53 Works

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: 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: 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: 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: 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: 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: 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: 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: Deconstructing Darwin’s naturalization conundrum in the San Juan Islands using community phylogenetics and functional traits

Hannah E. Marx, David E. Giblin, Peter W. Dunwiddie & David C. Tank
Aim: Darwin posed a conundrum about species invasions, postulating the importance of functional distinctiveness from the receiving native community to avoid competition, and, at the same time, the importance of shared similarity to pass environmental filters and successfully establish. Using phylogenetic distances and functional traits, we assessed this conundrum in the flora of 80 mostly uninhabited islands, where over 30% of the species are invasive. We highlight the importance of publicly available datasets to disentangle...

Data from: Playing 20 Questions with the mind: collaborative problem solving by humans using a brain-to-brain interface

Andrea Stocco, Chantel S. Prat, Darby M. Losey, Jeneva A. Cronin, Joseph Wu, Justin A. Abernethy & Rajesh P. N. Rao
We present, to our knowledge, the first demonstration that a non-invasive brain-to-brain interface (BBI) can be used to allow one human to guess what is on the mind of another human through an interactive question-and-answering paradigm similar to the “20 Questions” game. As in previous non-invasive BBI studies in humans, our interface uses electroencephalography (EEG) to detect specific patterns of brain activity from one participant (the “respondent”), and transcranial magnetic stimulation (TMS) to deliver functionally-relevant...

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

Devin Arbuthnott, Tera C. Levin & Daniel E. L. Promislow
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: The influence of adult attachment on patient self-management in primary care

Katja Brenk-Franz, Bernhard Strauß, Fabian Tiesler, Christian Fleischhauer, Paul Ciechanowski, Nico Schneider & Jochen Gensichen
Objective: Self-management strategies are essential elements of evidence-based treatment in patients with chronic conditions in primary care. Our objective was to analyse different self-management skills and behaviours and their association to adult attachment in primary care patients with multiple chronic conditions. Methods: In the apricare study (Adult Attachment in Primary Care) we used a prospective longitudinal design to examine the association between adult attachment and self-management in primary care patients with multimorbidity. The attachment dimensions...

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, Leo 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...

Data from: Temporal genetic variance and propagule-driven genetic structure characterize naturalized rainbow trout (Oncorhynchus mykiss) from a Patagonian lake impacted by trout farming

Javiera Nidia Benavente, Lisa Wishard Seeb, James Edward Seeb, Ivan Arismendi, Cristián Esteban Hernández, Gonzalo Gajardo, Ricardo Galleguillos, Maria Ignacia Cádiz, Selim Seman Musleh & Daniel Gomez-Uchida
Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). The species was introduced in Chile during the early twentieth century for stocking and promoting recreational fishing and, during the late twentieth century, for farming purposes...

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: 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: 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: 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: 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: 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: 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...

Registration Year

  • 2015
    53

Resource Types

  • Dataset
    53

Affiliations

  • University of Washington
    53
  • Stanford University
    3
  • Oregon State University
    3
  • CIUDAD
    2
  • University of Montana
    2
  • Princeton University
    2
  • University of Alberta
    2
  • University of Pittsburgh
    2
  • University of Zurich
    2
  • University of Colorado Boulder
    2