31 Works

Data from: The role of cis regulatory evolution in maize domestication

Zachary H. Lemmon, Robert Bukowski, Qi Sun & John F. Doebley
Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ~17,000 genes showing evidence of regulatory divergence between maize and teosinte. However,...

Data from: A Palaeozoic stem-group to mite harvestmen revealed through integration of phylogenetics and development

Russell J. Garwood, Prashant P. Sharma, Jason A. Dunlop & Gonzalo Giribet
Successfully placing fossils in phylogenies is integral to understanding the tree of life. Crown-group Paleozoic members of the arachnid order Opiliones are indicative of ancient origins and one of the earliest arthropod terrestrialization events. Opiliones epitomize morphological stasis, and all known fossils have been placed within the four extant suborders. Here we report a Carboniferous harvestman species, Hastocularis argusgen. nov., sp. nov., reconstructed with microtomography (microCT). Phylogenetic analysis recovers this species, and the Devonian Eophalangium...

Data from: Species richness of wild bees, but not the use of managed honey bees, increases fruit set of a pollinator-dependent crop

Rachel E. Mallinger & Claudio Gratton
1. Native, wild bees are important pollinators for both crop and wild plants. With concerns over the availability and cost of managed honey bees, attention has turned to native, wild bees as crop pollinators. However, the ability of native, wild bees to provide sufficient pollination may depend on their populations at local scales. 2. Therefore, at the farm scale, we examined the pollination contribution of both native, wild bees and managed honey bees to apples,...

Data from: The estimation of tree posterior probabilities using conditional clade probability distributions

Bret Larget
In this paper I introduce the idea of conditional independence of separated subtrees as a principle by which to estimate the posterior probability of trees using conditional clade probability distributions rather than simple sample relative frequencies. I describe an algorithm for these calculations and software which implements these ideas. I show that these alternative calculations are very similar to simple sample relative frequencies for high probability trees, but are substantially more accurate for relatively low...

Data from: The dual nature of hemocyanin in the establishment and persistence of the squid-vibrio symbiosis

Natacha Kremer, Julia Schwartzman, René Augustin, Lawrence Zhou, Edward G. Ruby, Stéphane Hourdez & Margaret J. McFall-Ngai
We identified and sequenced from the squid Euprymna scolopes two isoforms of haemocyanin that share the common structural/physiological characteristics of haemocyanin from a closely related cephalopod, Sepia officinalis, including a pronounced Bohr effect. We examined the potential roles for haemocyanin in the animal's symbiosis with the luminous bacterium Vibrio fischeri. Our data demonstrate that, as in other cephalopods, the haemocyanin is primarily synthesized in the gills. It transits through the general circulation into other tissues...

Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Kevin L. Childs, Aruna Nandety, Candice N. Hirsch, Elsa Góngora-Castillo, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum) is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing reads derived from crown, young shoot and leaf tissues, we generated sequence data from seven switchgrass cultivars,...

Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL

Zachary H. Lemmon & John F. Doebley
The domesticated crop maize and its wild progenitor, teosinte, have been used in numerous experiments to investigate the nature of divergent morphologies. This study examines a poorly understood region on the fifth chromosome of maize associated with a number of traits under selection during domestication using a QTL mapping population specific to the fifth chromosome. In contrast with other major domestication loci in maize where large effect, highly pleiotropic, single genes are responsible for phenotypic...

Data from: Insights into the maize pan-genome and pan-transcriptome

Candice N. Hirsch, Jillian M. Foerster, James M. Johnson, Rajandeep S. Sekhon, German Muttoni, Brieanne Vaillancourt, Francisco Peñagaricano, Erika Lindquist, Mary Ann Pedraza, Kerrie Barry, Natalia De Leon, Shawn M. Kaeppler & C. Robin Buell
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs...

Data from: Demographic history of a recent invasion of house mice on the isolated Island of Gough

Melissa M. Gray, Daniel Wegmann, Ryan J. Haasl, Michael A. White, Sofia I. Gabriel, Jeremy B. Searle, Richard J. Cuthbert, Peter G. Ryan & Bret A. Payseur
Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size, and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the...

Data from: Model-data assimilation of multiple phenological observations to constrain and predict leaf area index

Toni Viskari, Brady Hardiman, Ankur R. Desai & Michael C. Dietze
Our limited ability to accurately simulate leaf phenology is a leading source of uncertainty in models of ecosystem carbon cycling. We evaluate if continuously updating canopy state variables with observations is beneficial for predicting phenological events. We employed ensemble adjustment Kalman filter (EAKF) to update predictions of leaf area index (LAI) and leaf extension using tower-based photosynthetically active radiation (PAR) and moderate resolution imaging spectrometer (MODIS) data for 2002–2005 at Willow Creek, Wisconsin, USA, a...

Data from: QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

Kenneth D. Whitney, Karl W. Broman, Nolan C. Kane, Stephen M. Hovick, Rebecca A. Randell & Loren H. Rieseberg
The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H....

Data from: Spatial genetic structure in four understory Psychotria species and implications for tropical forest diversity

Terra J. Theim, Rebecca Y. Shirk & Thomas J. Givnish
Premise of the study: Tropical forests are the most species-rich terrestrial communities on Earth, and understory trees and shrubs comprise a large fraction of their plant species diversity, especially at high rainfalls. The mechanisms responsible for generating such high levels of diversity remain unknown. One hypothesis is that fleshy-fruited understory species should have limited seed dispersal due to the sedentary nature of their avian dispersers, resulting in restricted gene flow, population differentiation at small spatial...

Data from: Tree-hugging koalas demonstrate a novel thermoregulatory mechanism for arboreal mammals

Natalie J. Briscoe, Kathrine A. Handasyde, Stephen R. Griffiths, Warren P. Porter, Andrew Krockenberger & Michael R. Kearney
How climate impacts organisms depends not only on their physiology, but also whether they can buffer themselves against climate variability via their behaviour. One of the way species can withstand hot temperatures is by seeking out cool microclimates, but only if their habitat provides such refugia. Here, we describe a novel thermoregulatory strategy in an arboreal mammal, the koala Phascolarctos cinereus. During hot weather, koalas enhanced conductive heat loss by seeking out and resting against...

Data from: Pair bonding prevents reinforcing effects of testosterone in male California mice in an unfamiliar environment

Xin Zhao & Catherine A. Marler
Testosterone (T) can be released by stimuli such as social interactions, and thereby influence future social behaviours. Because the reinforcing effects of T can induce preferences for specific environmental locations, T has the potential to alter behaviour through space use. In a monogamous species, this T pulse may contribute differently to space use in sexually naive (SN) and pair-bonded (PB) males: SN males may be more likely to explore new areas to set up a...

Data from: Bayesian species delimitation combining multiple genes and traits in a unified framework

Claudia Solís-Lemus, L. Lacey Knowles & Cécile Ané
Delimitation of species based exclusively on genetic data has been advocated despite a critical knowledge gap: how might such approaches fail because they rely on genetic data alone, and would their accuracy be improved by using multiple data-types. We provide here the requisite framework for addressing these key questions. Because both phenotypic and molecular data can be analyzed in a common Bayesian framework with our program iBPP, we can compare the accuracy of delimited taxa...

Data from: Land-use history alters contemporary insect herbivore community composition and decouples plant-herbivore relationships

Philip G. Hahn & John L. Orrock
1. Past land use can create altered soil conditions and plant communities that persist for decades, although the effects of these altered conditions on consumers are rarely investigated. 2. Using a large-scale field study at 36 sites in longleaf pine (Pinus palustris) woodlands, we examined whether historic agricultural land use leads to differences in the abundance and community composition of insect herbivores (grasshoppers, families Acrididae and Tettigoniidae). 3. We measured the cover of six plant...

Data from: Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation

Marijan Posavi, Gregory William Gelembiuk, Bret Larget & Carol Eunmi Lee
Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the salt-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline...

Data from: Modeling avian biodiversity using raw, unclassified satellite imagery

Véronique St-Louis, Anna M. Pidgeon, Tobias Kuemmerle, Ruth Sonnenschein, Volker C. Radeloff, Murray K. Clayton, Brian A. Locke, Dallas Bash & Patrick Hostert
Applications of remote sensing for biodiversity conservation typically rely on image classifications that do not capture variability within coarse land cover classes. Here, we compare two measures derived from unclassified remotely sensed data, a measure of habitat heterogeneity and a measure of habitat composition, for explaining bird species richness and the spatial distribution of 10 species in a semi-arid landscape of New Mexico. We surveyed bird abundance from 1996 to 1998 at 42 plots located...

Data from: Synaptotagmin 7 functions as a Ca^2+ -sensor for synaptic vesicle replenishment

Huisheng Liu, Hua Bai, Enfu Hui, Lu Yang, Chantell S Evans, Zhao Wang, Sung E Kwon & Edwin R Chapman
Syt7 ms_eLIFE_Huisheng

Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).

Laurence R. Gesquiere, Toni E. Ziegler, Patricia A. Chen, Katherine A. Epstein, Susan C. Alberts & Jeanne Altmann
The development of non-invasive methods, particularly fecal determination, has made possible the assessment of hormone concentrations in wild animal populations. However, measuring fecal metabolites needs careful validation for each species and for each sex. We investigated whether radioimmunoassays (RIAs) previously used to measure fecal testosterone (fT) in male baboons and fecal estrogens (fE) in female baboons were well suited to measure these hormones in the opposite sex. We compared fE and fT concentrations determined by...

Data from: Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids

David Peris, Kayla Sylvester, Diego Libkind, Paula Gonçalves, José Paulo Sampaio, William G. Alexander & Chris Todd Hittinger
Reticulate evolution can be a major driver of diversification into new niches, especially in disturbed habitats and at the edges of ranges. Industrial fermentation strains of yeast provide a window into these processes, but progress has been hampered by a limited understanding of the natural diversity and distribution of Saccharomyces species and populations. For example, lager beer is brewed with Saccharomyces pastorianus, an alloploid hybrid of S. cerevisiae and S. eubayanus, a species only recently...

Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum

Joseph Evans, Jeongwoon Kim, Kevin L. Childs, Brieanne Vaillancourt, Emily Crisovan, Aruna Nandety, Daniel J. Gerhardt, Todd A. Richmond, Jeffrey A. Jeddeloh, Shawn M. Kaeppler, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic...

Data from: From refugia to rookeries: phylogeography of Atlantic green turtles

Eugenia Naro-Maciel, Brendan N. Reid, S. Elizabeth Alter, George Amato, Karen A. Bjorndal, Alan B. Bolten, Meredith Martin, Campbell J. Nairn, Brian Shamblin & Oscar Pineda-Catalan
Investigating species’ distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles (Chelonia mydas), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying...

Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus

Felipe S. Barreto, Sean D. Schoville & Ronald S. Burton
Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are...

Data from: Population dynamics of a northern-adapted mammal: disentangling the influence of predation and climate change

John W. Pokallus, Jonathan N. Pauli &
Community structure and interspecific interactions are particularly vulnerable to rapidly changing climatic regimes. Recent changes in both climate and vertebrate community assemblages have created a unique opportunity to examine the impacts of two dynamic forces on population regulation. We examined the effects of warming winter conditions and the reestablishment of a previously extirpated predator, the fisher (Martes pennanti), on regulatory mechanisms in a northern-adapted mammal, the porcupine (Erethizon dorsatum), along their southern range boundary. Using...

Registration Year

  • 2014
    31

Resource Types

  • Dataset
    31

Affiliations

  • University of Wisconsin-Madison
    31
  • Michigan State University
    5
  • Great Lakes Bioenergy Research Center
    2
  • Joint Genome Institute
    2
  • Cornell University
    2
  • City University of New York
    1
  • Fred Hutchinson Cancer Research Center
    1
  • Princeton University
    1
  • University of Michigan-Ann Arbor
    1
  • Duke University
    1