Data from: Simultaneous estimation of occupancy and detection probabilities an illustration using Cincinnatian brachiopodsLee 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...
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...
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses...
Data from: Evolution of static allometries: adaptive change in allometric slopes of eye span in stalk-eyed fliesKjetil Lysne Voje & Thomas F. Hansen
Julian Huxley showed that within-species (static) allometric (power-law) relations can arise from proportional growth regulation with the exponent in the power law equaling the factor of proportionality. Allometric exponents may therefore be hard to change and act as constraints on the independent evolution of traits. In apparent contradiction to this, many empirical studies have concluded that static allometries are evolvable. Many of these studies have been based, however, on a broad definition of allometry that...
Data from: Molecular characterization of sexual diversity in a population of Serpula lacrymans, a tetrapolar basidiomyceteInger Skrede, Sundy Maurice & Håvard Kauserud
Different mating systems have evolved in the fungal kingdom, including a tetrapolar multiallelic mating system in many basidiomycetes. In tetrapolar species, the presence of different alleles at two mating loci (MAT A and MAT B) is necessary for mating to occur. The tetrapolar fungus Serpula lacrymans causes wood-decay in buildings in temperate regions worldwide and is present in Europe with a genetically homogeneous founder population. Using genome sequence data, we annotated the two mating type...
Data from: The Azores Bullfinch (Pyrrhula murina) has the same unusual and size-variable sperm morphology as the Eurasian Bullfinch (Pyrrhula pyrrhula)Jan T. Lifjeld, Antje Hoenen, Lars Erik Johannessen, Terje Laskemoen, Ricardo J. Lopes, Pedro Rodrigues & Melissah Rowe
The Azores bullfinch is endemic to the island of São Miguel in the Azores archipelago and the sister species to the Eurasian bullfinch. Here we show that the spermatozoa of the two species have similar ultrastructure and gross morphology. Thus, the unusual and supposedly neotenous sperm morphology previously described for the Eurasian bullfinch appears to be an ancestral trait that evolved before the two taxa diverged. In addition, the coefficients of variation in total sperm...
Data from: Amplicon-pyrosequencing based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient.Marie L. Davey, Einar Heegaard, Rune Halvorsen, Håvard Kauserud & Mikael Ohlson
Although bryophytes are a dominant vegetation component of boreal and alpine ecosystems, little is known about their associated fungal communities. HPLC assays of ergosterol (fungal biomass) and amplicon pyrosequencing of the ITS2 region of rDNA were used to investigate how the fungal communities associated with four bryophyte species changed across an elevational gradient transitioning from conifer forest to the low alpine. Fungal biomass and OTU richness associated with the four moss hosts did not vary...
The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2...
Data from: Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) populationDimitar Serbezov, Per Erik Jorde, Louis Bernatchez, Esben Moland Olsen & L. Asbjørn Vøllestad
The effective population size (Ne) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate Ne are impacted variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, population substructure, as well as by the frequency patterns of genetic markers used and the...
To what extent within-species (static) allometries constitute a constraint on evolution is the subject of a long-standing debate in evolutionary biology. A prerequisite for the constraint hypothesis is that static allometries are hard to change. Several studies have attempted to test this hypothesis with artificial-selection experiments, but their results remain inconclusive due to various methodological issues. Here, we present results from an experiment in which we selected independently on the slope and the elevation of...
Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystemsLaura S. Epp, Sanne Boessenkool, Eva P. Bellemain, James Haile, Alfonso Esposito, Tiayyba Riaz, Christer Erséus, Vladimir I. Gusarov, Mary E. Edwards, Arild Johnsen, Hans K. Stenøien, Kristian Hassel, Håvard Kauserud, Nigel G. Yoccoz, Kari Anne Bråthen, Eske Willerslev, Pierre Taberlet, Eric Coissac & Christian Brochmann
Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds....
University of Oslo11
French National Centre for Scientific Research3
University of Southampton2
University of Gothenburg2
Norwegian University of Science and Technology2
Atomic Energy and Alternative Energies Commission1
Royal Botanic Gardens1
Natural History Museum1
University of Copenhagen1
University of Tartu1