422 Works

Diary, letters and poems of Marjory Fleming

The correlates of intraspecific variation in nest height and nest building duration in the Eurasian blue tit Cyanistes caeruleus

Dagmar Der Weduwen, Katharine Keogan, Jelmer Samplonius, Albert Phillimore & Jack Shutt
Birds build nests primarily as a receptacle to lay their eggs in, but they can also provide secondary benefits including structural support, camouflage, and adjustment of the microclimate surrounding the eggs and offspring. The factors underlying intraspecific variation in nest characteristics are poorly understood. In this study, we aim to identify the environmental factors that predict nest height variation and the duration of nest building in blue tits (Cyanistes caeruleus), evaluating latitude, elevation, temperature, and...

Rare missense functional variants at COL4A1 and COL4A2 in sporadic intracerebral hemorrhage

Jaeyoon Chung, Graham Hamilton, Minsup Kim, Sandro Marini, Bailey Montgomery, Jonathan Henry, Art Cho, Devin Brown, Bradford Worrall, James Meschia, Scott Silliman, Magdy Selim, David Tirschwell, Chelsea Kidwell, Brett Kissela, Steven Greenberg, Anand Viswanathan, Joshua Goldstein, Carl Langefeld, Kristiina Rannikmae, Catherine Sudlow, Neshika Samarasekera, Mark Rodrigues, Rustam Salman, James Prendergast … & Christopher Anderson
Objective To test the genetic contribution of rare missense variants in COL4A1 and COL4A2 in which common variants are genetically associated with sporadic intracerebral hemorrhage (ICH), we performed rare variant analysis in multiple sequencing data for the risk for sporadic ICH. Methods We performed sequencing across 559Kbp at 13q34 including COL4A1 and COL4A2 among 2,133 individuals (1,055 ICH cases; 1,078 controls) in US-based and 1,492 individuals (192 ICH cases; 1,300 controls) from Scotland-based cohorts, followed...

Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia

Kai Jiang, Xin Tong, Yan-Qian Ding, Zheng-Wei Wang, Li-Yuan Miao, Yue-E Xiao, Wei-Chang Huang, Yong-Hong Hu & Xiao-Yong Chen
This dataset contains one README file and two raw data files on the distribution and genetic data described in the paper: Jiang et al. (2021) Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia. Journal of Biogeography. Ecological niche modeling was employed to predict the potential distribution of M. thunbergii during the Last Glacial Maximum (LGM) and the last interglacial period. Nuclear microsatellite and chloroplast markers were...

Data from: RAD-mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

Suo Qiu, Roberta Bergero, Sara Guirao-Rico, Jose L. Campos, Timothée Cezard, Karim Gharbi & Deborah Charlesworth
How loss of genetic exchanges (recombination) evolves between sex chromosomes is a long-standing question. Suppressed recombination may evolve when a sexually antagonistic (SA) polymorphism occurs in a partially sex-linked, “pseudo-autosomal’ region (or “PAR”), maintaining allele frequency differences between the two sexes, and creating selection for closer linkage with the fully sex-linked region of the Y chromosome in XY systems, or the W in ZW sex chromosome systems. Most evidence consistent with the SA polymorphism hypothesis...

Data from: Rapid parallel evolution of aberrant traits in the diversification of the Gulf of Guinea white-eyes (Aves, Zosteropidae)

Martim Melo, Ben H. Warren & Peter J. Jones
Archipelago-endemic bird radiations are familiar to evolutionary biologists as key illustrations of evolutionary patterns. However, such radiations are in fact rare events. White-eyes (Zosteropidae) are birds with an exceptionally high colonization and speciation potential; they have colonized more islands globally than any other passerine group and include the most species-rich bird genus. The multiplication of white-eye island-endemics has been consistently attributed to independent colonisations from the mainland; the white-eyes of the Gulf of Guinea archipelago...

Data from: How integrated are behavioural and endocrine stress response traits? A repeated measures approach to testing the stress coping style model

Kay Boulton, Elsa Couto, Andrew J. Grimmer, Ryan L. Earley, Adelino V.M. Canario, Alastair J. Wilson, Craig A. Walling & Adelino V. M. Canario
It is widely expected that physiological and behavioral stress responses will be integrated within divergent stress-coping styles (SCS) and that these may represent opposite ends of a continuously varying reactive–proactive axis. If such a model is valid, then stress response traits should be repeatable and physiological and behavioral responses should also change in an integrated manner along a major axis of among-individual variation. While there is some evidence of association between endocrine and behavioral stress...

Data from: Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence

Melanie Clerc, D. Ebert & M. D. Hall
How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the...

Data from: Recombination changes at the boundaries of fully and partially sex-linked regions between closely related Silene species pairs

Jose L. Campos, Suo Qiu, Sara Guirao-Rico, Roberta Bergero & Deborah Charlesworth
The establishment of a region of suppressed recombination is a critical change during sex chromosome evolution, leading to such properties as Y (and W) chromosome genetic degeneration, accumulation of repetitive sequences and heteromorphism. Although chromosome inversions can cause large regions to have suppressed recombination, and inversions are sometimes involved in sex chromosome evolution, gradual expansion of the non-recombining region could potentially sometimes occur. We here test whether closer linkage has recently evolved between the sex-determining...

Data from: Early Plasmodium-induced inflammation does not accelerate aging in mice

Cédric Lippens, Emmanuel Guivier, Sarah E. Reece, Aidan J. O'Donnell, Stephane Cornet, Bruno Faivre & Gabriele Sorci
Aging is associated with a decline of performance leading to reduced reproductive output and survival. While the antagonistic pleiotropy theory of aging has attracted considerable attention, the molecular/physiological functions underlying the early-life benefits/late-life costs paradigm remain elusive. We tested the hypothesis that while early activation of the inflammatory response confers benefits in terms of protection against infection, it also incurs costs in terms of reduced reproductive output at old age, and shortened longevity. We infected...

Data from: How reliably can we infer diversity-dependent diversification from phylogenies?

Rampal S. Etienne, Alex L. Pigot, Albert Phillimore & Albert B. Phillimore
Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking. Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings – on survival of the birth–death process given the crown age, on...

Data from: Genetics and genomics of an unusual selfish sex ratio distortion in an insect

Phineas T. Hamilton, Christina N. Hodson, Caitlin I. Curtis & Steve J. Perlman
Diverse selfish genetic elements have evolved the ability to manipulate reproduction to increase their transmission, and this can result in highly distorted sex ratios. Indeed, one of the major explanations for why sex determination systems are so dynamic is because they are shaped by ongoing coevolutionary arms races between sex ratio distorting elements and the rest of the genome. Here, we use genetic crosses and genome analysis to describe an unusual sex ratio distortion with...

Data from: Measuring selection when parents and offspring interact

Caroline E. Thomson & Jarrod D. Hadfield
Non-social and social selection gradients are key evolutionary parameters in systems where individuals interact. They are most easily obtained by regressing an individual's fitness on the trait values of the individual and its social partner. In the context of parental care it is more common to regress the trait value of the parents (i.e. the social partner) on a ‘mixed’ fitness measure that is a function of the parent's and offspring's fitness (for example, the...

Data from: Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast‐Z effect in Heliconius

Ana Pinharanda, Marjolaine Rousselle, Simon H. Martin, Joseph J. Hanly, John W. Davey, Sujai Kumar, Nicolas Galtier & Chris D. Jiggins
Sex chromosomes have different evolutionary properties compared to autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution for a group of butterflies. First, we improve the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then, we analyse RNA from male and...

Data from: Estimating the number of sexual events per generation in a facultatively sexual haploid population

Richard A. Ennos & Xinsheng Hu
In populations of facultatively sexual organisms the proportion of sexually produced offspring contributed each generation is a critical determinant of their evolutionary potential. However, estimating this parameter in natural populations has proved difficult. Here we develop a population genetic model for estimating the number of sexual events occurring per generation for facultatively sexual haploids possessing a biallelic mating type locus (e.g. Chlamydomonas, ascomycete fungi). Our model treats the population as two subpopulations possessing opposite mating...

Data from: Inbred burying beetles suffer fitness costs from making poor decisions

Jon Richardson, Pauline Comin & Per T. Smiseth
There is a growing interest in how environmental conditions, such as resource availability, can modify the severity of inbreeding depression. However, little is known about whether inbreeding depression is associated with differences in individual decision-making. For example, decisions about how many offspring to produce are also often based upon the prevailing environmental conditions, such as resource availability, and getting these decisions wrong may have important fitness consequences for both parents and offspring. We tested for...

Data from: Genetic differentiation and species cohesion in two widespread Central American Begonia species

Alex D. Twyford, Catherine A. Kidner & Richard A. Ennos
Begonia is one of the ten largest plant genera, with over 1500 species. This high species richness may in part be explained by weak species cohesion, which has allowed speciation by divergence in allopatry. In this study, we investigate species cohesion in the widespread Central American Begonia heracleifolia and Begonia nelumbiifolia, by genotyping populations at microsatellite loci. We then test for post-zygotic reproductive barriers using experimental crosses, and assess whether sterility barriers are related to...

Data from: Patterns of mating and generation of diversity in a Geum hybrid swarm

Markus Ruhsam, Peter M. Hollingsworth & Richard A. Ennos
To understand the evolutionary consequences of hybridization between the outcrossing plant Geum rivale and the selfer G. urbanum we tested the predictions of two simple models which assume either A). low or B). high pollen fitness in hybrids. Model A predicts only four genotypic classes (G. rivale, G. rivale backcross (BCR), F1 and G. urbanum) and asymmetric introgression from inbreeding to outbreeding species. Model B predicts additional genotypic classes and potential generation of novel inbreeding...

Data from: Introgression and the fate of domesticated genes in a wild mammal population

Philine G. D. Feulner, Jacob Gratten, James W. Kijas, Peter M. Visscher, Josephine M. Pemberton, Jon Slate & Jon. Slate
When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re-introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high-throughput genotyping with 25 years of long-term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free-living Soay sheep of St Kilda, and more modern...

Data from: Substantial contribution of submicroscopical Plasmodium falciparum gametocyte carriage to the infectious reservoir in an area of seasonal transmission.

André Lin Ouédraogo, Teun Bousema, Petra Schneider, Sake J. De Vlas, Edith Ilboudo-Sanogo, Nadine Cuzin-Ouattara, Issa Nébié, Will Roeffen, Jan Peter Verhave, Adrian J.F. Luty & Robert Sauerwein
Background: Man to mosquito transmission of malaria depends on the presence of the sexual stage parasites, gametocytes, that often circulate at low densities. Gametocyte densities below the microscopical threshold of detection may be sufficient to infect mosquitoes but the importance of submicroscopical gametocyte carriage in different transmission settings is unknown. Methodology/Principal Findings: Membrane feeding experiments were carried out on 80 children below 14 years of age at the end of the wet season in an...

Data from: Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

Nian Wang, Marian Thomson, William J. A. Bodles, Robert M. M. Crawford, Harriet V. Hunt, Alan Watson Featherstone, Jaume Pellicer & Richard J. A. Buggs
New sequencing technologies allow development of genome-wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridisation. We present a de novo reference genome sequence assembly, from 67X short read coverage, of Betula nana (dwarf birch) – a diploid that is the keystone woody species of sub-arctic scrub communities but of conservation concern in Britain. We also present...

Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Simon H. Martin, Kanchon K. Dasmahapatra, Nicola J. Nadeau, Camilo Salazar, James R. Walters, Fraser Simpson, Mark Blaxter, Andrea Manica, James Mallet & Chris D. Jiggins
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole genome sequences of 31 individuals. Comparisons between...

Data from: Special features of RAD Sequencing data: implications for genotyping

John W. Davey, Timothée Cezard, Pablo Fuentes-Utrilla, Cathlene Eland, Karim Gharbi & Mark L. Blaxter
RAD Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools...

Data from: A framework for estimating the fixation time of an advantageous allele in stepping-stone models

Matthew Hartfield
Determining how population subdivision increases the fixation time of an advantageous allele is an important problem in evolutionary genetics as this influences many processes. Here, I lay out a framework for calculating the fixation time of a positively selected allele in a subdivided population, as a function of the number of demes present, the migration rate between them, and the manner in which they are connected. Using this framework it becomes clear that a beneficial...

Data from: The experimental evolution of herbicide-resistance in Chlamydomonas reinhardtii results in a positive correlation between fitness in the presence and absence of herbicides

Tom Vogwill, Nick Colegrave, Paul Neve & Mato Lagator
Pleiotropic fitness trade-offs will be key determinants of the evolutionary dynamics of selection for pesticide resistance. However, for herbicide resistance, empirical support for a fitness cost of resistance is mixed, and it is therefore also questionable what further ecological trade-offs can be assumed to apply to herbicide resistance. Here, we test the existence of trade-offs by experimentally evolving herbicide resistance in Chlamydomonas reinhardtii. Although fitness costs are detected for all herbicides, we find that, counterintuitively,...

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