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: Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

Marine S. O. Brieuc, Kotaro Ono, Daniel P. Drinan & Kerry A. Naish
Anadromous Chinook salmon populations vary in the period of river entry at the initiation of adult freshwater migration, facilitating optimal arrival at natal spawning. Run timing is a polygenic trait that shows evidence of rapid parallel evolution in some lineages, signifying a key role for this phenotype in the ecological divergence between populations. Studying the genetic basis of local adaptation in quantitative traits is often impractical in wild populations. Therefore, we used a novel approach,...

Data from: New evidence for hybrid zones of forest and savanna elephants in Central and West Africa

Samrat Mondol, Ida Moltke, John Hart, Michael Keigwin, Lisa Brown, Matthew Stephens & Samuel K. Wasser
The African elephant consists of forest and savanna subspecies. Both subspecies are highly endangered due to severe poaching and habitat loss, and knowledge of their population structure is vital to their conservation. Previous studies have demonstrated marked genetic and morphological differences between forest and savanna elephants and despite extensive sampling, genetic evidence of hybridization between them has been restricted largely to a few hybrids in the Garamba region of northeastern Democratic Republic of Congo (DRC)....

Data from: Evolution and maintenance of haploid-diploid life cycles in natural populations: the case of the marine brown alga Ectocarpus

Lucía Couceiro, Mickael Le Gac, Heather M. Hunsperger, Stéphane Mauger, Christophe Destombe, J. Mark Cock, Sophia Ahmed, Susana M. Coelho, Myriam Valero & Akira F. Peters
The evolutionary stability of haploid-diploid life cycles is still controversial. Mathematical models indicate that niche differences between ploidy phases may be a necessary condition for the evolution and maintenance of these life cycles. Nevertheless, experimental support for this prediction remains elusive. In the present work, we explored this hypothesis in natural populations of the brown alga Ectocarpus. Consistent with the life cycle described in culture, E. crouaniorum in NW France and E. siliculosus in SW...

Data from: Age specific survival rates of Steller sea lions at rookeries with divergent population trends in the Russian Far East

Alexey V. Altukhov, Russel D. Andrews, Donald G. Calkins, Thomas S. Gelatt, Eliezer D. Gurarie, Thomas R. Loughlin, Evgeny G. Mamaev, Victor S. Nikulin, Peter A. Permyakov, Sergey D. Ryazanov, Vladimir V. Vertyankin & Vladimir N. Burkanov
After a dramatic population decline, Steller sea lions have begun to recover throughout most of their range. However, Steller sea lions in the Western Aleutians and Commander Islands are continuing to decline. Comparing survival rates between regions with different population trends may provide insights into the factors driving the dynamics, but published data on vital rates have been extremely scarce, especially in regions where the populations are still declining. Fortunately, an unprecedented dataset of marked...

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: 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: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

Adam D. Leaché, Barbara L. Banbury, Joseph Felsenstein, Adrián Nieto-Montes De Oca & Alexandros Stamatakis
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD...

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: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

Owen A. Thompson, L. Basten Snoek, Harm Nijveen, Mark G. Sterken, Rita J. M. Volkers, Rachel Brenchley, Arjen Van't Hof, Roel P. J. Bevers, Andrew R. Cossins, Itai Yanai, Alex Hajnal, Tobias Schmid, Jaryn D. Perkins, David Spencer, Leonid Kruglyak, Erik C. Andersen, Donald G. Moerman, LaDeana W. Hillier, Jan E. Kammenga & Robert H. Waterston
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that...

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...

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