26 Works

Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences

Kessy Abarenkov, Panu Somervuo, R. Henrik Nilsson, Paul M. Kirk, Tea Huotari, Nerea Abrego & Otso Ovaskainen
• Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed PROTAX-fungi, a general tool for taxonomic placement of fungal ITS sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. • PROTAX-fungi outperformed the SINTAX and RDB classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence...

Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought

Andrés J. Cortés & Matthew W. Blair
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS)...

Data from: Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

Halvor Knutsen, Per Erik Jorde, Jeffrey A. Hutchings, Jakob Hemmer-Hansen, Peter Grønkjær, Kris-Emil Mose Jørgensen, Carl Andre, Marte Sodeland, Jon Albretsen, Esben M. Olsen & Peter Grønkjaer
Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification, and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analyzed genetic origin of...

Data from: Calcium transfer across the outer mantle epithelium in the Pacific oyster, Crassostrea gigas

J. Kirsikka Sillanpää, Henrik Sundh & Kristina S. Sundell
Calcium transport is essential for bivalves to be able to build and maintain their shells. Ionized calcium (Ca2+) is taken up from the environment and eventually transported through the outer mantle epithelium (OME) to the shell growth area. However, the mechanisms behind this process are poorly understood. The objective of the present study was to characterize the Ca2+ transfer performed by the OME of the Pacific oyster, Crassostrea gigas, as well as to develop an...

Data from: Allele phasing greatly improves the phylogenetic utility of ultraconserved elements

Tobias Andermann, Alexandre M. Fernandes, Urban Olsson, Mats Töpel, Bernard Pfeil, Bengt Oxelman, Alexandre Aleixo, Brant C. Faircloth & Alexandre Antonelli
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High...

Data from: Taxon cycle predictions supported by model-based inference in Indo-Pacific trap-jaw ants (Hymenoptera: Formicidae: Odontomachus)

Pável Matos-Maraví, Nicholas J. Matzke, Fredrick J. Larabee, Ronald M. Clouse, Ward C. Wheeler, Daniela Magdalena Sorger, Andrew V. Suarez & Milan Janda
Non-equilibrium dynamics and non-neutral processes, such as trait-dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential non-equilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework. Here, we test predictions of the taxon-cycle model using six expected phylogenetic patterns and a time-calibrated phylogeny of Indo-Pacific Odontomachus (Hymenoptera: Formicidae: Ponerinae), one of the ant genera...

Data from: Locality or habitat? Exploring predictors of biodiversity in Amazonia

Camila D. Ritter, Alexander Zizka, Christopher Barnes, R. Henrik Nilsson, Fabian Roger & Alexandre Antonelli
Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we...

Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes

Rui Faria, Pragya Chaube, Hernan E. Morales, Tomas Larsson, Alan R. Lemmon, Emily Moriarty Lemmon, Marina Rafajlovic, Marina Panova, Mark Ravinet, Kerstin Johannesson, Anja M. Westram & Roger K. Butlin
Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail,...

Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow

Anja Marie Westram, Marina Rafajlovic, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, Anders Blomberg, Bernhard Mehlig, Kerstin Johannesson & Roger Butlin
Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations...

Data from: Importance of the coronary circulation for cardiac and metabolic performance in rainbow trout (Oncorhynchus mykiss)

Andreas Ekström, Michael Axelsson, Albin Gräns, Jeroen Brijs & Erik Sandblom
Cardiac oxygenation is achieved via both coronary arterial and luminal venous oxygen supply routes in many fish species. However, the relative importance of these supplies for cardiac and aerobic metabolic performance is not fully understood. Here, we investigated how coronary artery ligation in rainbow trout (Oncorhynchus mykiss), implanted with heart rate loggers, affected cardiorespiratory performance in vivo. While coronary ligation significantly elevated resting heart rate, the standard metabolic rate was unchanged compared to sham treated...

Data from: Clitellate worms (Annelida) in lateglacial and Holocene sedimentary DNA records from the Polar Urals and northern Norway

Youri Lammers, Charlotte L. Clarke, Christer Erséus, Antony G. Brown, Mary E. Edwards, Ludovic Gielly, Haflidi Haflidason, Jan Mangerud, Emilia Rota, John Inge Svendsen & Inger Greve Alsos
While there are extensive macro- and microfossil records of a range of plants and animals from Quaternary records, earthworms and their close relatives among annelids are not preserved as fossils, and therefore we have limited knowledge of their Quaternary distributions. This lack of fossils means that clitellate worms (Annelida) are currently underused in palaeoecological research, even though they can provide valuable information about terrestrial and aquatic environmental conditions. Their DNA might be preserved in sediments,...

Data from: Inter-continental karyotype-environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly

Claire Mérot, Emma Berdan, Charles Babin, Eric Normandeau, Maren Wellenreuther, Louis Bernatchez & Emma L. Berdan
Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialisation. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic,...

Data from: Low fasting serum insulin and dementia in nondiabetic women followed for 34 years

Kirsten Mehlig, Leif Lapidus, Dag Steinar Thelle, Margda Waern, Henrik Zetterberg, Cecilia Björkelund, Ingmar Skoog & Lauren Lissner
Objective: A previous study reported a U-shaped association between fasting insulin and dementia in a 5-year follow-up of a male cohort, which was now re-investigated in a representative population of women followed over 34 years, and taking into account the incidence of diabetes. Methods: Fasting values for insulin and glucose were obtained from serum samples in 1212 non-diabetic women aged 38-60 at the 1968 baseline. Risk of dementia was assessed by Cox proportional hazard regression...

Data from: Expression profiling of human pluripotent stem cell-derived cardiomyocytes exposed to doxorubicin—integration and visualization of multi-omics data

Gustav Holmgren, Peter Sartipy, Christian X. Andersson, Anders Lindahl & Jane Synnergren
Anthracyclines, such as doxorubicin, are highly efficient chemotherapeutic agents against a variety of cancers. However, anthracyclines are also among the most cardiotoxic therapeutic drugs presently on the market. Chemotherapeutic-induced cardiomyopathy is one of the leading causes of disease and mortality in cancer survivors. The exact mechanisms responsible for doxorubicin-induced cardiomyopathy are not completely known, but the fact that the cardiotoxicity is dose-dependent and that there is a variation in time-to-onset of toxicity, and gender- and...

Data from: Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

Pierre De Wit, Evan Durland, Alexander Ventura & Chris J. Langdon
Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 hours post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with...

Data from: Long term effects of superoxide and DNA repair on lizard telomeres

Mats Olsson, Christopher R. Friesen, Nicky Rollings, Joanna Sudyka, Willow Lindsay, Camilla M. Whittington & Mark Wilson
Telomeres are the non-coding protein-nucleotide ‘caps’ at chromosome ends that contribute to chromosomal stability by protecting the coding parts of the linear DNA from shortening at cell division, and from erosion by reactive molecules. Recently, there has been some controversy between molecular and cell biologists, on the one hand, and evolutionary ecologists on the other, regarding whether reactive molecules erode telomeres during oxidative stress. Many studies of biochemistry and medicine have verified these relationships in...

Data from: Incubation temperature and parental identity determine sex in the Australian agamid lizard Ctenophorus pictus

Alexander Hansson & Mats Olsson
Sex determination in Australian agamid lizards show a complex framework of different mechanisms, varying even among closely related taxa. It is clear that discrete classification of these species as either having genetic (GSD) or environmental sex determination (ESD) does not agree with empirical data. Although many species in this group show temperature-dependent sex determination (TSD), recent evidence suggests additional genetic or epigenetic effects. A proposed model explaining the adaptive significance and evolution of TSD in...

Data from: Early arrival and climatically-linked geographic expansion of New World monkeys from tiny African ancestors

Daniele Silvestro, Marcelo F. Tejedor, Martha L. Serrano-Serrano, Oriane Loiseau, Victor Rossier, Jonathan Rolland, Alexander Zizka, Sebastian Höhna, Alexandre Antonelli & Nicolas Salamin
New World monkeys (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Here we integrate paleontological and molecular evidence to assess the evolutionary...

Data from: PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology

Søren Faurby, Matt Davis, Rasmus Østergaard Pedersen, Simon D. Schowanek, Alexandre Antonelli & Jens-Christian Svenning
Data needed for macroecological analyses are difficult to compile and often hidden away in supplementary material under non-standardized formats. Phylogenies, range data, and trait data often use conflicting taxonomies and require ad hoc decisions to synonymize species or fill in large amounts of missing data. Furthermore, most available data sets ignore the large impact that humans have had on species ranges and diversity. Ignoring these impacts can lead to drastic differences in diversity patterns and...

Data from: Abnormal CSF amyloid-β42 and tau levels in hip fracture patients without dementia

Esther S. Oh, Kaj Blennow, George E. Bigelow, Sharon K. Inouye, Edward R. Marcantonio, Karin J. Neufeld, Paul B. Rosenberg, Juan C. Troncoso, Nae-Yuh Wang, Henrik Zetterberg, Frederick Sieber, Constantine G. Lyketsos & Frederick E. Sieber
Background: There is strong association of Alzheimer's disease (AD) pathology with gait disorder and falls in older adults without dementia. The goal of the study was to examine the prevalence and severity of AD pathology in older adults without dementia who fall and sustain hip fracture. Methods: Cerebrospinal fluid (CSF) was obtained from 168 hip fracture patients. CSF Aβ42/40 ratio, p-tau, and t-tau measures were dichotomized into normal vs. abnormal, and categorized according to the...

Data from: Effects of male telomeres on probability of paternity in sand lizards

Angela Pauliny, Emily Miller, Nicky Rollings, Erik Wapstra, Donald Blomqvist, Christopher Friesen, Mats Olsson & Chris R. Friesen
Standardized swim-up trials are used in IVF clinics to select particularly motile spermatozoa in order to increase the probability of a successful fertilization. Such trials demonstrate that sperm with longer telomeres have higher motility and lower levels of DNA damage. Regardless of whether sperm motility, and successful swim-up to fertilization sites, is a direct or correlational effect of telomere length or DNA damage, covariation between telomere length and sperm performance predicts a relationship between telomere...

Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

Jonna Sofia Eriksson, Filipe De Sousa, Yann J.K. Bertrand, Alexandre Antonelli, Bengt Oxelman & Bernard E. Pfeil
Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs...

Data from: Are assortative mating and genital divergence driven by reinforcement?

Johan Hollander, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M. Westram, Ludovic Duvaux, David G. Reid & Roger K. Butlin
The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative...

Data from: Demography and selection shape transcriptomic divergence in field crickets

Thomas Blankers, Sibelle Torres Vilaça, Isabelle Waurick, David A. Gray, R. Matthias Hennig, Camilla J. Mazzoni, Frieder Mayer & Emma L. Berdan
Gene flow, demography, and selection can result in similar patterns of genomic variation and disentangling their effects is key to understanding speciation. Here, we assess transcriptomic variation to unravel the evolutionary history of Gryllus rubens and G. texensis, cryptic field cricket species with highly divergent mating behavior. We infer their demographic history and screen their transcriptomes for footprints of selection in the context of the inferred demography. We find strong support for a long history...

Data from: Disentangling structural genomic and behavioral barriers in a sea of connectivity

Julia M. I. Barth, David Villegas-Ríos, Carla Freitas, Even Moland, Bastiaan Star, Carl André, Halvor Knutsen, Ian Bradbury, Jan Dierking, Christoph Petereit, David Righton, Julian Metcalfe, Kjetill S. Jakobsen, Esben M. Olsen, Sissel Jentoft & Julia M.I. Barth
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question whether inversions play a role...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Gothenburg
  • University of Oslo
  • Harvard University
  • University of Sheffield
  • University of Wollongong
  • Lund University
  • Aarhus University
  • University of Sydney
  • University of Auckland
  • University of Agder