53 Works

Data from: Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate

Zena T. Wolf, Harrison A. Brand, John R. Shaffer, Elizabeth J. Leslie, Boaz Arzi, Cali E. Willet, Timothy C. Cox, Toby McHenry, Nicole Narayan, Eleanor Feingold, Xioajing Wang, Saundra Sliskovic, Nili Karmi, Noa Safra, Carla Sanchez, Frederic W. B. Deleyiannis, Jeffrey C. Murray, Claire M. Wade, Mary L. Marazita & Danika L. Bannasch
Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted...

Data from: Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Jesse A. Port, James L. O'Donnell, Ofelia C. Romero-Maraccini, Paul R. Leary, Steven Y. Litvin, Kerry J. Nickols, Kevan M. Yamahara & Ryan P. Kelly
Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource-intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by...

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: Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits

Andréa T. Thomaz, Dahiana Arcila, Guillermo Ortí & Luiz R. Malabarba
Background The subfamily Stevardiinae is a diverse and widely distributed clade of freshwater fishes from South and Central America, commonly known as “tetras” (Characidae). The group was named “clade A” when first proposed as a monophyletic unit of Characidae and later designated as a subfamily. Stevardiinae includes 48 genera and around 310 valid species with many species presenting inseminating reproductive strategy. No global hypothesis of relationships is available for this group and currently many genera...

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: Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing

Adam D. Leaché, Andreas S. Chavez, Leonard N. Jones, Jared A. Grummer, Andrew D. Gottscho & Charles W. Linkem
Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data,...

Data from: Phylogenomics of horned lizards (genus: Phrynosoma) using targeted sequence capture data

Adam D. Leaché & Charles W. Linkem
New genome sequencing techniques are enabling phylogenetic studies to scale-up from using a handful of loci to hundreds or thousands of loci from throughout the genome. In this study, we use targeted sequence capture (TSC) data from 540 ultraconserved elements and 44 protein-coding genes to estimate the phylogenetic relationships among all 17 species of horned lizards in the genus Phrynosoma. Previous molecular phylogenetic analyses of Phrynosoma based on a few nuclear genes, restriction site associated...

Data from: Keeping cool: enhanced optical reflection and heat dissipation in silver ants

Norman Nan Shi, Cheng-Chia Tsai, Fernando Camino, Gary D. Bernard, Nanfang Yu & Rüdiger Wehner
Saharan silver ants, Cataglyphis bombycina, forage under extreme temperature conditions in the African desert. We show that the ants’ conspicuous silvery appearance is created by a dense array of triangular hairs with two thermoregulatory effects. They enhance not only the reflectivity of the ant’s body surface in the visible and near-infrared range of the spectrum, where solar radiation culminates, but also the emissivity of the ant in the mid-infrared. The latter effect enables the animals...

Data from: Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America

John S. Sproul, Derek D. Houston, C. Riley Nelson, R. Paul Evans, Keith A. Crandall & Dennis K. Shiozawa
Background: Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data...

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: 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: Abiotic stress does not magnify the deleterious effects of spontaneous mutations

Jacob R. Andrew, Melody M. Dossey, Veniel O. Garza, Michelle Keller-Pearson, Charles F. Baer & Joanna Joyner-Matos
Although the effects of deleterious alleles often are predicted to be greater in stressful environments, there is no theoretical basis for this prediction and the empirical evidence is mixed. Here we characterized the effects of three types of abiotic stress (thermal, oxidative and hyperosmotic) on two sets of nematode (Caenorhabditis elegans) mutation accumulation (MA) lines that differ by threefold in fitness. We compared the survival and egg-to-adult viability between environments (benign and stressful) and between...

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

Registration Year

  • 2015

Resource Types

  • Dataset


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