215 Works

Data from: Molecular evolution of shattering loci in U.S. weedy rice

Carrie Thurber, Michael Reagon, Briana Gross, Kenneth Olsen, Yulin Jia & Ana Caicedo
Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well...

Data from: Modularity and scaling in fast movements: power amplification in mantis shrimp

Thomas Claverie, Elliot Chan & Sheila N. Patek
Extremely fast animal actions are accomplished with mechanisms that reduce the duration of movement. This process is known as power amplification. While many studies have examined the morphology and performance of power-amplified systems, little is known about their development and evolution. Here we examine scaling and modularity in the powerful predatory appendages of a mantis shrimp, Gonodactylaceus falcatus (Crustacea, Stomatopoda). We propose that power-amplified systems can be divided into three units: an engine (e.g., muscle),...

Data from: Vertebral evolution and the diversification of squamate reptiles

Philip J. Bergmann & Duncan J. Irschick
Taxonomic, morphological and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic...

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: Constraint and opportunity: the genetic basis and evolution of modularity in the cichlid mandible

Kevin J. Parsons, Eladio Márquez & R. Craig Albertson
Modular variation, whereby the relative degree of connectivity varies within a system, is sometimes thought to evolve through natural selection. In this way, modularity may facilitate evolution. Alternatively, conserved patterns of modularity may act to constrain evolution by preventing certain functions from evolving. A comprehensive understanding of the interplay between these phenomena will require knowledge of both the inheritance and genetic basis of modularity. Here we explore these ideas in the cichlid mandible by investigating...

Data from: Exploring possible human influences on the evolution of Darwin's finches

Luis Fernando De León, Joost A.M. Raeymaekers, Eldredge Bermingham, Jeffrey Podos, Anthony Herrel & Andrew P. Hendry
Humans are an increasingly common influence on the evolution of natural populations. Potential arenas of influence include altered evolutionary trajectories within populations and modifications of the process of divergence among populations. We consider this second arena in the medium ground finch (Geospiza fortis) on Santa Cruz Island, Galápagos, Ecuador. Our study compared the G. fortis population at a relatively undisturbed site, El Garrapatero, to the population at a severely disturbed site, Academy Bay, which is...

Data from: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

Zhao Lai, Nolan C. Kane, Alex Kozik, Kathryn A. Hodgins, Katrina M. Dlugosch, Michael S. Barker, Marta Matvienko, Qian Yu, Kathryn G. Turner, Stephanie A. Pearl, Graeme D.M. Bell, Yi Zou, Chris Grassa, Alessia Guggisberg, Keith L. Adams, James V. Anderson, David P. Horvath, Richard V. Kesseli, John M. Burke, Richard W. Michelmore, Loren H. Rieseberg, Stephanie Anne Pearl & Graeme D. M. Bell
PREMISE OF THE STUDY: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic...

Data from: Consequences of multiple flower-insect interactions for subsequent plant-insect interactions and plant reproduction

Nicole L. Soper Gorden & Lynn S. Adler
Premise of the study. Plants often interact simultaneously with multiple antagonists and mutualists that can alter plant traits at the phenotypic or genetic level, subsequent plant-insect interactions, and reproduction. Although many studies have examined the effects of single floral antagonisms on subsequent pollination and plant reproduction, we know very little about the combined, potentially non-additive effects of multiple flower-insect interactions. Methods. We simulated increased florivory, nectar robbing, and pollination on field-grown Impatiens capensis. This allowed...

Data from: Phase-dependent climate-predator interactions explain three decades of variation in neonatal caribou survival

Guillaume Bastille-Rousseau, James A. Schaefer, Keith P. Lewis, Matthew Mumma, E. Hance Ellington, Nathaniel D. Rayl, Shane P. Mahoney, Darren Pouliot, Dennis L. Murray & Matthew A. Mumma
1. Climate can have direct and indirect effects on population dynamics via changes in resource competition or predation risk, but this influence can be modulated by density- or phase-dependent processes. We hypothesized that for ungulates, climatic conditions close to parturition have a greater influence on the predation risk of neonates during population declines, when females are already under nutritional stress triggered by food limitation. 2. We examined the presence of phase-dependent climate-predator interactions on neonatal...

Data from: Phenotypic selection on floral traits in an urban landscape

Rebecca E. Irwin, Paige S. Warren & Lynn S. Adler
Native species are increasingly living in urban landscapes associated with abiotic and biotic changes that may influence patterns of phenotypic selection. However, measures of selection in urban and non-urban environments, and exploration of the mechanisms associated with such changes, are uncommon. Plant-animal interactions have played a central role in the evolution of flowering plants and are sensitive to changes in the urban landscape, and thus provide opportunities to explore how urban environments modify selection. We...

Data from: Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

Kevin J. Parsons, Moira Concannon, Dina Navon, Jason Wang, Ilene Ea, Kiran Groveas, Calum Campbell & R. Craig Albertson
Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F3 hybrid mapping population. At early juvenile...

Data from: Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow

Katherine A. Zeller, Tyler G. Creech, Katie L. Millette, Rachel S. Crowhurst, Robert A. Long, Helene H. Wagner, Niko Balkenhol & Erin L. Landguth
Mantel-based tests have been the primary analytical methods for understanding how landscape features influence observed spatial genetic structure. Simulation studies examining Mantel-based approaches have highlighted major challenges associated with the use of such tests and fueled debate on when the Mantel test is appropriate for landscape genetics studies. We aim to provide some clarity in this debate using spatially explicit, individual-based, genetic simulations to examine the effects of the following on the performance of Mantel-based...

Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

Kathryn A. Hodgins, Zhao Lai, Luiz O. Oliveira, David W. Still, Moira Scascitelli, Michael S. Barker, Nolan C. Kane, Hannes Dempewolf, Alex Kozik, Richard V. Kesseli, John M. Burke, Richard W. Michelmore & Loren H. Rieseberg
Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium...

Data from: Evidence of phenotypic plasticity of penis morphology and delayed reproductive maturation in response to male competition in waterfowl

Patricia L. R. Brennan, Richard O. Prum & Derek Feng
Ducks are an excellent group to study avian genital evolution. Penis morphology of ducks is diverse, and penis length and elaboration are positively correlated with levels of male competition resulting from forced extra-pair copulations, and with female genital elaboration resulting from sexual conflict. Here we examined whether penis morphology is affected by social environment. We found experimental evidence that in a male-biased social environment, consisting of several males and fewer females, the penis in Lesser...

Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia

Nathan P. Havill, Shigehiko Shiyake, Ashley Lamb Galloway, Robert G. Foottit, Guoyue Yu, Annnie Paradis, Joseph Elkinton, Michael E. Montgomery, Masakazu Sano, Adalgisa Caccone & Annie Paradis
Hemlock woolly adelgid, Adelges tsugae, is an invasive pest of hemlock trees (Tsuga) in eastern North America. We used 14 microsatellites and mitochondrial COI sequences to assess its worldwide genetic structure and reconstruct its colonization history. The resulting information about its life cycle, biogeography and host specialization could help predict invasion by insect herbivores. We identified eight endemic lineages of hemlock adelgids in central China, western China, Ulleung Island (South Korea), western North America, and...

Data from: Molecular evolution of shattering loci in U.S. weedy rice

Carrie Thurber, Michael Reagon, Briana Gross, Kenneth Olsen, Yulin Jia & Ana Caicedo
Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well...

Data from: Madagascar's ephemeral palaeo-grazer guild: who ate the ancient C4 grasses?

Laurie R. Godfrey & Brooke E. Crowley
Supplementary isotope and radiocarbon data on subfossil hippos and tortoises of MadagascarRaw and corrected d13C data and 14C and calibrated radiocarbon ages before present, and data sources for now-extinct Hippopotamus and Aldabrachelys on MadagascarSupplementary Table_for submission.xls

Data from: Vigor and skill in the acrobatic mating displays of a Neotropical songbird

Lilian T. Manica, Regina H. Macedo, Jefferson A. Graves & Jeffrey Podos
Animal social behaviors are often mediated by signals that provide information about signaler attributes. Although some signals are structurally simple, others are temporally dynamic and multifaceted. In such cases, exaggeration of some display components is likely to curtail the expression of others. We quantified features of the acrobatic, multimodal “leap display” of blue-black grassquits (Volatinia jacarina), which appears to entail moderate-to-high performance levels in terms of vigor and skill. We video recorded and quantified leap...

Data from: Selection for mechanical advantage underlies multiple cranial optima in new world leaf-nosed bats

Elizabeth R. Dumont, Krishna Samadevam, Ian R. Grosse, Omar M. Warsi, Brandon Baird, Liliana M. Davalos & Ian Grosse
Selection for divergent performance optima has been proposed as a central mechanism underlying adaptive radiation. Uncovering multiple optima requires identifying forms associated with different adaptive zones and linking those forms to performance. However, testing and modeling the performance of complex morphologies like the cranium is challenging. We introduce a three-dimensional finite element (FE) model of the cranium that can be morphed into different shapes by varying simple parameters to investigate the relationship between two engineering-based...

Data from: Unexpected spatial population ecology of a widespread terrestrial salamander near its southern range edge

Raisa Hernández-Pacheco, Chris Sutherland, Lily M. Thompson & Kristine Grayson
Under the current amphibian biodiversity crisis, common species provide an opportunity to measure population dynamics across a wide range of environmental conditions while examining the processes that determine abundance and structure geographic ranges. Studying species at their range limits also provides a window for understanding the dynamics expected in future environments under increasing climate change and human modification. We quantified patterns of seasonal activity, density, and space use in the Eastern red-backed salamander (Plethodon cinereus)...

Data from: First diagnosis of septic arthritis in a dinosaur

Jennifer Anné, Brandon P. Hedrick & Jason P. Schein
Identification and interpretation of pathologies in the fossil record allows for unique insights into the life histories of extinct organisms. However, the rarity of such finds limits not only the sample size for palaeopathologic studies, but also the types of analyses that may be performed. In this study, we present the first occurrence of a palaeopathology in a vertebrate from the Mesozoic of the East Coast of North America (Appalachia), a pathologic ulna and radius...

Data from: Correcting for missing and irregular data in home-range estimation

Christen H. Fleming, Daniel Sheldon, William F. Fagan, Peter Leimgruber, Thomas Mueller, Dejid Nandintsetseg, Michael J. Noonan, Kirk A. Olson, Edy Setyawan, Abraham Sianipar & Justin M. Calabrese
Home-range estimation is an important application of animal tracking data that is frequently complicated by autocorrelation, sampling irregularity, and small effective sample sizes. We introduce a novel, optimal weighting method that accounts for temporal sampling bias in autocorrelated tracking data. This method corrects for irregular and missing data, such that oversampled times are downweighted and undersampled times are upweighted to minimize error in the home-range estimate. We also introduce computationally efficient algorithms that make this...

Data from: Sexual conflict over mating in red-sided garter snakes (Thamnophis sirtalis) as indicated by experimental manipulation of genitalia

Christopher R. Friesen, Emily J. Uhrig, Mattie K. Squire, Robert T. Mason & Patricia L. R. Brennan
Sexual conflict over mating can result in sex specific morphologies and behaviors that allow each sex to exert control over the outcome of reproduction. Genital traits, in particular, are often directly involved in conflict interactions. Via genital manipulation, we experimentally investigated whether genital traits in red-sided garter snakes influence copulation duration and formation of a copulatory plug. The hemipenes of male red-sided garter snakes have a large basal spine that inserts into the female cloaca...

Data from: Baby fish working out: an epigenetic source of adaptive variation in the cichlid jaw

Yinan Hu & R. Craig Albertson
Understanding the developmental processes that underlie the production of adaptive variation (i.e. the ‘arrival of the fittest’) is a major goal of evolutionary biology. While most evo-devo studies focus on the genetic underpinnings of adaptive phenotypic variation, factors beyond changes in nucleotide sequence can also play a major role in shaping developmental outcomes. Here, we document a vigorous but enigmatic gaping behaviour during the early development of Lake Malawi cichlid larvae. The onset of the...

Data from: Trait compensation between boldness and the propensity for tail autotomy under different food availabilities in similarly-aged brown anole lizards

Chi-Yun Kuo, Duncan J. Irschick & Simon P. Lailvaux
1. Trait compensation denotes the situation in which individuals offset the costs of one trait with the benefits of another trait. The phenomenon of trait compensation is best exemplified by a negative correlation between the degree of predator avoidance and the strength of morphological defense. 2. In this study, we used the relationship between risk-taking tendency (boldness) and the propensity for tail autotomy in the brown anole lizards Anolis sagrei to address two important questions...

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