184 Works

Data from: Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Stefanie Hartmann, André Wehe & Todd J. Vision
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony is a phylogenetic optimization criterion in which a species tree is selected that minimizes the number of gene duplications induced among a set of gene trees. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic...

Data from: Seed transmission of soybean vein necrosis virus: the first Tospovirus implicated in seed transmission

Carol Groves, Thomas German, Ranjit Dasgupta, Daren Mueller & Damon L. Smith
Soybean vein necrosis virus (SVNV; genus Tospovirus; Family Bunyaviridae) is a negative-sense single-stranded RNA virus that has been detected across the United States and in Ontario, Canada. In 2013, a seed lot of a commercial soybean variety (Glycine max) with a high percentage of discolored, deformed and undersized seed was obtained. A random sample of this seed was planted in a growth room under standard conditions. Germination was greater than 90% and the resulting seedlings...

Data from: Hydric conditions during incubation influence phenotypes of neonatal reptiles in the field

Brooke L. Bodensteiner, Timothy S. Mitchell, Jeramie T. Strickland & Fredric J. Janzen
Phenotypic variation is strongly impacted by environmental conditions experienced during development. Substantial laboratory research has shown that reptiles with flexible-shelled eggs are particularly sensitive to hydric conditions, yet research on nests in the wild is sparse. In this two-year field experiment, we explore the influence of hydric conditions during incubation on phenotypic traits of hatchling painted turtles (Chrysemys picta). Using a split-clutch design, we created two artificial nests adjacent to each maternally-selected nest site. Half...

Data from: Macroevolution of Arboreality in Salamanders

Erica K. Baken & Dean C. Adams
Evolutionary theory predicts that selection in distinct microhabitats generates correlations between morphological and ecological traits, and may increase both phenotypic and taxonomic diversity. However, some microhabitats exert unique selective pressures that act as a restraining force on macroevolutionary patterns of diversification. In this study, we use phylogenetic comparative methods to investigate the evolutionary outcomes of inhabiting the arboreal microhabitat in salamanders. We find that arboreality has independently evolved at least five times in Caudata, and...

Data from: On the comparison of the strength of morphological integration across morphometric datasets

Dean C. Adams & Michael L. Collyer
Evolutionary morphologists frequently wish to understand the extent to which organisms are integrated, and whether the strength of morphological integration among subsets of phenotypic variables differ among taxa or other groups. However, comparisons of the strength of integration across datasets are difficult, in part because the summary measures that characterize these patterns (RV and rPLS) are dependent both on sample size and on the number of variables. As a solution to this issue we propose...

Data from: A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species

Dean C. Adams & John D. Nason
Evaluating trait correlations across species within a lineage via phylogenetic regression is fundamental to comparative evolutionary biology, but when traits of interest are derived from two sets of lineages that co-evolve with one another, methods for evaluating such patterns in a dual-phylogenetic context remain underdeveloped. Here we extend multivariate permutation-based phylogenetic regression to evaluate trait correlations in two sets of interacting species while accounting for their respective phylogenies. This extension is appropriate for both univariate...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

Jared Egan Decker, Stephanie D. McKay, Megan M. Rolf, JaeWoo Kim, Antonio Molina Alcalá, Tad S. Sonstegard, Olivier Hanotte, Anders Götherström, Christopher M. Seabury, Lisa Praharani, Masroor Ellahi Babar, Luciana Correia De Almieda Regitano, Mehmet Ali Yildiz, Michael P. Heaton, Wan-Sheng Liu, Chu-Zhao Lei, James M. Reecy, Muhammad Saif-Ur-Rehman, Robert D. Schnabel & Jeremy F. Taylor
The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns...

Data from: Genome-wide discovery and characterization of maize long non-coding RNAs

Lin Li, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng-Ting Yeh, Wei Wu, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C. P. Timmermans, Nathan M. Springer & Gary J. Muehlbauer
Background: Long noncoding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. Results: By exploiting available public ESTs, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNA. Of these lncRNAs, more than 90% are predicted to be...

Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila

Lori R. Shapiro, Erin D. Scully, Timothy J. Straub, Jihye Park, Andrew G. Stephenson, Gwyn A. Beattie, Mark L. Gleason, Roberto Kolter, Miguel C. Coelho, Consuelo M. De Moraes, Mark C. Mescher & Olga Zhaxybayeva
Modern industrial agriculture depends on high density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared to ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and...

Data from: Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)

Young Jin Chun, John Nason & Kirk Moloney
Study of adaptive evolutionary changes in populations of invasive species can be advanced through the joint application of quantitative and population genetic methods. Using purple loosestrife as a model system, we investigated the relative roles of natural selection, genetic drift, and gene flow in the invasive process by contrasting phenotypic and neutral genetic differentiation among native European and invasive North American populations (QST - FST analysis). Our results indicate that invasive and native populations harbor...

Data from: Energy demand and the context-dependent effects of genetic interactions underlying metabolism

Luke A. Hoekstra, Cole R. Julick, Katelyn M. Mika & Kristi L. Montooth
Genetic effects are often context-dependent, with the same genotype differentially affecting phenotypes across environments, life stages, and sexes. We used an environmental manipulation designed to increase energy demand during development to investigate energy demand as a general physiological explanation for context-dependent effects of mutations, particularly for those mutations that affect metabolism. We found that increasing the period during which Drosophila larvae are active during development phenocopies a temperature-dependent developmental delay in a mitochondrial-nuclear genotype with...

Data from: Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding

Joseph L. Gage, Michael R. White, Jode W. Edwards, Shawn Kaeppler & Natalia De Leon
Inflorescence capacity plays a crucial role in reproductive fitness in plants, and in production of hybrid crops. Maize is a monoecious species bearing separate male and female flowers (tassel and ear, respectively). The switch from open-pollinated populations of maize to hybrid-based breeding schemes in the early 20th century was accompanied by a dramatic reduction in tassel size, and the trend has continued with modern breeding over the recent decades. The goal of this study was...

Data from: Brazilian sugarcane ethanol as an expandable green alternative to crude oil use

Deepak Jaiswal, Amanda P. De Souza, Søren Larsen, David S. LeBauer, Fernando E. Miguez, Gerd Sparovek, Germán Bollero, Marcos S. Buckeridge & Stephen P. Long
Reduction of CO2 emissions will require a transition from fossil fuels to alternative energy sources. Expansion of Brazilian sugarcane ethanol1, 2 provides one near-term scalable solution to reduce CO2 emissions from the global transport sector. In contrast to corn ethanol, the Brazilian sugarcane ethanol system may offset 86% of CO2 emissions compared to oil use, and emissions resulting from land-use change to sugarcane are paid back in just 2–8 years3, 4. But, it has been...

Data from: Introgression between divergent corn borer species in a region of sympatry: implications on the evolution and adaptation of pest arthropods

Yangzhou Wang, Kyung Seok Kim, Wenchao Guo, Qiyun Li, Yunyue Zhang, Zhenying Wang & Brad S. Coates
The Asian corn borer, Ostrinia furnacalis, and European corn borer, O. nubilalis (Lepidoptera: Crambidae), cause damage to cultivated maize in spatially distinct geographies, and have evolved divergent hydrocarbons as the basis of sexual communication. The Yili area of Xinjiang Uyghur Autonomous Region in China represents the only known region where O. furnacalis has invaded a native O. nubilalis range, and these two corn borer species have made secondary contact. Genetic differentiation was estimated between Ostrinia...

Data from: Among-individual heterogeneity in maternal behaviour and physiology affects reproductive allocation and offspring life-history traits in the garter snake Thamnophis elegans

Eric J. Gangloff, Amanda M. Sparkman & Anne M. Bronikowski
Accumulating evidence suggests that within-individual plasticity of behavioural and physiological traits is limited, resulting in stable among-individual differences in these aspects of the phenotype. Furthermore, these traits often covary within individuals, resulting in a continuum of correlated phenotypic variation among individuals within populations and species. This heterogeneity, in turn, affects individual fitness and can have cross-generational effects. Patterns of trait covariation, among-individual differences, and subsequent fitness consequences have long been recognized in reptiles. Here, we...

Data from: Infection reduces anti-predator behaviors in house finches

James S. Adelman, Corinne Mayer & Dana M. Hawley
Infectious diseases can cause host mortality through direct or indirect mechanisms, including altered behavior. Diminished anti-predator behavior is among the most-studied causes of indirect mortality during infection, particularly for systems in which a parasite's life-cycle requires transmission from prey to predator. Significantly less work has examined whether directly-transmitted parasites and pathogens also reduce anti-predator behaviors. Here we test whether the directly-transmitted bacterial pathogen, Mycoplasma gallisepticum (MG), reduces responses to predation-related stimuli in house finches Haemorhous...

Data from: Rates of morphological evolution are correlated with species richness in salamanders

Daniel L. Rabosky & Dean C. Adams
The tempo and mode of species diversification and phenotypic evolution vary widely across the tree of life, yet the relationship between these processes is poorly known. Previous tests of the relationship between rates of phenotypic evolution and rates of species diversification have assumed that species richness increases continuously through time. If this assumption is violated, simple phylogenetic estimates of net diversification rate may bear no relationship to processes that influence the distribution of species richness...

Data from: Predation drives morphological convergence in the Gambusia panuco species group among lotic and lentic habitats

Eric K. Moody & M.L. Lozano-Vilano
Fish morphology is often constrained by a trade-off between optimizing steady vs. unsteady swimming performance due to opposing effects of caudal peduncle size. Lotic environments tend to select for steady swimming performance, leading to smaller caudal peduncles, while predators tend to select for unsteady swimming performance, leading to larger caudal peduncles. However, it is unclear which aspect of performance should be optimized across heterogeneous flow and predation environments and how this heterogeneity may affect parallel...

Data from: A range-wide domino effect and resetting of the annual cycle in a migratory songbird

Elizabeth A. Gow, Lauren Burke, David W. Winkler, Samantha M. Knight, Robert G. Clark, Marc Bélisle, Lisha L. Berzins, Tricia Blake, Eli S. Bridge, Russell D. Dawson, Peter O. Dunn, Dany Garant, Geoff Holroyd, Andrew G. Horn, David J.T. Hussell, Olga Lansdorp, Andrew J. Laughlin, Marty L. Leonard, Fanie Pelletier, Dave Shutler, Lynn Siefferman, Caz M. Taylor, Helen Trefry, Carol M. Vleck, David Vleck … & D. Ryan Norris
Latitudinal differences in timing of breeding are well documented but how such differences carry over to influence timing of events in the annual cycle of migratory birds is not well understood. We examined geographic variation in timing of events throughout the year using light-level geolocator tracking data from 133 migratory tree swallows (Tachycineta bicolor) originating from 12 North American breeding populations. A swallow’s breeding latitude influenced timing of breeding, which then carried over to affect...

Data from: Permutation tests for phylogenetic comparative analyses of high-dimensional shape data: what you shuffle matters

Dean C. Adams & Michael L. Collyer
Evaluating statistical trends in high-dimensional phenotypes poses challenges for comparative biologists, because the high-dimensionality of the trait data relative to the number of species can prohibit parametric tests from being computed. Recently, two comparative methods were proposed to circumvent this difficulty. One obtains phylogenetic independent contrasts for all variables, and statistically evaluates the linear model by permuting the PICs of the response data. The other uses a distance-based approach to obtain coefficients for generalized least...

Data from: Ecomorphological variation in male and female wall lizards and the macroecolution of sexual dimorphism in relation to habitat use

Antigoni Kaliontzopoulou, Miguel A. Carretero & Dean C. Adams
Understanding how phenotypic diversity evolves is a major interest of evolutionary biology. Habitat use is an important factor in the evolution of phenotypic diversity of many animal species. Interestingly, male and female phenotypes have been frequently shown to respond differently to environmental variation. At the macroevolutionary level, this difference between the sexes is frequently analyzed by using phylogenetic comparative tools to assess variation in sexual dimorphism (SD) across taxa in relation to habitat. A shortcoming...

Data from: Sexual selection targets cetacean pelvic bones

James P. Dines, Erik Otárola-Castillo, Peter Ralph, Jesse Alas, Timothy Daley, Andrew D. Smith & Matthew D. Dean
Male genitalia evolve rapidly, probably as a result of sexual selection. Whether this pattern extends to the internal infrastructure that influences genital movements remains unknown. Cetaceans (whales and dolphins) offer a unique opportunity to test this hypothesis: since evolving from land-dwelling ancestors, they lost external hind limbs and evolved a highly reduced pelvis which seems to serve no other function except to anchor muscles that maneuver the penis. Here we create a novel morphometric pipeline...

Data from: Bayesian total-evidence dating reveals the recent crown radiation of penguins

Alexandra Gavryushkina, Tracy A. Heath, Daniel T. Ksepka, Tanja Stadler, David Welch & Alexei J. Drummond
The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This...

Data from: Clothing color mediates lizard responses to humans in a tropical forest

Andrea Fondren, Lindsey Swierk & Breanna Putman
Identifying how ecotourism affects wildlife can lower its environmental impact. Human presence is an inherent component of ecotourism, which can impact animal behavior because animals often perceive humans as predators and, consequently, spend more time on human-directed antipredator behaviors and less on other fitness-relevant activities. We tested whether human clothing color affects water anole (Anolis aquaticus) behavior at a popular ecotourism destination in Costa Rica, testing the hypothesis that animals are more tolerant of humans...

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