List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)Melanie Lindner, Veronika N Laine & Marcel E Visser
The profiling of epigenetic marks like DNA methylation has become a central aspect of studies in evolution and ecology. Bisulfite sequencing is commonly used for assessing genome-wide DNA methylation at single nucleotide resolution but these data can also provide information on genetic variants like single nucleotide polymorphisms (SNPs). However, bisulfite conversion causes unmethylated cytosines to appear as thymines, complicating the alignment and subsequent SNP calling. Several tools have been developed to overcome this challenge, but...
Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowiGustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...
Population performance is predicted to be more strongly influenced by detrimental species interactions such as predation under benign climatic conditions, and by climate forcing under harsh conditions, reflected in geographical gradients in biotic interaction strength. Less appreciated is the potential for site-specific changes in drivers with the advent of anthropogenic alteration of predator-prey relationships, including apex predator restoration and spread of invasive predators. Particularly interesting is the relative impact of climate and biotic interactions on...
Gulf of Maine genotypes for 'Species identification based on a semi-diagnostic marker: evaluation of a simple conchological test for distinguishing blue mussels Mytilus edulis L. and M. trossulus Gould'Sarah Kingston, Vadim Khaitov, Julia Marchenko, Marina Katolikova, Risto Väinölä, David Carlon, Michael Gantsevich & Petr Strelkov
These are genotype calls for Gulf of Maine samples associated with the paper 'Species identification based on a semi-diagnostic marker: evaluation of a simple conchological test for distinguishing blue mussels Mytilus edulis L. and M. trossulus Gould'.
Data from: Titmice are a better indicator of bird density in Northern European than in Western European forestsMira H. Kajanus, Jukka T. Forsman, Maximilian G. R. Vollstädt, Vincent Devictor, Merja Elo, Aleksi Lehikoinen, Mikko Mönkkönen, James T. Thorson & Sami M. Kivelä
Population sizes of many birds are declining alarmingly and methods for estimating fluctuations in species’ abundances at a large spatial scale are needed. The possibility to derive indicators from the tendency of specific species to co-occur with others has been overlooked. Here we tested whether the abundance of resident titmice can act as a general ecological indicator of forest bird density in European forests. Titmice species are easily identifiable and have a wide distribution, which...
Data from: Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forestsAku Korhonen, Otto Miettinen, Johan Kotze & Leena Hamberg
Data from: Korhonen, A., Miettinen, O., Kotze, D.J., & Hamberg, L. (2022). Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests. Environmental Microbiology. DOI: 10.1111/1462-2920.15903 This dataset contains occurrence data of 475 fungal ITS2 sequence clusters (OTUs) across 360 sequenced samples originating from dead wood of Norway spruce (Picea abies). Wood samples were collected from 90 downed spruce trunks, at four points from each trunk. Trunks were at...
You eat what you find – local patterns in vegetation structure control diets of African fungus-growing termitesRisto Vesala, Aleksi Rikkinen, Petri Pellikka, Jouko Rikkinen & Laura Arppe
Fungus-growing termites and their symbiotic Termitomyces fungi are critically important carbon and nutrient recyclers in arid and semiarid environments of sub-Saharan Africa. A major proportion of plant litter produced in these ecosystems is decomposed within nest chambers of termite mounds, where temperature and humidity are kept optimal for the fungal symbionts. While fungus-growing termites are generally believed to exploit a wide range of different plant substrates, the actual diets of most species remain elusive. We...
Data from: Cycles of trans‐Arctic dispersal and vicariance, and diversification of the amphi‐boreal marine faunaHanna Laakkonen, Risto Väinölä, Petr Strelkov & Michael Hardman
The amphi‐boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans‐Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further dispersal have risen at times however, and molecular data now expose more...
This dataset contains data for a manuscript titled 'Urban forests host rich polypore assemblages in a Nordic metropolitan area' where we have studied associations between the diversity of dead-wood inhabiting fungi and urbanization. The included spreadsheets contain data used in the analyses, i.e. polypore species occurrences, species richness and environmental data, accompanied by annotations about the characteristics of the study sites and individual dead-wood units. Data is given at two spatial scales on two separate...
Genome sequencing of spatially distributed individuals sheds light on how evolution structures genetic variation. Populations of Phellopilus nigrolimitatus, a red-listed wood-inhabiting fungus associated with old-growth coniferous forests, have decreased in size over the last century due to a loss of suitable habitats. We assessed the population genetic structure and investigated local adaptation in P. nigrolimitatus, by establishing a reference genome and genotyping 327 individuals sampled from 24 locations in Northern Europe by RAD sequencing. We...
Finnish Museum of Natural History14
University of Lisbon4
Meise Botanic Garden4
Natural History Museum4
Museum für Naturkunde4
Natural Resources Institute Finland3
Botanischer Garten und Botanisches Museum Berlin2
Senckenberg Nature Research Society2
Royal Belgian Institute of Natural Sciences2
Royal Botanic Garden Edinburgh2