535 Works

Data from: Fine-scale population structure, inbreeding risk and avoidance in a wild insect population

Amanda Bretman, Rolando Rodríguez-Muñoz, Craig Walling, Jon Slate & Tom Tregenza
The ecological and evolutionary importance of fine scale genetic structure within populations is increasingly appreciated. However, available data are largely restricted to wild vertebrates and eusocial insects. In addition there is the expectation that most insects tend to have such large and high density populations and are so mobile that they are unlikely to face inbreeding risks through fine scale population structuring. This has made the growing body of evidence for inbreeding avoidance in insects...

Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

Andrea J. Betancourt, Bernardo Blanco-Martin & Brian Charlesworth
We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available data sets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore...

Data from: Genetic analysis of life-history constraint and evolution in a wild ungulate population

Michael B. Morrissey, Craig A. Walling, Alastair J. Wilson, Josephine M. Pemberton, Tim H. Clutton-Brock & Loeske E. B. Kruuk
Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in...

Data from: Plasticity predicts evolution in a marine alga

C. Elisa Schaum & Sinéad Collins
Under global change, populations have four possible responses: ‘migrate, acclimate, adapt or die’ (Gienapp et al. 2008 Climate change and evolution: disentangling environmental and genetic response. Mol. Ecol. 17, 167–178. (doi:10.1111/j.1365-294X.2007.03413.x)). The challenge is to predict how much migration, acclimatization or adaptation populations are capable of. We have previously shown that populations from more variable environments are more plastic (Schaum et al. 2013 Variation in plastic responses of a globally distributed picoplankton species to ocean...

Data from: Crowdsourcing the identification of organisms: a case-study of iSpot

Jonathan Silvertown, Martin Harvey, Richard Greenwood, Mike Dodd, Jon Rosewell, Tony Rebelo, Janice Ansine & Kevin McConway
Accurate species identification is fundamental to biodiversity science, but the natural history skills required for this are neglected in formal education at all levels. In this paper we describe how the web application ispotnature.org and its sister site ispot.org.za (collectively, "iSpot") are helping to solve this problem by combining learning technology with crowdsourcing to connect beginners with experts. Over 94% of observations submitted to iSpot receive a determination. To date (2014), iSpot has crowdsourced the...

Data from: The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation

Matthew Hartfield, Sarah P. Otto & Peter David Keightley
Although there is no known general explanation as to why sexual populations resist asexual invasion, previous work has shown that sexuals can outcompete asexuals in structured populations. However, it is currently unknown whether costly sex can be maintained with the weak structure that is commonly observed in nature. We investigate the conditions under which obligate sexuals resist asexual invasion in structured populations subject to recurrent mutation. We determine the level of population structure needed to...

Data from: Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach

Emily A. Brown, Jill G. Pilkington, Dan H. Nussey, Kathryn A. Watt, Adam D. Hayward, Rachel Tucker, Andrea L. Graham, Steve Paterson, Dario Beraldi, Josephine M. Pemberton & Jon Slate
Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. Here we test the candidate gene approach to identifying loci involved in variation in gastrointestinal parasite burden, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources were used to generate a list of candidate genes. In a pilot study these candidates, along with 50 random genes, were then sequenced...

Data from: Detecting slow introgression of invasive alleles in an extensively restocked game bird

Ines Sanchez-Donoso, Jisca Huisman, Jorge Echegaray, Manel Puigcerver, José Domingo Rodríguez-Teijeiro, Frank Hailer & Carles Vilà
Interbreeding of two species in the wild implies introgression of alleles from one species into the other only when admixed individuals survive and successfully backcross with the parental species. Consequently, estimating the proportion of first generation hybrids in a population may not inform about the evolutionary impact of hybridization. Samples obtained over a long time span may offer a more accurate view of the spreading of introgressed alleles in a species’ gene pool. Common quail...

Data from: Understanding genetic variation in in vivo tolerance to artesunate: implications for treatment efficacy and resistance monitoring

Laura C. Pollitt, Derek Sim, Rahel Salathé & Andrew F. Read
Artemisinin-based drugs are the front-line weapon in the treatment of human malaria cases, but there is concern that recent reports of slow clearing infections may signal developing resistance to treatment. In the absence of molecular markers for resistance, current efforts to monitor drug efficacy are based on the rate at which parasites are cleared from infections. However, some knowledge of the standing variation in parasite susceptibility is needed to identify a meaningful increase in infection...

Data from: The effect of funding sources on donepezil randomised controlled trial outcome: a meta-analysis

Lewis O. J. Killin, Tom C. Russ, John M. Starr, Sharon Abrahams & Sergio Della Sala
Objective: To investigate whether there is a difference in the treatment effect of donepezil on cognition in Alzheimer disease between industry-funded and independent randomised controlled trials. Design: Fixed effects meta-analysis of standardised effects of donepezil on cognition as measured by the Mini Mental State Examination and the Alzheimer’s Disease Assessment Scale-cognitive subscale. Data sources: Studies included in the meta-analyses reported in the National Institute for Health and Care Excellence (NICE) technical appraisal 217 updated with...

Data from: The evolutionary dynamics of sexually antagonistic mutations in pseudoautosomal regions of sex chromosomes

Brian Charlesworth, Crispin Y. Jordan & Deborah Charlesworth
Sex chromosomes can evolve gene contents that differ from the rest of the genome, as well as larger sex differences in gene expression compared with autosomes. This probably occurs because fully sex-linked beneficial mutations substitute at different rates from autosomal ones, especially when fitness effects are sexually antagonistic (SA). The evolutionary properties of genes located in the recombining pseudo-autosomal region (PAR) of a sex chromosome have not previously been modelled in detail. Such PAR genes...

Data from: The action of stabilizing selection, mutation and drift on epistatic quantitative traits

Victoria Ávila, Andrés Pérez-Figueroa, Armando Caballero, William G. Hill, Aurora García-Dorado & Carlos López-Fanjul
For a quantitative trait under stabilizing selection, the effect of epistasis on its genetic architecture and on the changes of genetic variance caused by bottlenecking were investigated using theory and simulation. Assuming empirical estimates of the rate and effects of mutations and the intensity of selection, we assessed the impact of two-locus epistasis (synergistic/antagonistic) among linked or unlinked loci on the distribution of effects and frequencies of segregating loci in populations at the mutation-selection-drift balance....

Data from: RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene

Paul M. Richards, M. Maureen Liu, Natalie Lowe, John W. Davey, Mark L. Blaxter & Angus Davison
Studies on the classic shell colour and banding polymorphism of the land snail Cepaea played a crucial role in establishing the importance of natural selection in maintaining morphological variation. Cepaea is also a pre-eminent model for ecological genetics because the outward colour and banding phenotype is entirely genetically determined, primarily by a ‘supergene’ of at least five loci. Unfortunately, progress in understanding the evolution and maintenance of the Cepaea polymorphism stalled, partly because of a...

Data from: Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine.

Jarrod D. Hadfield, Elizabeth A. Heap, Florian Bayer, Elizabeth A. Mittell & Nicholas M. A. Crouch
Cross-fostering experiments are widely used by quantitative geneticists to study genetics and by behavioral ecologists to study the effects of prenatal in- vestment. Generally, the effects of genes and prenatal investment are confounded and the interpretation given to such experiments is largely dependent on the in- terests of the researcher. Using a large-scale well controlled experiment on a wild population of blue tits (Cyanistes caeruleus) we are able to partition variation in body mass across...

Data from: Variation in plastic responses of a globally distributed picoplankton species to ocean acidification

Elisa Schaum, Rost Björn, J. Millar Andrew & Collins Sinéad
Phytoplankton are the basis of marine food webs, and affect biogeochemical cycles. As CO2 levels increase, shifts in the frequencies and physiology of ecotypes within phytoplankton groups will affect their nutritional value and biogeochemical function. However, studies so far are based on a few representative genotypes from key species. Here, we measure changes in cellular function and growth rate at atmospheric CO2 concentrations predicted for the year 2100 in 16 ecotypes of the marine picoplankton...

Data from: Hybridisation in closely related Rhododendron species: half of all species differentiating markers experience serious transmission ratio distortion

Tobias Marczewski, David F. Chamberlain & Richard I. Milne
An increasing number of studies of hybridization in recent years have revealed that complete reproductive isolation between species is frequently not finalized in more or less closely related organisms. Most of these species do, however, seem to retain their phenotypical characteristics despite the implication of gene flow, highlighting the remaining gap in our knowledge of how much of an organism's genome is permeable to gene flow, and which factors promote or prevent hybridization. We used...

Data from: The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees

Josh A. Firth, Jarrod D. Hadfield, Anna W. Santure, Jon Slate & Ben C. Sheldon
Quantitative genetic analysis is often fundamental for understanding evolutionary processes in wild populations. Avian populations provide a model system due to the relative ease of inferring relatedness amongst individuals through observation. However, extra-pair paternity (EPP) creates erroneous links within the social pedigree. Previous work has suggested this causes minor underestimation of heritability if paternal misassignment is random and hence not influenced by the trait being studied. Nevertheless, much literature suggests numerous traits are associated with...

Data from: Faster-X Effects in two Drosophila lineages

Victoria Ávila, Sophie Marion De Procé, José L. Campos, Helen Borthwick, Brian Charlesworth & Andrea J. Betancourt
Under certain circumstances, X-linked loci are expected to experience more adaptive substitutions than similar autosomal loci. To look for evidence of faster-X evolution, we analyzed the evolutionary rates of coding sequences in two sets of Drosophila species, the melanogaster and pseudoobscura clades, using whole-genome sequences. One of these, the pseudoobscura clade, contains a centric 15 fusion between the ancestral X chromosome and the autosomal arm homologous to 3L in D.melanogaster. This offers an opportunity to...

Measurements of respiration and microbial assimilation of carbon substrates and priming of soil organic matter mineralisation in tropical lowland and montane forest soils

J. Whitaker, N. Ostle, N. McNamara, A.T. Nottingham, A.W. Stott, R.D. Bardgett, N. Salinas, A.J.Q. Ccahuana & P. Meir
This dataset includes measurements of microbial community composition by phospholipid fatty acid (PLFA) analysis, soil respiration (Carbon dioxide (CO2)), soil physico-chemical properties and 13C enrichment in CO2 samples and microbial Phospholipid Fatty Acids (PLFAs). Data were produced for an investigation of the effects of carbon (C) substrate addition on soil carbon cycling processes in ten tropical soils from the Peruvian Andes. Soils were amended with 13C labelled substrates (xylose, glycine, vanillin and hemicellulose) and incubated...

Data from: Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird

Alexandra Pavlova, J. Nevil Amos, Leo Joseph, Kate Loynes, Jeremy J. Austin, J. Scott Keogh, Graham N. Stone, James Allan Nicholls & Paul Sunnucks
Relationships among multi-locus genetic variation, geography and environment can reveal how evolutionary processes affect genomes. We examined the evolution of an Australian bird, the eastern yellow robin Eopsaltria australis, using mitochondrial (mtDNA) and nuclear (nDNA) genetic markers, and bioclimatic variables. In southeastern Australia, two divergent mtDNA lineages occur east and west of the Great Dividing Range, perpendicular to latitudinal nDNA structure. We evaluated alternative scenarios to explain this striking discordance in landscape genetic patterning. Stochastic...

Data from: Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Pablo Fuentes-Utrilla, Martin Venturas, Peter M. Hollingsworth, Jane Squirrell, Carmen Collada, Graham N. Stone & Luis Gil
Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity...

Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates

Simon Aeschbacher, Andreas Futschik & Mark A. Beaumont
We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland....

Data from: Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome

Yann X. C. Bourgeois, Emeline Lhuillier, Timothée Cézard, Joris A. M. Bertrand, Boris Delahaie, Josselin Cornuault, Thomas Duval, Olivier Bouchez, Borja Milá & Christophe Thébaud
Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white-eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18–25 individuals using a single sequencing lane. This allowed us to build around 600 000 contigs, among which at least...

Soil temperature profiles from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset consists of soil temperature profiles from permafrost in subarctic Canada. Soil temperature profiles were monitored during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus, thawing features of peatland plateaus, unburnt and burnt black spruce forests, and additional sites.

Soil thaw depth from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This datasets contains measures of soil thaw depth from permafrost in subarctic Canada. Soil thaw depth was measured in 2013 and 2014 in sites from Yukon and Northwest Territories.

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