42 Works

Data from: Divergence in DNA photorepair efficiency among genotypes from contrasting UV radiation environments in nature

Brooks E. Miner, Paige M. Kulling, Karlyn D. Beer & Benjamin Kerr
Populations of organisms routinely face abiotic selection pressures, and a central goal of evolutionary biology is to understand the mechanistic underpinnings of adaptive phenotypes. Ultraviolet radiation (UVR) is one of earth’s most pervasive environmental stressors, potentially damaging DNA in any organism exposed to solar radiation. We explored mechanisms underlying differential survival following UVR exposure in genotypes of the water flea Daphnia melanica derived from natural ponds of differing in UVR intensity. The UVR tolerance of...

Data from: Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

Ryan K. Waples, Lisa W. Seeb, Jim E. Seeb, R. K. Waples, L. W. Seeb & J. E. Seeb
Gene sequence similarity due to shared ancestry after a duplication event, that is paralogy, complicates the assessment of genetic variation, as sequences originating from paralogs can be difficult to distinguish. These confounded sequences are often removed prior to further analyses, leaving the underlying loci uncharacterized. Salmonids have only partially rediploidized subsequent to a whole-genome duplication; residual tetrasomic inheritance has been observed in males. We present a maximum-likelihood-based method to resolve confounded paralogous loci by observing...

Data from: Biotic and climatic velocity identify contrasting areas of vulnerability to climate change

Carlos Carroll, Joshua J. Lawler, David R. Roberts & Andreas Hamann
Metrics that synthesize the complex effects of climate change are essential tools for mapping future threats to biodiversity and predicting which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extirpation. The most commonly used of such metrics is the velocity of climate change, which estimates the speed at which species must migrate over the earth’s surface to maintain...

Data from: Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change

James L. Dimond & Steven B. Roberts
DNA methylation is an epigenetic mark that plays an inadequately understood role in gene regulation, particularly in non-model species. Because it can be influenced by the environment, DNA methylation may contribute to the ability of organisms to acclimatize and adapt to environmental change. We evaluated the distribution of gene body methylation in reef-building corals, a group of organisms facing significant environmental threats. Gene body methylation in six species of corals was inferred from in silico...

Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

Charles D. Waters, Jeffrey J. Hard, Marine S. O. Brieuc, David E. Fast, Kenneth I. Warheit, Robin Waples, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish & Robin S. Waples
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal...

Data from: Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic data

Morten T. Limborg, Ryan K. Waples, Fred W. Allendorf & James E. Seeb
Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in...

Data from: Effects of spatial scale of sampling on food web structure

Spencer A. Wood, Roly Russell, Dieta Hanson, Richard J. Williams & Jennifer A. Dunne
This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network structure is important for both fundamental ecological knowledge and the application of network analysis in conservation and management. Using a highly resolved food web for the marine intertidal ecosystem of the Sanak Archipelago in the...

Data from: Forage species in predator diets: synthesis of data from the California Current

Amber I. Szoboszlai, Julie A. Thayer, Spencer A. Wood, William J. Sydeman & Laura E. Koehn
Characterization of the diets of upper-trophic pelagic predators that consume forage species is a key ingredient in the development of ecosystem-based fishery management plans, conservation of marine predators, and ecological and economic modeling of trophic interactions. Here we present the California Current Predator Diet Database (CCPDD) for the California Current region of the Pacific Ocean over the past century, assimilating over 190 published records of predator food habits for over 100 predator species and 32...

Data from: How many routes lead to migration? Comparison of methods to assess and characterise migratory movements

Francesca Cagnacci, Stefano Focardi, Anne Ghisla, Bram Van Moorter, Eliezer Gurarie, Marco Heurich, Atle Mysterud, John Linnell, Manuela Panzacchi, Evelyn Merrill, Roel May, Torgeir Nygård, Christer Rolandsen, Mark Hebblewhite & Evelyn H. Merrill
1. Decreasing rate of migration in several species as a consequence of climate change and anthropic pressure, together with increasing evidence of space-use strategies intermediate between residency and complete migration, are very strong motivations to evaluate migration occurrence and features in animal populations. 2. The main goal of this paper was to perform a relative comparison between methods for identifying and characterising migration at the individual and population level on the basis of animal location...

Data from: Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey

Charlotte Boyd, Ramiro Castillo, Hunt Jr., George L., André E. Punt, Glenn R. VanBlaricom, Henri Weimerskirch, Sophie Bertrand & George L. Hunt
1. Understanding the ecological processes that underpin species distribution patterns is a fundamental goal in spatial ecology. However, developing predictive models of habitat use is challenging for species that forage in marine environments, as both predators and prey are often highly mobile and difficult to monitor. Consequently, few studies have developed resource selection functions for marine predators based directly on the abundance and distribution of their prey. 2. We analysed contemporaneous data on the diving...

Data from: Injuries, death, and disability associated with 11 years of conflict in Baghdad, Iraq: a randomized household cluster survey

Riyadh Lafta, Sahar Al-Shatari, Megan Cherewick, Lindsay Galway, Charles Mock, Amy Hagopian, Abraham Flaxman, Tim Takaro, Anna Greer, Adam Kusner & Gilbert Burnham
Background: The objective of this study was to characterize injuries, deaths, and disabilities arising during 11 years of conflict in Baghdad. Methods: Using satellite imagery and administrative population estimated size for Baghdad, 30 clusters were selected, proportionate to population size estimates. Interviews were conducted during April and May 2014 in 900 households containing 5148 persons. Details about injuries and disabilities occurring from 2003 through May 2014 and resultant disabilities were recorded. Findings: There were 553...

Data from: Calibrating animal-borne proximity loggers

Christian Rutz, Michael B. Morrissey, Zackory T. Burns, John Burt, Brian Otis, James J. H. St Clair & Richard James
1. Growing interest in the structure and dynamics of animal social networks has stimulated efforts to develop automated tracking technologies that can reliably record encounters in free-ranging subjects. A particularly promising approach is the use of animal-attached ‘proximity loggers’, which collect data on the incidence, duration and proximity of spatial associations through inter-logger radio communication. While proximity logging is based on a straightforward physical principle – the attenuation of propagating radio waves with distance –...

Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

John R. Candy, Nathan R. Campbell, Terry D. Beacham, Matthew H. Grinnell, Shawn R. Narum & Wesley A. Larson
Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively...

Data from: Dual dimensionality reduction reveals independent encoding of motor features in a muscle synergy for insect flight control

Simon N. Sponberg, Thomas L. Daniel, Adrienne L. Fairhall & Simon Sponberg
What are the features of movement encoded by changing motor commands? Do motor commands encode movement independently or can they be represented in a reduced set of signals (i.e. synergies)? Motor encoding poses a computational and practical challenge because many muscles typically drive movement, and simultaneous electrophysiology recordings of all motor commands are typically not available. Moreover, during a single locomotor period (a stride or wingstroke) the variation in movement may have high dimensionality, even...

Data from: Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Jared A. Grummer, Martha L. Calderón-Espinosa, Adrián Nieto-Montes De Oca, Eric N. Smith, Fausto R. Méndez De La Cruz & Adam D. Leaché
Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the...

Data from: Community-wide changes in inter-taxonomic temporal co-occurrence resulting from phenological shifts

Fangyuan Hua, Junhua Hu, Yang Liu, Xingli Giam, Tien Ming Lee, Hao Luo, Jia Wu, Qiaoyi Liang, Jian Zhao, Xiaoyan Long, Hong Pang, Biao Wang, Wei Liang, Zhengwang Zhang, Xuejie Gao & Jiang Zhu
Global climate change is known to affect the assembly of ecological communities by altering species’ spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species’ temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon...

Data from: Climate interacts with anthropogenic drivers to determine extirpation dynamics

Lise Comte, Bernard Hugueny & Gaël Grenouillet
Theoretical studies suggest that the dynamics of a species’ range during a period of climate change depends upon the existence and interplay of various ecological and evolutionary processes. Here we tested how anthropogenic pressures contribute to climate-mediated extirpation patterns of 32 freshwater fish species over the last 20 yr. We contrasted two extreme cases to determine whether extirpations were governed by patterns of climate exposure, assuming full adaptation of species to local climate, or instead...

Data from: Quantifying the effect of gape and morphology on bite force: biomechanical modeling and in vivo measurements in bats

Sharlene E. Santana
Maximum bite force is an important metric of feeding performance that defines the dietary ecology of many vertebrates. In mammals, theoretical analyses and empirical studies suggest a trade-off between maximum bite force and gape at behavioural and evolutionary scales; in vivo bite force is expected to decrease at wide gapes, and cranial morphologies that enable high mechanical advantage are thought to have a lower ability to generate high bite forces at wide gapes, and vice...

Data from: Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss

Garrett J. McKinney, Matthew C. Hale, Giles Goetz, Michael Gribskov, Frank P. Thrower & Krista M. Nichols
Little information has been gathered regarding the ontogenetic changes that contribute to differentiation between resident and migrant individuals, particularly before the onset of gross morphological and physiological changes in migratory individuals. The aim of this study was to evaluate gene expression during early development in Oncorhynchus mykiss populations with different life histories, in a tissue known to integrate environmental cues to regulate complex developmental processes and behaviours. We sampled offspring produced from migrant and resident...

Data from: Oxygen supply limits the heat tolerance of lizard embryos

Colton Smith, Rory S. Telemeco, Michael J. Angilletta, John M. VandenBrooks, M. J. Angilletta, C. Smith, R. S. Telemeco & J. M. VandenBrooks
The mechanisms that set the thermal limits to life remain uncertain. Classically, researchers thought that heating kills by disrupting the structures of proteins or membranes, but an alternative hypothesis focuses on the demand for oxygen relative to its supply. We evaluated this alternative hypothesis by comparing the lethal temperature for lizard embryos developing at oxygen concentrations of 10–30%. Embryos exposed to normoxia and hyperoxia survived to higher temperatures than those exposed to hypoxia, suggesting that...

Data from: Thermoregulatory behavior limits local adaptation of thermal niches and confers sensitivity to climate change

Lauren B. Buckley, Joseph C. Ehrenberger, Angilletta Jr., Michael J. & Michael J. Angilletta
1. Thermoregulation buffers environmental variation, which enables a species to persist during climate change but ultimately hinders adaptation of thermal tolerance by weakening selective pressure. 2. We used a model of optimal thermal physiology to demonstrate how thermoregulatory behaviour limits local adaptation of thermal physiology in a widespread group of lizards, the Sceloporus undulatus complex. 3. Empirical data for seven populations demonstrates conservatism of thermal tolerance, consistent with the model's prediction in the case of...

Data from: Elevational differences in developmental plasticity determine phenological responses of grasshoppers to recent climate warming

Lauren B. Buckley, César R. Nufio, Evan M. Kirk & Joel G. Kingsolver
Annual species may increase reproduction by increasing adult body size through extended development, but risk being unable to complete development in seasonally limited environments. Synthetic reviews indicate that most, but not all, species have responded to recent climate warming by advancing the seasonal timing of adult emergence or reproduction. Here, we show that 50 years of climate change have delayed development in high-elevation, season-limited grasshopper populations, but advanced development in populations at lower elevations. Developmental...

Data from: Performance of Encounternet tags: field tests of miniaturized proximity loggers for use on small animals

Iris I. Levin, David M. Zonana, John M. Burt & Rebecca J. Safran
Proximity logging is a new tool for understanding social behavior as it allows for accurate quantification of social networks. We report results from field calibration and deployment tests of miniaturized proximity tags (Encounternet), digital transceivers that log encounters between tagged individuals. We examined radio signal behavior in relation to tag attachment (tag, tag on bird, tag on saline-filled balloon) to understand how radio signal strength is affected by the tag mounting technique used for calibration...

Data from: The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster

Devin Arbuthnott, Tera C. Levin, Daniel E. L. Promislow, D. Arbuthnott, D. E. L. Promislow & T. C. Levin
Symbionts and parasites can manipulate their hosts’ reproduction to their own benefit, profoundly influencing patterns of mate choice and evolution of the host population. Wolbachia is one of the most widespread symbionts among arthropods, and one that alters its hosts’ reproduction in diverse and dramatic ways. While we are beginning to appreciate how Wolbachia's extreme manipulations of host reproduction can influence species diversification and reproductive isolation, we understand little about how symbionts and Wolbachia, in...

Data from: Sizing ocean giants: patterns of intraspecific size variation in marine megafauna

Craig R. McClain, Meghan A. Balk, Mark C. Benfield, Trevor A. Branch, Catherine Chen, James Cosgrove, Alistair D. M. Dove, Lindsay C. Gaskins, Rebecca Helm, Frederick G. Hochberg, Frank B. Lee, Andrea Marshall, Steven E. McMurray, Caroline Schanche, Shane N. Stone, Andrew D. Thaler & Rebecca R. Helm
What are the greatest sizes that the largest marine megafauna obtain? This is a simple question with a difficult and complex answer. Many of the largest-sized species occur in the world’s oceans. For many of these, rarity, remoteness, and quite simply the logistics of measuring these giants has made obtaining accurate size measurements difficult. Inaccurate reports of maximum sizes run rampant through the scientific literature and popular media. Moreover, how intraspecific variation in the body...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Washington
  • Stanford University
  • University of Montana
  • Princeton University
  • Oregon State University
  • University of Alberta
  • University of Pittsburgh
  • University of Colorado Boulder
  • Arizona State University
  • University of Maryland, College Park
  • Northwest Fisheries Science Center
  • National Evolutionary Synthesis Center
  • University of Bath
  • Sun Yat-sen University