336 Works

Data from: A practical introduction to random forest for genetic association studies in ecology and evolution

Marine S.O. Brieuc, Charles D. Waters, Daniel P. Drinan, Kerry Ann Naish & Marine S. O. Brieuc
Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here we explore the use of Random Forest (RF), a powerful machine learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild...

Data from: Mating patterns and determinants of individual reproductive success in brown trout (Salmo trutta) revealed by parentage analysis of an entire stream living population

Dimitar Serbezov, Louis Bernatchez, Esben Olsen & Leif Vøllestad
Reproductive success and its determinants are difficult to infer for wild populations of species with no parental care where behavioral observations are difficult or impossible. In this study, we characterized the breeding system and provide estimates of individual reproductive success under natural conditions for a stream-resident, semi-isolated brown trout (Salmo trutta) population. We inferred parentage using a full probability Bayesian model that combines genetic (microsatellite) with phenotypic data. We had tried to exhaustively sample all...

Data from: Positive feedback between ecological and reproductive character displacement in a young avian hybrid zone

Niclas Vallin, Amber M. Rice, Richard I. Bailey, Arild Husby & Anna Qvarnström
Character displacement can reduce costly interspecific interactions between young species. We investigated the mechanisms behind divergence in three key traits - breeding habitat choice, timing of breeding and plumage coloration - in Ficedula flycatchers. We found that male pied flycatchers became expelled from the preferred deciduous habitat into mixed forest as the superior competitor, collared flycatchers, increased in numbers. The peak in food abundance differs between habitats, and the spatial segregation was paralleled by an...

Data from: Simultaneous estimation of occupancy and detection probabilities an illustration using Cincinnatian brachiopods

Lee Hsiang Liow
Preservation in the fossil record is never perfect in the sense that we cannot sample all individuals of a given population in time and space. Incomplete detection (i.e., preservation and modern-day sampling of fossils) often affects estimates of other paleobiological parameters of interest, such as occupancy and turnover. Here, I simultaneously model the occupancy and detection probability of taxa, teasing apart the zeros in data that reflect true absences and those that imply non-detection of...

Data from: A giant spurrey on a tiny island: on the phylogenetic position of Sanctambrosia manicata (Caryophyllaceae) and the generic circumscriptions of Spergula, Spergularia and Rhodalsine

Anneleen Kool & Mats Thulin
The only member of the generally herbaceous family Caryophyllaceae that may grow to a small tree is Sanctambrosia manicata, endemic to remote San Ambrosio Island, off the coast of Chile. The monospecific Sanctambrosia has been suggested to be closely related to Spergula and Spergularia (spurreys) on the basis of morphology, despite its treelike habit and gynodioecy. A plastid DNA dataset (ndhF, rps16, trnL-F) is used to investigate the relationships of Sanctambrosia and other members of...

Data from: Is telomere length associated with mate choice in a songbird with a high rate of extra-pair paternity?

Arild Johnsen, Angela Pauliny, Jan T. Lifjeld & Donald Blomqvist
Telomere length is related to aging in many eukaryotes and the rate of telomere attrition has been suggested to reflect individual genetic quality. Telomere length could thus have implications for mate choice. We investigated telomere length variation in bluethroat Luscinia svecica families with mixed paternity, including social parents, extra-pair fathers and nestlings, testing whether telomere length is associated with social and/or extra-pair mate choice through assortative mating or selection of mates with relatively long telomeres....

Data from: Walk the line: 600,000 years of molar evolution constrained by allometry in the fossil rodent Mimomys savini

Cyril Firmat, Iván Lozano-Fernández, Jordi Agustí, Geir H. Bolstad, Gloria Cuenca-Bescós, Thomas F. Hansen & Christophe Pélabon
The allometric-constraint hypothesis states that evolutionary divergence of morphological traits is restricted by integrated growth regulation. In this study, we test this hypothesis on a time-calibrated and well-documented palaeontological sequence of dental measurements on the Pleistocene arvicoline rodent species Mimomys savini from the Iberian Peninsula. Based on 507 specimens representing nine populations regularly spaced over 600 000 years, we compare static (within-population) and evolutionary (among-population) allometric slopes between the width and the length of the...

Data from: Serum-free and xenobiotic-free preservation of cultured human limbal epithelial cells

Oeygunn A. Utheim, Rakibul Islam, Torstein Lyberg, Borghild Roald, Jon Roger Eidet, Maria Fideliz De La Paz, Darlene A. Dartt, Sten Raeder, Tor Paaske Utheim & Oeygunn Utheim
Aim/Purpose of the Study: To develop a one-week storage method, without serum and xenobiotics, that would maintain cell viability, morphology, and phenotype of cultured human limbal epithelial sheets. Materials and Methods: Human limbal explants were cultured on intact human amniotic membranes for two weeks. The sheets were stored in a hermetically sealed container at 23°C in either a serum-free medium with selected animal serum-derived compounds (Quantum 286) or a xenobiotic-free medium (Minimal Essential Medium) for...

Data from: Examining community stability in the face of mass extinction in communities of digital organisms

Tian-Tong Luo, Lise Heier, Zaki Ahmad Khan, Faraz Hasan, Trond Reitan, , Zi-Xuan Xie, Jian-Long Zhu & Gabriel Yedid
Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent platform for addressing topics in long-term evolution and paleobiology, such as mass extinction and recovery, with experimental evolutionary approaches. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an...

Data from: Millions of years behind: slow adaptation of ruminants to grasslands

Olja Toljagić, Kjetil L. Voje, Michael Matschiner, Lee H. Liow & Thomas F. Hansen
The Late-Cretaceous appearance of grasses, followed by the Cenozoic advancement of grasslands as dominant biomes, has contributed to the evolution of a range of specialized herbivores adapted to new diets, as well as to increasingly open and arid habitats. Many mammals including ruminants, the most diversified ungulate suborder, evolved high–crowned (hypsodont) teeth as an adaptation to tooth–wearing diets and habitats. The impact of different causes of tooth wear is still a matter of debate, and...

Data from: Host and tissue variation overshadow the response of boreal moss-associated fungal communities to increased nitrogen load

Marie L. Davey, Marte J. Skogen, Einar Heegaard, Rune Halvorsen, Håvard Kauserud & Mikael Ohlson
Human activity has more than doubled the amount of nitrogen entering the global nitrogen cycle, and the boreal forest biome is a nitrogen-limited ecosystem sensitive to nitrogen load perturbation. Although bryophyte-associated microbes contribute significantly to boreal forest ecosystem function, particularly in carbon and nitrogen cycling, little is known about their responses to anthropogenic global change. Amplicon pyrosequencing of the ITS2 region of rDNA was used to investigate how fungal communities associated with three bryophyte species...

Data from: Mismatch between fishway operation and timing of fish movements: a risk for cascading effects in partial migration systems

Casper H. A. Van Leeuwen, Jon Museth, Odd Terje Sandlund, Tore Qvenild & Leif Asbjørn Vøllestad
Habitat fragmentation is a growing problem worldwide. Particularly in river systems, numerous dams and weirs hamper the movement of a wide variety of species. With the aim to preserve connectivity for fish, many barriers in river systems are equipped with fishways (also called fish passages or fish ladders). However, few fishways provide full connectivity. Here we hypothesized that restricted seasonal opening times of fishways can importantly reduce their effectiveness by interfering with the timing of...

Data from: Fungal communities in Scandinavian lakes along a longitudinal gradient

Maryia Khomich, Marie L. Davey, Håvard Kauserud, Serena Rasconi & Tom Andersen
This study investigates the diversity and distribution of fungal communities in 77 oligotrophic lakes in southern Norway and Sweden using 454-sequencing with fungal-specific primers targeting ITS2 region of the rRNA gene. A total of 232 operational taxonomic units (OTUs) belonging to four recognized phyla were detected. A large proportion (70.69%) of the detected OTUs were Dikarya (Ascomycota and Basidiomycota), while Chytridiomycota dominated quantitatively (63.37% reads). The most abundant aquatic fungi were taxonomically assigned to Chytridiomycota,...

Data from: Size, weapons and armor as predictors of competitive outcomes in fossil and contemporary marine communities

Lee Hsiang Liow, Trond Reitan, Kjetil Voje, Paul Taylor & Emanuela Di Martino
Inter- and intraspecific competition are usually observed over a few generations but their patterns and consequences are seldom tractable in natural systems over longer timescales relevant to macroevolutionary change. Here, we use win-draw-lose competitive overgrowths for a marine benthic community of encrusting bryozoans that have evolved together in New Zealand for at least 2.3 million years to investigate battles for substrate space, a resource that is limiting for these colonial organisms. Using more than 6000...

Data from: Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum

Jon Bråte, Marcin Adamski, Ralf Neumann, Kamran Shalchian-Tabrizi, Maja Adamska & Ralf S. Neumann
Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation has been important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analyzed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the...

Data from: Sperm head abnormalities are more frequent in songbirds with more helical sperm: A possible trade-off in sperm evolution

Hanna N. Støstad, Melissah Rowe, Arild Johnsen & Jan T. Lifjeld
Sperm morphology varies enormously across the animal kingdom. While knowledge of the factors that drive the evolution of interspecific variation in sperm morphology is accumulating, we currently have little understanding of factors that may constrain evolutionary change in sperm traits. We investigated whether susceptibility to sperm abnormalities could represent such a constraint in songbirds, a group characterised by a distinctive helical sperm head shape. Specifically, using 36 songbird species and data from light- and scanning...

Data from: Comparative analyses of plastid and AFLP data suggest different colonization history and asymmetric hybridisation between Betula pubescens and B. nana

Pernille Bronken Eidesen, Inger Greve Alsos & Christian Brochmann
Birches (Betula spp.) hybridize readily, confounding genetic signatures of refugial isolation and postglacial migration. We aimed to distinguish hybridization from range-shift processes in the two widespread and cold-adapted species B. nana and B. pubescens, previously shown to share a similarly east–west-structured variation in plastid DNA (pDNA). We sampled the two species throughout their ranges and included reference samples of five other Betula species and putative hybrids. We analysed 901 individual plants using mainly nuclear high-resolution...

Data from: Testing classical species properties with contemporary data: how 'bad species' in the brassy ringlets (Erebia tyndarus complex, Lepidoptera) turned good

Paolo Gratton, Emiliano Trucchi, Alessandra Trasatti, Giorgio Riccarducci, Silvio Marta, Giuliana Allegrucci, Donatella Cesaroni & Valerio Sbordoni
All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods i) rely on simplified demographic models that may fail to capture some attributes of biological species, ii) do not...

Data from: Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding

Eeva M. Soininen, Gilles Gauthier, Frédéric Bilodeau, Dominique Berteaux, Ludovic Gielly, Pierre Taberlet, Galina Gussarova, Eva Bellemain, Kristian Hassel, Hans K. Stenøien, Laura Epp, Audun Schrøder-Nilsen, Christian Brochmann, Nigel G. Yoccoz & Audun Schrøder-Nielsen
Sympatric species are expected to minimize competition by partitioning resources, especially when these are limited. Herbivores inhabiting the High Arctic in winter are a prime example of a situation where food availability is anticipated to be low, and thus reduced diet overlap is expected. We present here the first assessment of diet overlap of high arctic lemmings during winter based on DNA metabarcoding of feces. In contrast to previous analyses based on microhistology, we found...

Data from: Convergent evolution of the ladder-like ventral nerve cord in Annelida

Conrad Helm, Patrick Beckers, Thomas Bartolomaeus, Stephan H. Drukewitz, Ioannis Kourtesis, Anne Weigert, Günter Purschke, Katrine Worsaae, Torsten H. Struck & Christoph Bleidorn
Background: A median, segmented, annelid nerve cord has repeatedly been compared to the arthropod and vertebrate nerve cords and became the most used textbook representation of the annelid nervous system. Recent phylogenomic analyses, however, challenge the hypothesis that a subepidermal rope-ladder-like ventral nerve cord (VNC) composed of a paired serial chain of ganglia and somata-free connectives represents either a plesiomorphic or a typical condition in annelids. Results: Using a comparative approach by combining phylogenomic analyses...

Data from: A consistent species richness-climate relationship for oaks across the Northern Hemisphere

Xiaoting Xu, Dimitar Dimitrov, Nawal Shrestha, Carsten Rahbek & Zhiheng Wang
Aim: Although the effects of climate on species richness are known, regional processes may lead to different species richness-climate relationships across continents resulting in species richness anomalies, especially for tropical groups. Phylogenetic niche conservatism may also influence species richness-climate relationships of different lineages. Here, we tested whether regional effects also exist for temperate lineages using the genus Quercus. Location: Northern Hemisphere Time period: Present day Major taxa studied: Quercus (Fagaceae) Methods: We used a dated...

Data from: Bayesian estimation of speciation and extinction from incomplete fossil occurrence data

Daniele Silvestro, Jan Schnitzler, Lee Hsiang Liow, Alexandre Antonelli & Nicolas Salamin
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here,...

Data from: Inferring the demographic history of European Ficedula flycatcher populations

Niclas Backström, Glenn-Peter Sætre & Hans Ellegren
Background: Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results: We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between...

Data from: Comparative authentication of Hypericum perforatum herbal products using DNA metabarcoding, TLC and HPLC-MS

Ancuta Cristina Raclariu, Ramona Paltinean, Laurian Vlase, Aurelie Labarre, Vincent Manzanilla, Mihael Cristin Ichim, Gianina Crisan, Anne Krag Brysting & Hugo De Boer
Many herbal products have a long history of use, but there are increasing concerns over product efficacy, safety and quality in the wake of recent cases exposing discrepancies between labeling and constituents. When it comes to St. John’s wort (Hypericum perforatum L.) herbal products, there is limited oversight, frequent off-label use and insufficient monitoring of adverse drug reactions. In this study, we use amplicon metabarcoding (AMB) to authenticate 78 H. perforatum herbal products and evaluate...

Data from: Mapping and analysis of the connectome of sympathetic premotor neurons in the rostral ventrolateral medulla of the rat using a volumetric brain atlas

Bowen Dempsey, Sheng Le, Anita Turner, Phill Bokiniec, Radhika Ramadas, Jan G. Bjaalie, Clement Menuet, Rachael Neve, Andrew Allen, Ann Goodchild, Simon McMullan, Phil Bokiniec, Ann K. Goodchild & Andrew M. Allen
Spinally projecting neurons in the rostral ventrolateral medulla (RVLM) play a critical role in the generation of vasomotor sympathetic tone and are thought to receive convergent input from neurons at every level of the neuraxis; the factors that determine their ongoing activity remain unresolved. In this study we use a genetically restricted viral tracing strategy to definitively map their spatially diffuse connectome. We infected bulbospinal RVLM neurons with recombinant rabies variant that drives reporter expression...

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