403 Works

Data from: Quantifying effects of environmental and geographical factors on patterns of genetic differentiation

Cheng-Ruei Lee & Thomas Mitchell-Olds
Elucidating the factors influencing genetic differentiation is an important task in biology, and the relative contribution from natural selection and genetic drift has long been debated. In this study, we used a regression-based approach to simultaneously estimate the quantitative contributions of environmental adaptation and isolation by distance on genetic variation in Boechera stricta, a wild relative of Arabidopsis. Patterns of discrete and continuous genetic differentiation coexist within this species. For the discrete differentiation between two...

Data from: Genetic structure in a dynamic baboon hybrid zone corroborates behavioral observations in a hybrid population

Marie J.E. Charpentier, Michael C. Fontaine, Julien P. Renoult, Thomas Jenkins, Erwan Cherel, Laure Benoit, Nicolas Barthès, Susan C. Alberts & Jenny Tung
Behavior and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behavior of the hybridizing taxa can also have an important impact on the incidence and outcome of hybridization events. Hybridization between yellow baboons and anubis baboons has been well-documented in the Amboseli basin of Kenya, where more anubis-like...

Data from: Inferring the history of interchromosomal gene transposition in Drosophila using n-Dimensional parsimony

Mira V. Han & Matthew W. Hahn
Gene transposition puts a new gene copy in a novel genomic environment. Moreover, genes moving between the autosomes and the X chromosome experience change in several evolutionary parameters. Previous studies of gene transposition have not utilized the phylogenetic framework that becomes possible with the availability of whole genomes from multiple species. Here we used parsimonious reconstruction on the genomic distribution of gene families to analyze interchromosomal gene transposition in Drosophila. We identified 782 genes that...

Data from: Classification tree methods provide a multifactorial approach to predicting insular body size evolution in rodents

Paul A. P. Durst & V. Louise Roth
Many hypotheses have been proposed to explain size changes in insular mammals, but no single variable suffices to explain the diversity of responses, particularly within Rodentia. Here in a dataset on insular rodents we observe strong consistency in the direction of size change within islands and within species, but (outside of Heteromyidae) little consistency at broader taxonomic scales. Using traits of islands and of species in a classification-tree analysis we find the most important factor...

Data from: Long-term data reveal patterns and controls on streamwater chemistry in a forested stream: Walker Branch, Tennessee

Brian D. Lutz, Patrick J. Mulholland & Emily S. Bernhardt
We present 20 years of weekly streamwater chemistry, hydrology, and climate data for the Walker Branch watershed in eastern Tennessee, USA. Since 1989, the watershed has experienced a ~1.0˚C increase in mean annual temperature, a ~20% decline in precipitation, and a ~30% increase in forest evapotranspiration rates. As a result, runoff has declined by ~34%. We evaluate long-term trends in streamwater concentrations and fluxes for 9 solutes and use wet deposition data to calculate approximate...

Data from: Interploidal hybridization and mating patterns in the Sphagnum subsecundum complex

Mariana Ricca, P. Szövényi, Matthew G Johnson, A Jonathan Shaw & Eva M. Temsch
Polyploidization is thought to result in instant sympatric speciation, but several cases of hybrid zones between one of the parental species and its polyploid derivative have been documented. Previous work showed that diploid Sphagnum lescurii is an allopolyploid derived from the haploids S. lescurii (maternal progenitor) and S. subsecundum (paternal progenitor). Here we report the results from analyses of a population where allodiploid and haploid S. lescurii co-occur and produce sporophytes. We tested (1) whether...

Data from: Life-history QTLs and natural selection on flowering time in Boechera stricta, a perennial relative of Arabidopsis

Jill Theresa Anderson, Cheng-Ruei Lee & Thomas Mitchell-Olds
Plants must precisely time flowering to capitalize on favorable conditions. Although we know a great deal about the genetic basis of flowering phenology in model species under controlled conditions, the genetic architecture of this ecologically-important trait is poorly understood in non-model organisms. Here, we evaluated the transition from vegetative growth to flowering in Boechera stricta, a perennial relative of Arabidopsis thaliana. We examined flowering time QTLs using 7,920 recombinant inbred individuals, across seven lab and...

Data from: Genetic population structure of U.S. Atlantic coastal striped bass (Morone saxatilis)

David T. Gauthier, Corinne A. Audemard, Jeanette E. L. Carlsson, Tanya L. Darden, Michael R. Denson, Kimberly S. Reece & Jens Carlsson
Genetic population structure of anadromous striped bass along the US Atlantic coast was analyzed using 14 neutral nuclear DNA microsatellites. Young-of-the-year and adult striped bass (n = 1114) were sampled from Hudson River, Delaware River, Chesapeake Bay, North Carolina, and South Carolina. Analyses indicated clear population structure with significant genetic differentiation between all regions. Global multilocus F ST was estimated at 0.028 (P < 0.001). Population structure followed an isolation-by-distance model and temporal sampling indicated...

Data from: Female competition in chimpanzees

Anne E. Pusey & Kara Schroepfer-Walker
Female chimpanzees exhibit exceptionally slow rates of reproduction and raise their offspring without direct paternal care. Therefore, their reproductive success depends critically on long-term access to high-quality food resources over a long lifespan. Chimpanzee communities contain multiple adult males, multiple adult females and their offspring. Because males are philopatric and jointly defend the community range while most females transfer to new communities before breeding, adult females are typically surrounded by unrelated competitors. Communities are fission–fusion...

Data from: Predictability and irreversibility of genetic changes associated with flower color evolution in Penstemon barbatus

Carolyn A. Wessinger & Mark D. Rausher
Two outstanding questions in evolutionary biology are whether, and how often, the genetic basis of phenotypic evolution is predictable; and whether genetic change constrains evolutionary reversibility. We address these questions by studying the genetic basis of red flower color in Penstemon barbatus. The production of red flowers often involves the inactivation of one or both of two anthocyanin pathway genes, Flavonoid 3',5'-hydroxylase (F3'5'h) and Flavonoid 3'-hydroxylase (F3'h). We used gene expression and enzyme function assays...

Data from: Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

Eric P. Palkovacs, Daniel J. Hasselman, Emily E. Argo, Stephen R. Gephard, Karin E. Limburg, David M. Post, Thomas F. Schultz & Theodore V. Willis
A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for...

Data from: Role of grooming in reducing tick load in wild baboons (Papio cynocephalus)

Mercy Y. Akinyi, Susan C. Alberts, Jeanne Altmann, Nilesh B. Patel, Jenny Tung & Maamun Jeneby
Nonhuman primate species spend a conspicuous amount of time grooming during social interactions, a behaviour that probably serves both social and health-related functions. While the social implications of grooming have been relatively well studied, less attention has been paid to the health benefits, especially the removal of ectoparasites, which may act as vectors in disease transmission. In this study, we examined whether grooming behaviour reduced tick load (number of ticks) and haemoprotozoan infection status in...

Data from: Biogeographic consequences of nutrient enrichment for plant-herbivore interactions in coastal wetlands

Qiang He & Brian R. Silliman
A major challenge in ecology is to understand broadscale trends in the impact of environmental change. We provide the first integrative analysis of the effects of eutrophication on plants, herbivores, and their interactions in coastal wetlands across latitudes. We show that fertilisation strongly increases herbivory in salt marshes, but not in mangroves, and that this effect increases with increasing latitude in salt marshes. We further show that stronger nutrient effects on plant nitrogen concentration at...

Data from: Newspaper coverage of maternal health in Bangladesh, Rwanda, and South Africa: a quantitative and qualitative content analysis

Frey Gugsa, Ellora Karmarkar, Andrew Cheyne & Gavin Yamey
Objective: To examine newspaper coverage of maternal health in three countries that have made varying progress towards Millennium Development Goal 5 (MDG 5): Bangladesh (on track), Rwanda (making progress, but not on track) and South Africa (no progress). Design: We analysed each country's leading national English-language newspaper: Bangladesh's The Daily Star, Rwanda's The New Times/The Sunday Times, and South Africa's Sunday Times/The Times. We quantified the number of maternal health articles published from 1 January...

Data from: Unraveling the determinants of insular body size shifts

Craig R. McClain, Paul A. P. Durst, Alison G. Boyer & Clinton D. Francis
The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological, and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species’ ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak...

Data from: Multilocus coalescent analyses reveal the demographic history and speciation patterns of mouse lemur sister species

Christopher Blair, Kellie L. Heckman, Amy L. Russell & Anne D. Yoder
Background: Debate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in which evolution has generated a large number of species over a relatively recent time frame. Here, we examine speciation patterns in a pair of sister species of mouse lemur, Microcebus murinus and M. griseorufus. These two species have ranges that are disparately proportioned...

Data from: Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis

Heath Blackmon & Jeffery P. Demuth
Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems....

Data from: Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Fay-Wei Li
Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor—neochrome—that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome...

Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)

Kristina M. Cammen, Thomas F. Schultz, Patricia E. Rosel, Randall S. Wells & Andrew J. Read
Harmful algal blooms (HABs), which can be lethal in marine species and cause illness in humans, are increasing worldwide. In the Gulf of Mexico, HABs of Karenia brevis produce neurotoxic brevetoxins that cause large-scale marine mortality events. The long history of such blooms, combined with the potentially severe effects of exposure, may have produced a strong selective pressure for evolved resistance. Advances in next-generation sequencing, in particular genotyping-by-sequencing, greatly enable the genomic study of such...

Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs

Scott Hotaling, Mary Foley, Nicolette Lawrence, Jose Bocanegra, Marina B. Blanco, Rodin Rasoloarison, Peter M. Kappeler, Meredith A. Barrett, Anne D. Yoder, David W. Weisrock, Mary E. Foley & Nicolette M. Lawrence
Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each...

Data from: Young inversion with multiple linked QTLs under selection in a hybrid zone

Thomas Mitchell-Olds
Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose...

Data from: From the track to the ocean: using flow control to improve marine bio-logging tags for cetaceans

Giovani Fiore, Erik Anderson, C. Spencer Garborg, Mark Murray, Mark Johnson, Michael J. Moore, Laurens Howle & K. Alex Shorter
Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force...

Data from: A classification system for zebrafish adipose tissues

James E. N. Minchin & John F. Rawls
The zebrafish model system offers significant utility for in vivo imaging of adipose tissue (AT) dynamics and for screening to identify chemical and genetic modifiers of adiposity. In particular, AT can be quantified accurately in live zebrafish using fluorescent lipophilic dyes. Although this methodology offers considerable promise, the comprehensive identification and classification of zebrafish ATs has not been performed. Here, we use fluorescent lipophilic dyes and in vivo imaging systematically to identify, classify and quantify...

Data from: Candidate genes mediating magnetoreception in rainbow trout (Oncorhynchus mykiss)

Robert R. Fitak, Benjamin R. Wheeler, David A. Ernst, Kenneth J. Lohmann & Sonke Johnsen
Diverse animals use Earth's magnetic field in orientation and navigation, but little is known about the molecular mechanisms that underlie magnetoreception. Recent studies have focused on two possibilities: (i) magnetite-based receptors; and (ii) biochemical reactions involving radical pairs. We used RNA sequencing to examine gene expression in the brain of rainbow trout (Oncorhynchus mykiss) after exposure to a magnetic pulse known to disrupt magnetic orientation behaviour. We identified 181 differentially expressed genes, including increased expression...

Data from: The quick and the dead: microbial demography at the yeast thermal limit

Colin S. Maxwell & Paul M. Magwene
The niche of microorganisms is determined by where their populations can expand. Populations can fail to grow because of high death or low birth rates, but these are challenging to measure in microorganisms. We developed a novel technique that enables single cell measurement of age-structured birth and death rates in the budding yeast, Saccharomyces cerevisiae, and used this method to study responses to heat stress in a genetically diverse panel of strains. We find that...

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