53 Works

Data from: Luminance-dependent visual processing enables moth flight in low light

Simon Sponberg, Jonathan P. Dyhr, Robert W. Hall & Thomas L. Daniel
Animals must operate under an enormous range of light intensities. Nocturnal and twilight flying insects are hypothesized to compensate for dim conditions by integrating light over longer times. This slowing of visual processing would increase light sensitivity but should also reduce movement response times. Using freely hovering moths tracking robotic moving flowers, we showed that the moth’s visual processing does slow in dim light. These longer response times are consistent with models of how visual...

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

Colton Smith, Rory S. Telemeco, Michael J. Angilletta & John 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: 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: 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: Large scale determination of previously unsolved protein structures using evolutionary information

Sergey Ovchinnikov, Lisa Kinch, Hahnbeom Park, Yuxing Liao, Jimin Pei, David E. Kim, Hetunandan Kamisetty, Nick V. Grishin & David Baker
The prediction of the structures of proteins without detectablesequence similarity to any protein of known structure remains anoutstanding scientific challenge. Here we describe de novo blindstructure predictions of unprecedented accuracy for two proteins in large families made in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then use the method to generate structure models for 58 of the 121 large protein...

Data from: Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

Joseph Manthey, John Klicka & Garth Spellman
With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North...

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: 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: An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

Garrett J. McKinney, Lisa W. Seeb, Wesley A. Larson, Daniel Gomez-Uchida, Morten T. Limborg, Marine S. O. Brieuc, Meredith V. Everett, Kerry-Ann Naish, Ryan K. Waples, Jim E. Seeb & K. A. Naish
Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14,620 SNP loci including 2,336 paralogs in...

Data from: Past tree influence and prescribed fire mediate biotic interactions and community reassembly in a grassland-restoration experiment

Charles B. Halpern, Joseph A. Antos, Donald McKenzie & Annette M. Olson
Woody plant encroachment of grasslands is occurring globally, with profound ecological consequences. Attempts to restore herbaceous dominance may fail if the woody state is resilient or if intervention leads to an alternate, undesirable state. Restoration outcomes often hinge on biotic interactions – particularly on priority effects that inhibit or promote community reassembly. Following experimental tree removal from conifer-invaded grasslands, we documented substantial variation in community reassembly associated with the changing abundance of the native clonal...

Data from: Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

Richard E. Lenski, Michael J. Wiser, Noah Ribeck, Zachary D. Blount, Joshua R. Nahum, James Jeffrey Morris, Luis Zaman, Caroline B. Turner, Brian D. Wade, Rohan Maddamsetti, Alita R. Burmeister, Elizabeth J. Baird, Jay Bundy, Nkrumah A. Grant, Kyle J. Card, Maia Rowles, Kiyana Weatherspoon, Spiridon E. Papoulis, Rachel Sullivan, Colleen Clark, Joseph S. Mulka & Neerja Hajela
Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines...

Data from: Bulk genotyping of biopsies can create spurious evidence for heterogeneity in mutation content

Rumen Kostadinov, Carlo C. Maley & Mary K. Kuhner
When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones....

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: Genetic assignment of large seizures of elephant ivory reveals Africa’s major poaching hotspots

Samuel K. Wasser, Lisa Brown, Celia Mailand, Samrat Mondol, William Clark, Cathy Laurie & Bruce S. Weir
Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa’s major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 tons) made between 1996-2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law...

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
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: Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

Heather M. Hunsperger, Tejinder Randhawa & Rose Ann Cattolico
Background: Two non-homologous, isofunctional enzymes catalyze the penultimate step of chlorophyll a synthesis in oxygenic photosynthetic organisms such as cyanobacteria, eukaryotic algae and land plants: the light-independent (LIPOR) and light-dependent (POR) protochlorophyllide oxidoreductases. Whereas the distribution of these enzymes in cyanobacteria and land plants is well understood, the presence, loss, duplication, and replacement of these genes have not been surveyed in the polyphyletic and remarkably diverse eukaryotic algal lineages. Results: A phylogenetic reconstruction of the...

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

Lauren B. Buckley, Joseph C. Ehrenberger, & 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: Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey

Charlotte Boyd, Ramiro Castillo, , 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: 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: The ecology and economics of shorebird conservation in a tropical human-modified landscape

Jonathan M. H. Green, Siriya Sripanomyom, Xingli Giam & David S. Wilcove
1. Rapid and extensive land-use change in intertidal foraging habitat and coastal roosting habitat is thought to be driving major population declines of shorebirds migrating through the East Asian-Australasian Flyway. Along the Inner Gulf of Thailand, a critical stopover and wintering ground for these birds, artificial wetlands (saltpans and aquaculture ponds) have replaced much of the natural coastal ecosystem. 2. We conducted a two-part study to: (i) assess the importance of saltpans and semi-traditional aquaculture...

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: 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: 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: 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...

Registration Year

  • 2015
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Resource Types

  • Dataset
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Affiliations

  • University of Washington
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  • Stanford University
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  • Oregon State University
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  • CIUDAD
    2
  • University of Montana
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  • Princeton University
    2
  • University of Alberta
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  • University of Pittsburgh
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  • University of Zurich
    2
  • University of Colorado Boulder
    2