114 Works

Data from: Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Andrey A. Yurchenko, Hans D. Daetwyler, Nikolay Yudin, Robert D. Schnabel, Christy J. Vander Jagt, Vladimir Soloshenko, Bulat Lhasaranov, Ruslan Popov, Jeremey F. Taylor & Denis M. Larkin
Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data...

Data from: Leader preference in Neoconocephalus ensiger katydids: a female preference for a non-heritable male trait

Megan A. Murphy, Howard C. Gerhardt, Johannes Schul, M. A. Murphy, H. C. Gerhardt & J. Schul
Leader preferences, which result in greater mating success of males that produce their signals just ahead of those of their neighbors, are common in acoustically communicating insects and anurans (e.g. Whitney and Krebs 1975, Greenfield and Roizen 1993, Grafe 1996, Römer et al. 1997, Greenfield et al. 2004). These preferences are unusual in that they do not act on a property of the male signal itself but rather on its timing relative to that of...

Data from: Land use change increases climatic vulnerability of migratory birds: insights from integrated population modelling

Qing Zhao, Todd W. Arnold, James H. Devries, David W. Howerter, Robert G. Clark & Mitch D. Weegman
1. Knowledge of land use patterns that could affect animal population resiliency or vulnerability to environmental threats such as climate change is essential, yet the interactive effects of land use and climate on demography across space and time can be difficult to study. This is particularly true for migratory species, which rely on different landscapes throughout the year. 2. Unlike most North American migratory waterfowl, populations of northern pintails (Anas acuta; hereafter pintails) have not...

Data from: Hummingbirds control turning velocity using body orientation and turning radius using asymmetrical wingbeat kinematics

Tyson J. G. Read, Paolo S. Segre, Kevin M. Middleton & Douglas L. Altshuler
Turning in flight requires reorientation of force, which birds, bats and insects accomplish either by shifting body position and total force in concert or by using left–right asymmetries in wingbeat kinematics. Although both mechanisms have been observed in multiple species, it is currently unknown how each is used to control changes in trajectory. We addressed this problem by measuring body and wingbeat kinematics as hummingbirds tracked a revolving feeder, and estimating aerodynamic forces using a...

Data from: A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

Michael R. McKain, Haibao Tang, Joel R. McNeal, Saravanaraj Ayyampalayam, Jerrold I. Davis, Claude W. DePamphilis, Thomas J. Givnish, J. Chris Pires, Dennis Wm. Stevenson & Jim H. Leebens-Mack
Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intra-genomic syntenic blocks. Three such whole genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein coding sequences. The timing of...

Data from: A multispecies occupancy model for two or more interacting species

Christopher T. Rota, Marco A. R. Ferreira, Roland W. Kays, Tavis D. Forrester, Elizabeth L. Kalies, William J. McShea, Arielle W. Parsons & Joshua J. Millspaugh
Species occurrence is influenced by environmental conditions and the presence of other species. Current approaches for multispecies occupancy modelling are practically limited to two interacting species and often require the assumption of asymmetric interactions. We propose a multispecies occupancy model that can accommodate two or more interacting species. We generalize the single-species occupancy model to two or more interacting species by assuming the latent occupancy state is a multivariate Bernoulli random variable. We propose modelling...

Data from: Parents face quantity-quality tradeoffs between reproduction and investment in offspring in Iceland

Robert Francis Lynch
How to optimally allocate time, energy and investment in an effort to maximize one's reproductive success is a fundamental problem faced by all organisms. This effort is complicated when the production of each additional offspring dilutes the total resources available for parental investment. Although a quantity–quality trade-off between producing and investing in offspring has long been assumed in evolutionary biology, testing it directly in humans is difficult, partly owing to the long generation time of...

Data from: Resource predictability and specialization in avian malaria parasites

Maria Svensson-Coelho, Bette A. Loiselle, John G. Blake & Robert E. Ricklefs
We tested the hypothesis that avian haemosporidian (malaria) parasites specialize on hosts that can be characterized as predictable resources at a site in Amazonian Ecuador. We incorporated host phylogenetic relationship and relative abundance in assessing parasite specialization, and we examined associations between parasite specialization and three host characteristics – abundance, mass and longevity – using quantile regression, phylogenetic logistic regression and t-tests. Hosts of specialist malaria parasite lineages were on average more abundant than hosts...

Data from: Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants

Dieter Hackenberg, Michael McKain, Soon-Goo Lee, Swarup Roy Choudhury, Tyler McCann, Spencer Schreier, Alex Harkess, J. Chris Pires, Gane Ka-Shu Wong, Joseph Jez, Elizabeth Kellogg, Sona Pandey, Soon Goo Lee, Joseph M. Jez, Michael R. McKain & Elizabeth A. Kellogg
Signaling pathways regulated by heterotrimeric G-proteins exist in all eukaryotes. The regulator of G-protein signaling (RGS) proteins are key interactors and critical modulators of the Gα protein of the heterotrimer. However, while G-proteins are widespread in plants, RGS proteins have been reported to be missing from the entire monocot lineage, with two exceptions. A single amino acid substitution-based adaptive coevolution of the Gα:RGS proteins was proposed to enable the loss of RGS in monocots. We...

Data from: Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer

Pascal-Antoine Christin, Erika J. Edwards, Guillaume Besnard, Susanna F. Boxall, Richard Gregory, Elizabeth A. Kellogg, Colin P. Osborne & James Hartwell
C4 photosynthesis is a complex trait that confers higher productivity under warm and arid conditions. It has evolved more than 60 times via the co-option of genes present in C3 ancestors followed by alteration of the patterns and levels of expression, and adaptive changes in the coding sequences, but the evolutionary path to C4 photosynthesis is still poorly understood. The grass lineage Alloteropsis offers unparalleled opportunities for studying C4 evolution, because it includes a C3...

Data from: Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes

Jared E. Decker, Jeremy F. Taylor, Leeson J. Alexander, Juha Kantanen, Ann Millbrooke, Robert D. Schnabel & Michael D. MacNeil
Feral livestock may harbor genetic variation of commercial, scientific, historical or esthetic value. The origins and uniqueness of feral cattle on Chirikof Island, Alaska, are uncertain. The island is now part of the Alaska Maritime Wildlife Refuge and Federal wildlife managers want grazing to cease, presumably leading to demise of the cattle. Here we characterize the cattle of Chirikof Island relative to extant breeds and discern their origins. Our analyses support the inference that Yakut...

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, Jared E. Decker & Antonio Molina Alcalá
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: Three decades of cultural evolution in Savannah sparrow songs

Heather Williams, Iris I. Levin, D. Ryan Norris, Amy E. M. Newman, Nathaniel T. Wheelwright & Amy E.M. Newman
Cultural evolution can result in changes in the prevalence not only of different learned song types within bird populations but also of different segments within the song. Between 1980 and 2011, we examined changes within different segments of the single songs of male Savannah sparrows, Passerculus sandwichiensis, in an island population. Introductory notes did not change. The buzz segment showed similar stability; although a rare low-frequency variant appeared and then disappeared, the buzz segments from...

Data from: Rivers, refuges, and population divergence of fire-eye antbirds (Pyriglena) in the Amazon Basin

Marcos Maldonado-Coelho, John G. Blake, Luis F. Silveira, Henrique Batalha-Filho, Robert E. Ricklefs, R. E. Ricklefs, H. Batalha-Filho & L. F. Silveira
The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white-backed fire-eye (Pyriglena leuconota) populations along...

RNA-sequencing endometrium intact, vasectomized, and control heifers

Sandra Recuero, José María Sánchez, Yentel Mateo-Otero, Sandra Bagés-Arnal, Michael McDonald, Susanta K Behura, Thomas E Spencer, David A Kenny, Marc Yeste, Pat Lonergan & Beatriz Fernandez-Fuertes
An appropriate female reproductive environment is essential for pregnancy success. In several species, including mice, pigs and horses, seminal plasma (SP) components have been shown to modulate this environment, leading to increased embryo viability and implantation. Due to the characteristics of mating in the aforementioned species, SP comes into direct contact with the uterus. However, it is questionable whether any SP reaches the uterus in species that ejaculate inside the vagina, such as humans and...

Data from: More than one way to be a giant: convergence and disparity in the hip joints of saurischian dinosaurs

Henry P. Tsai, Kevin M. Middleton, John Hutchinson & Casey M. Holliday
Saurischian dinosaurs evolved seven orders of magnitude in body mass, as well as a wide diversity of hip joint morphology and locomotor postures. The very largest saurischians possess incongruent bony hip joints, suggesting that large volumes of soft tissues mediated hip articulation. To understand the evolutionary trends and functional relationships between body size and hip anatomy of saurischians, we tested the relationships among discrete and continuous morphological characters using phylogenetically corrected regression. Giant theropods and...

Data from: Ecological resistance surfaces predict fine scale genetic differentiation in a terrestrial woodland salamander

William E. Peterman, Grant M. Connette, Raymond D. Semlitsch & Lori S. Eggert
Landscape genetics has seen tremendous advances since its introduction, but parameterization and optimization of resistance surfaces still poses significant challenges. Despite increased availability and resolution of spatial data, few studies have integrated empirical data to directly represent ecological processes as genetic resistance surfaces. In our study, we determine the landscape and ecological factors affecting gene flow in the western slimy salamander (Plethodon albagula). We used field data to derive resistance surfaces representing salamander abundance and...

Data from: Competition for hummingbird pollination shapes flower color variation in Andean Solanaceae

Nathan Muchhala, Sönke Johnsen & Stacey Dewitt Smith
One classic explanation for the remarkable diversity of flower colors across angiosperms involves evolutionary shifts among different types of pollinators with different color preferences. However, the pollinator shift model fails to account for the many examples of color variation within clades that share the same pollination system. An alternate explanation is the competition model, which suggests that color divergence evolves in response to interspecific competition for pollinators, as a means to decrease interspecific pollinator movements....

Data from: Bumble bee nest abundance, foraging distance, and host-plant reproduction: implications for management and conservation

Jennifer C. Geib, James P. Strange & Candace Galen
Recent reports of global declines in pollinator species imply an urgent need to assess the abundance of native pollinators and density-dependent benefits for linked plants. In this study, we investigated (1) pollinator nest distributions and estimated colony abundances, (2) the relationship between abundances of foraging workers and the number of nests they represent, (3) pollinator foraging ranges, and (4) the relationship between pollinator abundance and plant reproduction. We examined these questions in an alpine ecosystem...

Data from: European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Federica Mattucci, Rita Oliveira, Leslie A. Lyons, Paulo C. Alves & Ettore Randi
Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and...

Data from: Elephant damage, not fire or rainfall, explains mortality of overstorey trees in Serengeti

Thomas A. Morrison, Ricardo M. Holdo & T. Michael Anderson
Generalizations about the drivers of tree demography in tropical savannahs continue to prove difficult because of the complex and dynamic interactions involved, and because multi-year datasets spanning meaningful gradients in potential drivers are lacking. Overstorey trees play disproportionate roles in the long-term dynamics and functioning of savannah ecosystems. Understanding demographic patterns in these trees is complicated by their resprouting ability after being top-killed and few studies have attempted to separate top-kill from true mortality events....

Data from: Non-additive effects of intra- and interspecific competition between two larval salamanders

Thomas Anderson, Howard Whiteman, Howard H. Whiteman & Thomas L. Anderson
1) Assessment of the relative strengths of intra- and interspecific competition has increased in recent years, and is critical to understanding the importance of competition. Yet, whether intra- and interspecific competition can have non-additive effects has rarely been tested. The resulting fitness consequences of such non-additive interactions are important to provide the context necessary to advance our understanding of competition theory. 2) We compared the strength of additive and non-additive intra- and interspecific competition by...

Data from: The influence of a working memory task on affective perception of facial expressions

Seung-Lark Lim, Amanda S. Bruce & Robin L. Aupperle
In a dual-task paradigm, participants performed a spatial location working memory task and a forced two-choice perceptual decision task (neutral vs. fearful) with gradually morphed emotional faces (neutral ~ fearful). Task-irrelevant word distractors (negative, neutral, and control) were experimentally manipulated during spatial working memory encoding. We hypothesized that, if affective perception is influenced by concurrent cognitive load using a working memory task, task-irrelevant emotional distractors would bias subsequent perceptual decision-making on ambiguous facial expression. We...

Data from: Thinking outside the box: problem-solving in free-living lizards

Levi Storks & Manuel Leal
Despite evidence that organisms are more likely to exhibit their full range of cognitive abilities under conditions found in nature, studies evaluating cognition under such conditions remain rare, particularly in vertebrate species. Here we conducted an experiment to evaluate problem solving and motor-self regulation in free-living arboreal lizards, Anolis sagrei, under natural conditions. We presented lizards with a novel detour problem which challenged individuals to circumvent a transparent barrier in order to obtain a food...

Data from: Forkhead box a2 (FOXA2) impacts uterine decidualization and fetoplacental development

Pramod Dhakal, Andrew Kelleher, Susanta Behura & Thomas Spencer
Glands of the uterus are essential for the establishment of pregnancy in mice and likely humans. Forkhead box a2 (FOXA2) is a transcription factor expressed specifically in the glands of the uterus and a critical regulator of uterine gland differentiation, development and function. Mice with a conditional deletion of FOXA2 in the adult uterus, created using the lactotransferrin iCre (Ltf-iCre) model, have a morphologically normal uterus with glands, but lack a considerable number of FOXA2-dependent...

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