleyi is a unicellular alga that forms massive oceanic blooms covering thousands of square kilometers (Tyrrell & Merico 2004). The intricate calcite exoskeleton of E. huxleyi accounts for ~1/3 of total marine CaCO3 production (Monteiro et al. 2016). E. huxleyi blooms are an important source of DMS, which is, by far, the most abundant volatile sulfur compound in the surface ocean and the best studied aerosol precursor (Simó 2001) with a...

2m, raw 20Hz data of wind, sonic temperature and humidity at EastGRIP site on Greenland Ice Sheet, summer 2019

Hans Christian Steen-Larsen & Sonja Wahl
IRGASON raw 20Hz data stored directly as measured by the instrument, in plain text .dat files. The IRGASON was installed at 2.15m facing the prevailing wind direction. Data columns correspond to: date and time (TIMESTAMP) u, y and z components of wind vector in m/s (Ux, Uy, Uz), sonic temperature in degrees Celsius (T_SONIC), absolute humidity (H2O-density), and diagnostic flags for sonic temperature and humidity (diag_sonic, diag_irga).

Exploring protocol bias in airway microbiome studies: One versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

Christine Drengenes, Rune Nielsen, Ingvild Haaland, Harald Wiker & Tomas Eagan
Background: Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2-steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups:...

Data from: Spatial covariance of herbivorous and predatory guilds of forest canopy arthropods along a latitudinal gradient

Ondřej Mottl
In arthropod community ecology, species richness studies tend to be prioritized over those investigating patterns of abundance. Consequently, the biotic and abiotic drivers of arboreal arthropod abundance are still relatively poorly known. In this cross-continental study, we employ a theoretical framework in order to examine patterns of covariance among herbivorous and predatory arthropod guilds. Leaf-chewing and leaf-mining herbivores, and predatory ants and spiders, were censused on > 1,000 trees in nine 0.1 ha forest plots....

Data from: Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological “hotspot”

Inger Alsos, Per Sjögren, Antony Brown, Ludovic Gielly, Marie Merkel, Aage Paus, Youri Lammers, Mary Edwards, Torbjørn Alm, Melanie Leng, Tomasz Goslar, Catherine Langdon, Jostein Bakke & Willem Van Der Bilt
Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and add newly analysed ancient sedimentary DNA, pollen, macrofossils, geochemistry and stable isotopes from three lake sediment cores from Øvre...

Data from: The evolutionary history of Afrocanarian blue tits inferred from genome-wide SNPs

Jostein Gohli, Erica Leder, Eduardo Garcia-Del-Rey, Lars Erik Johannessen, Arild Johnsen, Terje Laskemoen, Magnus Popp, Jan T. Lifjeld & Erica H. Leder
A common challenge in phylogenetic reconstruction is to find enough suitable genomic markers to reliably trace splitting events with short internodes. Here we present phylogenetic analyses based on genome-wide single-nucleotide polymorphisms (SNPs) of an enigmatic avian radiation, the subspecies complex of Afrocanarian blue tits (Cyanistes teneriffae). The two sister species, the Eurasian blue tit (Cyanistes caeruleus) and the azure tit (Cyanistes cyanus), constituted the outgroup. We generated a large data set of SNPs for analysis...

Data from: Regional environmental pressure influences population differentiation in turbot (Scophthalmus maximus)

S. G. Vandamme, G. E. Maes, J. A. M. Raeymaekers, K. Cottenie, A. K. Imsland, B. Hellemans, G. Lacroix, E. Mac Aoidh, J. T. Martinsohn, P. Martínez, J. Robbens, R. Vilas & F. A. M. Volckaert
Unravelling the factors shaping the genetic structure of mobile marine species is challenging due to the high potential for gene flow. However, genetic inference can be greatly enhanced by increasing the genomic, geographic or environmental resolution of population genetic studies. Here we investigated the population structure of turbot (Scophthalmus maximus) by screening 17 random and gene-linked markers in 999 individuals at 290 geographical locations throughout the Northeast Atlantic Ocean. A seascape genetics approach with the...

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