145 Works

Data from: A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait

Peter C. Zee, Helena Mendes-Soares, Yuen-Tsu Nicco Yu, Susanne A. Kraemer, Heike Keller, Stephan Ossowski, Korbinian Schneeberger & Gregory J. Velicer
While the importance of epistasis in evolution has long been recognized, remarkably little is known about the processes by which epistatic interactions evolve in real time in specific biological systems. Here, we have characterized how the epistatic fitness relationship between a social gene and an adapting genome changes radically over a short evolutionary time frame in the social bacterium Myxococcus xanthus. We show that a highly beneficial effect of this social gene in the ancestral...

Data from: The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

Desiree E. Allen & Michael Lynch
Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study we utilized a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex...

Data from: Joint effects of habitat, zooplankton, host stage structure and diversity on amphibian chytrid

Jessica L. Hite, Jaime Bosch, Saioa Fernández-Beaskoetxea, Daniel Medina & Spencer R. Hall
Why does the severity of parasite infection differ dramatically across habitats? This question remains challenging to answer because multiple correlated pathways drive disease. Here, we examined habitat–disease links through direct effects on parasites and indirect effects on parasite predators (zooplankton), host diversity and key life stages of hosts. We used a case study of amphibian hosts and the chytrid fungus, Batrachochytrium dendrobatidis, in a set of permanent and ephemeral alpine ponds. A field experiment showed...

Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages

Maurine Neiman, Dorota Paczesniak, Deanna M Soper, Austin T Baldwin & Gery Hehman
Natural animal populations are rarely screened for ploidy-level variation at a scale that allows detection of potentially important aberrations of common ploidy patterns. This type of screening can be especially important for the many mixed sexual/asexual systems where sexuals are presumed to be dioecious diploids and asexuals are assumed to be triploid and all-female. For example, elevation of ploidy level above triploidy can be a source of genetic variation and raises the possibility of gene...

Data from: Alternative paths to success in a parasite community: within-host competition can favor higher virulence or direct interference

Farrah Bashey-Visser, Hadas Hawlena & Curtis M. Lively
Selection imposed by coinfection may vary with the mechanism of within-host competition between parasites. Exploitative competition is predicted to favor more virulent parasites, while interference competition may result in lower virulence. Here, we examine whether exploitative or interference competition determines the outcome of competition between two nematode species (Steinernema spp.), which in combination with their bacterial symbionts (Xenorhabdus spp.), infect and kill insect hosts. Multiple isolates of each nematode species, carrying their naturally associated bacteria,...

Data from: Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers

Julianno Bergoch Monteiro Sambatti, Jared L. Strasburg, Daniel Ortiz-Barrientos, Eric J. Baack & Loren Henry Rieseberg
In several cases, estimates of gene flow between species appears to be higher than predicted given the strength of interspecific barriers. However, as far as we are aware, detailed measurements of reproductive isolation have not previously been compared with a coalescent-based assessment of gene flow. Here, we contrast these two measures in two species of sunflower, Helianthus annuus and Helianthus petiolaris. We quantified the total reproductive barrier strength between these species by compounding the contributions...

Data from: Gene-tree reconciliation with MUL-trees to resolve polyploidy events

Gregg W.C. Thomas, S. Hussain Ather & Matthew W. Hahn
Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together...

Data from: Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals

Gregg W. C. Thomas & Matthew W. Hahn
Convergent evolution occurs when the same trait arises independently in multiple lineages. In most cases of phenotypic convergence such transitions are adaptive, so finding the underlying molecular causes of convergence can provide insight into the process of adaptation. Convergent evolution at the genomic level also lends itself to study by comparative methods, though molecular convergence can also occur by chance, adding noise to this process. Parker et al. (2013) studied convergence across the genomes of...

Data from: Global database of matched Plasmodium falciparum and P. vivax incidence and prevalence records from 1985–2013

Katherine E. Battle, Carlos A. Guerra, Nick Golding, Kirsten A. Duda, Ewan Cameron, Rosalind E. Howes, Iqbal R. F. Elyazar, J. Kevin Baird, , Peter W. Gething, David L. Smith & Simon I. Hay
Measures of clinical incidence are necessary to help estimate the burden of a disease. Incidence is a metric not commonly measured in malariology because the longitudinal surveys required are costly and labour intensive. This database is an effort to collate published incidence records obtained using active case detection for Plasmodium falciparum and Plasmodium vivax malaria. The literature search methods, data abstraction procedures and data processing procedures are described here. A total of 1,680 spatio-temporally unique...

Data from: Hybrid incompatibility between D. virilis and D. lumei is stronger in the presence of transposable elements

Dean Castillo & Leonie Moyle
Mismatches between parental genomes in selfish elements are frequently hypothesized to underlie hybrid dysfunction and drive speciation. However, because the genetic basis of most hybrid incompatibilities is unknown, testing the contribution of selfish elements to reproductive isolation is difficult. Here we evaluated the role of transposable elements (TEs) in hybrid incompatibilities between Drosophila virilis and D. lummei by experimentally comparing hybrid incompatibility in a cross where active TEs are present in D. virilis (TE+) and...

Data from: Connecting the sun to flowering in sunflower adaptation

Benjamin K Blackman, Scott D Michaels & Loren H Rieseberg
Species living in seasonal environments often adaptively time their reproduction in response to photoperiod cues. We characterized the expression of genes in the flowering-time regulatory network across wild populations of the common sunflower, Helianthus annuus, that we found to be adaptively differentiated for photoperiod response. The observed clinal variation was associated with changes at multiple hierarchical levels in multiple pathways. Paralog-specific changes in FT homolog expression and tissue-specific changes in SOC1 homolog expression were associated...

Data from: Sexual, fecundity, and viability selection on flower size and number in a sexually dimorphic plant

Lynda F. Delph & Christopher R. Herlihy
The evolution of sexual dimorphism will depend on how sexual, fecundity and viability selection act within each sex, with the different forms of selection potentially operating in opposing directions. We examined selection in the dioecious plant Silene latifolia using planted arrays of selection lines that differed in flower size (small vs. large). In this species a flower size/number tradeoff exists within each sex, and males produce smaller and more numerous flowers than females. Moreover, floral...

Data from: Surprising complexity of the ancestral apoptosis network

Christian M. Zmasek, Qing Zhang, Yuzhen Ye & Adam Godzik
Apoptosis, one of the main types of programmed cell death, is regulated and performed by a complex protein network. Studies in model organisms, mostly in the nematode C. elegans, identified a relatively simple apoptotic network consisting of only a few proteins. However, analysis of several recently sequenced invertebrate genomes, ranging from the cnidarian sea anemone Nematostella vectensis, representing one of the morphologically simplest metazoans, to the deuterostomes sea urchin and amphioxus, contradicts the current paradigm...

Data from: Morphological integration in the hominin dentition: evolutionary, developmental, and functional factors.

Aida Gómez-Robles & P. David Polly
As the most common and best preserved remains in the fossil record, teeth are central to our understanding of evolution. However, many evolutionary analyses based on dental traits overlook the constraints that limit dental evolution. These constraints are diverse, ranging from developmental interactions between the individual elements of a homologous series (the whole dentition) to functional constraints related to occlusion. This study evaluates morphological integration in the hominin dentition and its effect on dental evolution...

Data from: Directional cultural change by modification and replacement of memes

Gonçalo C Cardoso & Jonathan W Atwell
Evolutionary approaches to culture remain contentious. A source of contention is that cultural mutation may be substantial and, if it drives cultural change, then current evolutionary models are not adequate. But we lack studies quantifying the contribution of mutations to directional cultural change. We estimated the contribution of one type of cultural mutations – modification of memes - to directional cultural change using an amenable study system: learned birdsongs in a species that recently entered...

Data from: Running with the Red Queen: host-parasite coevolution selects for biparental sex

Levi T. Morran, Olivia G. Schmidt, Ian A. Gelarden, & Curtis M. Lively
Most organisms reproduce through outcrossing, even though it comes with significant costs. The Red Queen hypothesis proposes that selection from coevolving pathogens facilitates the persistence of outcrossing in spite of these costs. We utilized experimental coevolution to test the Red Queen hypothesis, and found that coevolution with a bacterial pathogen (Serratia marcescens) resulted in significantly more outcrossing in mixed mating experimental populations of the nematode Caenorhabditis elegans. Furthermore, we found that coevolution with the pathogen...

Data from: Population genomics of wild and laboratory zebrafish (Danio rerio)

Andrew R Whiteley, Anuradha Bhat, Emilia P Martins, Richard L Mayden, M Arunachalam, Silva Uusi-Heikkilä, A.T.A. Ahmed, Jiwan Shrestha, Matthew Clark, Derek Stemple & Louis Bernatchez
Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and...

Data from: The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

Desiree E. Allen & Michael Lynch
Cyclical parthenogens are a valuable system in which to empirically test theoretical predictions as to the genetic consequences of sexual reproduction in natural populations, particularly if the frequency of sexual relative to asexual reproduction can be quantified. In this study we utilized a series of lake populations of the cyclical parthenogen, Daphnia pulicaria, that vary consistently in their investment in sexual reproduction, to address the questions of whether the ecological variation in investment in sex...

Data from: Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers

Julianno Bergoch Monteiro Sambatti, Jared L. Strasburg, Daniel Ortiz-Barrientos, Eric J. Baack & Loren Henry Rieseberg
In several cases, estimates of gene flow between species appears to be higher than predicted given the strength of interspecific barriers. However, as far as we are aware, detailed measurements of reproductive isolation have not previously been compared with a coalescent-based assessment of gene flow. Here, we contrast these two measures in two species of sunflower, Helianthus annuus and Helianthus petiolaris. We quantified the total reproductive barrier strength between these species by compounding the contributions...

Data from: Wide variation in ploidy level and genome size in a New Zealand freshwater snail with coexisting sexual and asexual lineages

Maurine Neiman, Dorota Paczesniak, Deanna M Soper, Austin T Baldwin & Gery Hehman
Natural animal populations are rarely screened for ploidy-level variation at a scale that allows detection of potentially important aberrations of common ploidy patterns. This type of screening can be especially important for the many mixed sexual/asexual systems where sexuals are presumed to be dioecious diploids and asexuals are assumed to be triploid and all-female. For example, elevation of ploidy level above triploidy can be a source of genetic variation and raises the possibility of gene...

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