191 Works

Data from: How does ascertainment bias in SNP analyses affect inferences about population history?

Emily Jane McTavish & David M. Hillis
Background: The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection;...

Data from: Sympatric, temporally isolated populations of the pine white butterfly Neophasia menapia, are morphologically and genetically differentiated

Katherine L. Bell, Christopher A. Hamm, Arthur M. Shapiro & Chris C. Nice
Temporal isolation remains an understudied, and potentially under-appreciated, mechanism of reproductive isolation. Phenological differences have been discovered in populations of the pine white butterfly (Neophasia menapia), a typically univoltine species found throughout western North America. At two locations in the Coast Range of California there are two periods of adult emergence per year, one in early summer (July) and one in late summer/autumn (September/October). Differences in flight time are accompanied by differences in wing shape...

Data from: Loci contributing to boric acid toxicity in two reference populations of Drosophila melanogaster

Michael A. Najarro, Jennifer L. Hackett & Stuart J. Macdonald
Populations maintain considerable segregating variation in the response to toxic, xenobiotic compounds. To identify variants associated with resistance to boric acid, a commonly-used household insecticide with a poorly understood mechanism of action, we assayed thousands of individuals from hundreds of strains. Using the Drosophila Synthetic Population Resource (DSPR), a multi-parental population (MPP) of inbred genotypes, we mapped six QTL to short genomic regions containing few protein-coding genes (3–188), allowing us to identify plausible candidate genes...

Data from: Antagonistic pleiotropy and mutation accumulation contribute to age-related decline in stress response

Elizabeth Rose Everman & Theodore J. Morgan
As organisms age, the effectiveness of natural selection weakens, leading to age-related decline in fitness-related traits. The evolution of age-related changes associated with senescence is likely influenced by mutation accumulation (MA) and antagonistic pleiotropy (AP). MA predicts that age-related decline in fitness components is driven by age-specific sets of alleles, non-negative genetic correlations within trait across age, and an increase in the coefficient of genetic variance. AP predicts that age-related decline in a trait is...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Conservation genetics of Australasian sailfin lizards: flagship species threatened by coastal development and insufficient protected area coverage

Cameron D. Siler, Andrés Lira-Noriega & Rafe M. Brown
Despite rampant coastal development throughout Southeast Asia and the Pacific, studies of conservation genetics and ecology of vulnerable, coastal species are rare. Large bodied vertebrates with highly specialized habitat requirements may be at particular risk of extinction due to habitat degradation and fragmentation, especially if these habitats are naturally patchily distributed, marginal, or otherwise geographically limited, or associated in space with high human population densities or heavy anthropogenic disturbance. Particularly telling examples of these conservation...

Data from: From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis

James C. Lamsdell & Paul A. Selden
Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to...

Data from: Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas

Lawrence William Sheppard, Emma J. Defriez, Philip Christopher Reid & Daniel C. Reuman
Large-scale spatial synchrony is ubiquitous in ecology. We examined 56 years of data representing chlorophyll density in 26 areas in British seas monitored by the Continuous Plankton Recorder survey. We used wavelet methods to disaggregate synchronous fluctuations by timescale and determine that drivers of synchrony include both biotic and abiotic variables. We tested these drivers for statistical significance by comparison with spatially synchronous surrogate data. We generated timescale-specific models, accounting for 61% of long-timescale (>...

Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Anthony J. Barley, Patrick J. Monnahan, Robert C. Thomson, L. Lee Grismer & Rafe M. Brown
Incorporating genomic data sets into landscape genetic analyses allows for powerful insights into population genetics, explicitly geographical correlates of selection, and morphological diversification of organisms across the geographical template. Here, we utilize an integrative approach to examine gene flow and detect selection, and we relate these processes to genetic and phenotypic population differentiation across South-East Asia in the common sun skink, Eutropis multifasciata. We quantify the relative effects of geographic and ecological isolation in this...

Data from: Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Robert G. Moyle, Carl H. Oliveros, Michael J. Andersen, Peter A. Hosner, Brett W. Benz, Joseph D. Manthey, Scott L. Travers, Rafe M. Brown & Brant C. Faircloth
Songbirds (oscine passerines) are the most species rich and cosmopolitan bird group, comprising almost half of global avian species diversity. Because of their diversity and ubiquity, songbirds are used extensively in studies of evolutionary ecology, diversification, and ethology. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Prior research suggested songbird diversification scenarios that are largely uncoupled from Earth history, including extensive...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

Self-organising cicada choruses respond to the local sound and light environment

Lawrence Sheppard, Brandon Mechtley, Jonathan Walter & Daniel Reuman
1. Periodical cicadas exhibit an extraordinary capacity for self-organising spatially synchronous breeding behavior. The regular emergence of periodical cicada broods across the US is a phenomenon of longstanding public and scientific interest, as the cicadas of each brood emerge in huge numbers and briefly dominate their ecosystem. During the emergence, the 17-year periodical cicada species Magicicada cassini is found to form synchronised choruses, and we investigated their chorusing behavior from the standpoint of spatial synchrony....

Data from: Ornithogenic vegetation: How significant has the seabird influence been on the Aleutian Island vegetation during the Holocene?

Olesya Smyshlyaeva, Elena Severova, Olga Krylovich, Evgeniya Kuzmicheva, Arkady Savinetsky, Dixie West & Virginia Hatfield
In the Aleutian Islands during the Holocene, terrestrial predators were actually absent; as a result, large seabird colonies thrived along the coasts or across entire islands. Bird guano enriches the soil with nitrogen, which can lead to the formation of highly modified ornithogenic (bird-formed) ecosystems. For a more detailed investigation of avian influence, we reconstructed more than 10,000-year-old vegetation dynamics of the coast of Shemya Island (Near Islands) by pollen analysis. At the initial stages...

Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal

Maria Paniw, Dylan Childs, Kenneth Armitage, Daniel Blumstein, Julien Martin, Madan Oli & Arpat Ozgul
Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that...

Data from: Helianthus maximiliani and species fine-scale spatial pattern affect diversity interactions in reconstructed tallgrass prairies

Thomas McKenna, Jack McDonnell, Kathryn Yurkonis & Caroline Brophy
1. Biodiversity and Ecosystem Function analyses aim to explain how individual species and their interactions affect ecosystem function. With this study we asked in what ways do species interact, are these interactions affected by species planting pattern, and are initial (planted) proportions or previous year (realized) proportions a better reference point for characterizing grassland diversity effects? 2. We addressed these questions with experimental communities compiled from a pool of 16 tallgrass prairie species. We planted...

An animal without a mitochondrial genome: the salmon parasite Henneguya salminicola (Cnidaria: Myxozoa)

Dorothée Huchon, Dayana Yahalomi, Stephen D. Atkinson, Moran Neuhof, E. Sally Chang, Hervé Philippe, Paulyn Cartwright & Jerri L. Bartholomew
Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no...

Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)

Kin Onn Chan, Carl Hutter, Perry Wood, Lee Grismer & Rafe Brown
Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to utilize traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention is given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets...

Soil microbial legacy drives crop diversity advantage: linking ecological plant-soil feedback with agricultural intercropping

Guangzhou Wang, Shuikuan Bei, Jianpeng Li, Xingguo Bao, Jiudong Zhang, Peggy Schultz, Haigang Li, Long Li, Fusuo Zhang, James Bever & Junling Zhang
Although the importance of the soil microbiome in mediating plant community structures and functions has been increasingly emphasized in ecological studies, the biological processes driving crop diversity overyielding remain unexplained in agriculture. Based on the plant-soil feedback (PSF) theory and method, we quantified how much soil microbes contributed to intercropping overyielding and detected which microbial groups mediated this effect. Soils were collected as inocula and sequenced from a unique 10-year field experiment, consisting of monoculture,...

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

Perry Wood, Xianguang Guo, Scott Travers, Yong-Chao Su, Karen Olson, Aaron Bauer, Lee Grismer, Cameron Siler, Robert Moyle, Michael Andersen & Rafe Brown
Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread “generalist” clades. This is especially true in Australasia, where monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately “derived” parachute geckos...

A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species

Ella Vázquez-Domínguez, Carlos Luna‐Aranguré & Jorge Soberón
Aim: Assessing the relevance of niche evolution in the diversification patterns and geographical distribution of species driven by climate remains a challenge. We apply an integrative approach to evaluate the role of the environment on the phylogeography of bear species, incorporating fossil data to characterize the changes in the ecological niche through time. We evaluate our approach with the four extant species of bears within Ursus, the best represented taxon in the fossil record of...

Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness

Tim Cooper, Kelly Phillips, Scott Widmann, Jennifer Nguyen, Christian Ray, Gabor Balazsi & Huei-Yi Lai
Transcription of bacterial genes is controlled by the coordinated action of cis- and trans-acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in different environments. A well-studied example is the regulatory function that integrates the environmental availability of glucose and lactose to control the Escherichia coli lac operon. Most studies of lac operon regulation have focused on a few closely related strains. To determine the range...

Data from: Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense

Bryan G. Falk, Richard E. Glor & Susan L. Perkins
The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in...

Data from: Range-wide ecological niche comparisons of parasite, hosts and dispersers in a vector-borne plant parasite system

Andrés Lira-Noriega & A. Townsend Peterson
Aim: To test whether the distribution of the mistletoe Phoradendron californicum is mediated by host distributions (host niche hypothesis, HNH), or by factors such as the mistletoe’s autecology (parasite niche hypothesis, PNH) or that of its vectors (vector niche hypothesis, VNH). Our null hypothesis is that the ecological niche of the mistletoe will not be distinct from that of its hosts or vectors; alternatively, mistletoe infections might appear in hosts only in regions where host...

Data from: Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation inter-cross population

Tara N. Marriage, Elizabeth G. King, Anthony D. Long & Stuart J. Macdonald
Animals in nature are frequently challenged by toxic compounds, from those that occur naturally in plants as a defense against herbivory, to pesticides used to protect crops. On exposure to such xenobiotic substances, animals mount a transcriptional response, generating detoxification enzymes and transporters that metabolize and remove the toxin. Genetic variation in this response can lead to variation in the susceptibility of different genotypes to the toxic effects of a given xenobiotic. Here we use...

Data from: Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Joseph D. Manthey & Robert G. Moyle
Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms...

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