25 Works

Data from: The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae

Joshua A. Granek, Debra Murray, Ömür Kayıkçı & Paul M. Magwene
Biofilms are microbial communities that form on surfaces. They are the primary form of microbial growth in nature and can have detrimental impacts on human health. Some strains of the budding yeast Saccharomyces cerevisiae form colony biofilms, and there is substantial variation in colony architecture between biofilm-forming strains. To identify the genetic basis of biofilm variation, we developed a novel version of quantitative trait locus mapping, which leverages cryptic variation in a clinical isolate of...

Data from: Genetics of gene expression responses to temperature stress in a sea urchin gene network

Daniel E. Runcie, David A. Garfield, Courtney C. Babbitt, Jennifer A. Wygoda, Gregory A. Wray & Sayan Mukherjee
Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress. We found that an increase from 12...

Data from: Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (Genus Oplurus)

Lauren M. Chan, Dean Choi, Achille P. Raselimanana, Hery A. Rakotondravony & Anne D. Yoder
Understanding the remarkably high species diversity and levels of endemism found among Madagascar’s flora and fauna has been the focus of many studies. One hypothesis that has received much attention proposes that Pleistocene climate fluctuations spurred diversification. However, while spatial patterns of distribution and phylogenetic relationships can provide support for biogeographic predictions, temporal estimates of divergence are required to determine the fit of these geospatial patterns to climatic or biogeographic mechanisms. We use multilocus DNA...

Data from: Unraveling the determinants of insular body size shifts

Craig R. McClain, Paul A. P. Durst, Alison G. Boyer & Clinton D. Francis
The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological, and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species’ ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak...

Data from: Role of grooming in reducing tick load in wild baboons (Papio cynocephalus)

Mercy Y. Akinyi, Susan C. Alberts, Jeanne Altmann, Nilesh B. Patel, Jenny Tung & Maamun Jeneby
Nonhuman primate species spend a conspicuous amount of time grooming during social interactions, a behaviour that probably serves both social and health-related functions. While the social implications of grooming have been relatively well studied, less attention has been paid to the health benefits, especially the removal of ectoparasites, which may act as vectors in disease transmission. In this study, we examined whether grooming behaviour reduced tick load (number of ticks) and haemoprotozoan infection status in...

Data from: Long-term data reveal patterns and controls on streamwater chemistry in a forested stream: Walker Branch, Tennessee

Brian D. Lutz, Patrick J. Mulholland & Emily S. Bernhardt
We present 20 years of weekly streamwater chemistry, hydrology, and climate data for the Walker Branch watershed in eastern Tennessee, USA. Since 1989, the watershed has experienced a ~1.0˚C increase in mean annual temperature, a ~20% decline in precipitation, and a ~30% increase in forest evapotranspiration rates. As a result, runoff has declined by ~34%. We evaluate long-term trends in streamwater concentrations and fluxes for 9 solutes and use wet deposition data to calculate approximate...

Data from: Inferring the history of interchromosomal gene transposition in Drosophila using n-Dimensional parsimony

Mira V. Han & Matthew W. Hahn
Gene transposition puts a new gene copy in a novel genomic environment. Moreover, genes moving between the autosomes and the X chromosome experience change in several evolutionary parameters. Previous studies of gene transposition have not utilized the phylogenetic framework that becomes possible with the availability of whole genomes from multiple species. Here we used parsimonious reconstruction on the genomic distribution of gene families to analyze interchromosomal gene transposition in Drosophila. We identified 782 genes that...

Data from: Predicting the response to simultaneous selection: genetic architecture and physiological constraints

Goggy Davidowitz, H. Frederik Nijhout & Derek A. Roff
A great deal is known about the evolutionary significance of body size and development time. They are determined by the non-linear interaction of three physiological traits: two hormonal events and growth rate. In this study we investigate how the genetic architecture of the underlying three physiological traits affects the simultaneous response to selection on the two life history traits in the hawk moth Manduca sexta. The genetic architecture suggests that when the two life history...

Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

Fredrik Ronquist, Seraina Klopfstein, Lars Vilhelmsen, Susanne Schulmeister, Debra L. Murray & Alexandr P. Rasnitsyn
Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically,...

Data from: Amount or pattern? Grassland responses to the heterogeneity and availability of two key resources

Fernando T. Maestre & James F. Reynolds
Patterns of resource availability and heterogeneity shape the composition, productivity, and dynamics of plant assemblages in a wide variety of terrestrial ecosystems. Despite this, the responses of plant assemblages to simultaneous changes in the availability and heterogeneity of more than a single resource are virtually unknown. To fill this gap, microcosms consisting of assemblages formed by Lolium perenne, Plantago lanceolata, Anthoxantum odoratum, Holcus lanatus, and Trifolium repens were grown in a factorial experiment with the...

Data from: Spatial heterogeneity in soil nutrient supply modulates nutrient and biomass responses to multiple global change drivers in model grassland communities

Fernando T. Maestre & James F. Reynolds
Changes in the atmospheric concentration of carbon dioxide ([CO2]), nutrient availability and biotic diversity are three major drivers of the ongoing global change impacting terrestrial ecosystems worldwide. While it is well established that soil nutrient heterogeneity exerts a strong influence on the development of plant individuals and communities, it is virtually unknown how nutrient heterogeneity and global change drivers interact to affect plant performance and ecosystem functioning. We conducted a microcosm experiment to evaluate the...

Data from: Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika.

Jason L. Brown & L. Lacey Knowles
A central goal of phylogeography is to identify and characterize the processes underlying divergence. One of the biggest impediments currently faced is how to capture the spatiotemporal dynamic under which a species evolved. Here we described an approach that couples species distribution models (SDMs), demographic and genetic models in a spatiotemporally explicit manner. Analyses of American Pika (Ochotona priniceps) from the sky islands of the central Rocky Mountains of North America are used to provide...

Data from: Ecological selection as the cause and sexual differentiation as the consequence of species divergence?

Elen Oneal & L. Lacey Knowles
Key conceptual issues about speciation go unanswered without consideration of non-mutually exclusive factors. With tests based on speciation theory, we exploit the island distribution and habitat differences exhibited by the Caribbean cricket Amphiacusta sanctaecrucis, and with an analysis of divergent ecological selection, sexually selected differentiation, and geographic isolation, address how these different factors interact. After testing for divergent selection by comparing neutral genetic and morphological divergence in one ecological (mandible shape) and one sexual (male...

Data from: Long distance dispersal and genetic structure of natural populations: an assessment of the inverse isolation hypothesis in peat mosses

Peter Szovenyi, A. Jonathan Shaw & Sebastian Surdberg
It is well accepted that the shape of the dispersal kernel, especially its tail, has a substantial effect on the genetic structure of species. Theory predicts that dispersal by fat-tailed kernels reshuffles genetic material and thus preserves genetic diversity during colonization. Moreover, if efficient long distance dispersal is coupled with random colonization, an inverse isolation effect is predicted to develop in which increasing genetic diversity per colonizer is expected with increasing distance from a genetically...

Data from: Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events

Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron David Siler, Mark T. Holder & Rafe M. Brown
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the...

Data from: Spatially and temporally varying selection on intrapopulation quantitative trait loci for a life history trade-off in Mimulus guttatus

Julius P. Mojica, Young Wha Lee, John H. Willis & John K. Kelly
Why do populations remain genetically variable despite strong continuous natural selection? Mutation reconstitutes variation eliminated by selection and genetic drift, but theoretical and experimental studies each suggest that mutation-selection balance insufficient to explain extant genetic variation in most complex traits. The alternative hypothesis of balancing selection, wherein selection maintains genetic variation, is an aggregate of multiple mechanisms (spatial and temporal heterogeneity in selection, frequency-dependent selection, antagonistic pleiotropy, etc.). Most of these mechanisms have been demonstrated...

Data from: A new perspective on Punctelia subrudecta (Parmeliaceae) in North America: previously rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem

James C. Lendemer & Brendan P. Hodkinson
In North America the names Punctelia subrudecta and P. perreticulata have variously been applied to corticolous sorediate Punctelia specimens with lecanoric acid and a pale lower surface. ITS1, 5.8S, and ITS2 sequence data were generated from a geographically and morphologically broad sampling from within these specimens, and a molecular phylogeny was inferred. A combined approach using morphology, geography, and phylogeny was used to circumscribe three distinct species in North America, one of which is described...

Data from: High diversity and widespread occurrence of mitotic spore mats in ectomycorrhizal Pezizales

Rosanne A. Healy, Matthew E. Smith, Gregory M. Bonito, Donald H. Pfister, Gonzalo G. Guevara, Caroline Hobart, Leticia Kumar, Thai Lee, Katherine Stafford, Zai-Wei Ge, Rytas Vilgalys, Gwendolyn Williams, James Trappe, David J. McLaughlin &
Fungal mitospores may function as dispersal units and/ or spermatia and thus play a role in distribution and/or mating of species that produce them. Mitospore production in ectomycorrhizal (EcM) Pezizales is rarely reported, but here we document mitospore production by a high diversity of EcM Pezizales on three continents, in both hemispheres. We sequenced the internal transcribed spacer (ITS) and partial large subunit (LSU) nuclear rDNA from 292 spore mats (visible mitospore clumps) collected in...

Data from: Biomass responses to elevated CO2, soil heterogeneity and diversity: an experimental assessment with grassland assemblages

Fernando T. Maestre & James F. Reynolds
While it is well-established that the spatial distribution of soil nutrients (soil heterogeneity) influences the competitive ability and survival of individual plants, as well as the productivity of plant communities, there is a paucity of data on how soil heterogeneity and global change drivers interact to affect plant performance and ecosystem functioning. To evaluate the effects of elevated CO2, soil heterogeneity and diversity (species richness and composition) on productivity, patterns of biomass allocation and root...

Data from: Mapping of within-species segregation distortion in D. persimilis and hybrid sterility between D. persimilis and D. pseudoobscura

Shannon R. McDermott & Mohamed A. F. Noor
In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids which may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work by using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL...

Data from: Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

Heather M. Hines, Riccardo Papa, Mayte Ruiz, Alexie Papanicolaou, Charles Wang, H. Frederik Nijhout, W. Owen McMillan & Robert D. Reed
BACKGROUND: Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of...

Data from: A gain-of-function polymorphism controlling complex traits and fitness in nature

Kasavajhala V. S. K. Prasad, Bao-Hua Song, Carrie Olson-Manning, Jill T. Anderson, Cheng-Ruei Lee, M. Eric Schranz, Aaron J. Windsor, Maria J. Clauss, Antonio J. Manzaneda, Ibtehaj Naqvi, Michael Reichelt, Jonathan Gershenzon, Sanjeewa G. Rupasinghe, Mary A. Schuler & Thomas Mitchell-Olds
Identification of the causal genes that control complex trait variation remains challenging, limiting our appreciation of the evolutionary processes that influence polymorphisms in nature. We cloned a quantitative trait locus that controls plant defensive chemistry, damage by insect herbivores, survival, and reproduction in the natural environments where this polymorphism evolved. These ecological effects are driven by duplications in the BCMA (branched-chain methionine allocation) loci controlling this variation and by two selectively favored amino acid changes...

Data from: Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change

Jill T. Anderson, David W. Inouye, Amy M. McKinney, Robert I. Colautti & Thomas Mitchell-Olds
Anthropogenic climate change has already altered the timing of major life history transitions, such as the initiation of reproduction. Both phenotypic plasticity and adaptive evolution can underlie rapid phenological shifts in response to climate change but their relative contributions are poorly understood. Here, we combine a continuous 38-year field survey with quantitative genetic field experiments to assess adaptation in the context of climate change. We focused on Boechera stricta (Brassicaeae), a mustard native to the...

Data from: Rapid change in the thermal tolerance of a tropical lizard

Manuel Leal & Alex R. Gunderson
The predominant view is that the thermal physiology of tropical ectotherms, including lizards, is not labile over ecological timescales. We used the recent introduction (∼35 years ago) of the Puerto Rican lizard Anolis cristatellus to Miami, Florida, to test this thermal rigidity hypothesis. We measured lower (critical thermal minimum [CTmin]) and upper (critical thermal maximum [CTmax]) thermal tolerances and found that the introduced population tolerates significantly colder temperatures (by ∼3°C) than does the Puerto Rican...

Data from: The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

Thomas L. Parchman, Zachariah Gompert, Michael J. Braun, Robb T. Brumfield, D. B. McDonald, J. Albert C. Uy, G. Zhang, Erich D. Jarvis, B. A. Schlinger & C. A. Buerkle
The processes of adaptation and speciation are expected to shape genomic variation within and between diverging species. Here we analyze genomic heterogeneity of genetic differentiation and introgression in a hybrid zone between two bird species (Manacus candei and M. vitellinus) using 59 100 SNPs, a whole genome assembly, and Bayesian models. Measures of genetic differentiation (inline image) and introgression (genomic cline center [α] and rate [β]) were highly heterogeneous among loci. We identified thousands of...

Registration Year

  • 2012
    25

Resource Types

  • Dataset
    25

Affiliations

  • Duke University
    25
  • University of Kansas
    2
  • University of Michigan-Ann Arbor
    2
  • National Evolutionary Synthesis Center
    1
  • University of South Dakota
    1
  • University of Washington
    1
  • Princeton University
    1
  • Oregon State University
    1
  • University of Wyoming
    1
  • Natural History Museum
    1