54 Works

Data from: Genetic architecture of quantitative flower and leaf traits in a pair of sympatric sister species of Primulina

Chen Feng, Chao Feng, Lihua Yang, Ming Kang & Mark D. Rausher
Flowers and leaves each represent suites of functionally interrelated traits that are often involved in species divergence and local adaptation. However, a major unresolved issue is how the individual component traits that make up a complex trait such as a flower evolve in a coordinated fashion to retain a high degree of functionality. We use a quantitative trait loci (QTL) approach to elucidate the genetic architecture of divergence in flower and leaf traits between sister...

Data from: Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex

Jennifer M. Coughlan & John H. Willis
Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We...

Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta

Maggie R. Wagner & Thomas Mitchell-Olds
Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection (“adaptive plasticity”) or disfavored (“nonadaptive” plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho,...

Data from: Gene signature of the human pancreatic ε-cell

Giselle Dominguez Gutierrez, Jinrang Kim, Ann-Hwee Lee, Jenny Tong, JingJing Niu, Sarah Gray, Yi Wei, Yueming Ding, Min Ni, Christina Adler, Andrew J. Murphy, Jesper Gromada, Yurong Xin & Sarah M Gray
The ghrelin producing ε-cell represents the fifth endocrine cell type in human pancreatic islets. The abundance of ε-cells in adult pancreas is extremely low, which has hampered the investigation on the molecular pathways regulating the development and the function of this cell type. In this study, we explored the molecular features defining the function of pancreatic ε-cells isolated from adult non-diabetic donors using single-cell RNA sequencing technology. We focus on transcription factors, cell surface receptors...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: Estimating infection prevalence: best practices and their theoretical underpinnings

Ian F. Miller, India Schneider-Crease, Charles L. Nunn & Michael P. Muehlenbein
Accurately estimating infection prevalence is fundamental to the study of population health, disease dynamics, and infection risk factors. Prevalence is estimated as the proportion of infected individuals (“individual-based estimation”), but is also estimated as the proportion of samples from which the disease-causing organisms are recovered (“anonymous estimation”). The latter method is often used when researchers lack information on individual host identity, which can occur during noninvasive sampling of wild populations or when the individual that...

Data from: Assessing cetacean surveys throughout the Mediterranean Sea: a gap analysis in environmental space

Laura Mannocci, Jason J. Roberts, Patrick N. Halpin, Matthieu Authier, Olivier Boisseau, Mohamed Nejmeddine Bradai, Ana Cañadas, Carla Chicote, Léa David, Nathalie Di-Méglio, Caterina M. Fortuna, Alexandros Frantzis, Manel Gazo, Tilen Genov, Philip S. Hammond, Drasko Holcer, Kristin Kaschner, Dani Kerem, Giancarlo Lauriano, Tim Lewis, Giuseppe Notarbartolo Di Sciara, Simone Panigada, Juan Antonio Raga, Aviad Scheinin, Vincent Ridoux … & Joseph Vella
Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481...

Data from: Mutual visual signalling between the cleaner shrimp Ancylomenes pedersoni and its client fish

Eleanor M. Caves, Patrick A. Green & Sonke Johnsen
Cleaner shrimp and their reef fish clients are an interspecific mutualistic interaction that is thought to be mediated by signals, and a useful system for studying the dynamics of interspecific signalling. To demonstrate signalling, one must show that purported signals at minimum (a) result in a consistent state change in the receiver and (b) contain reliable information about the sender’s intrinsic state or future behaviour. Additionally, signals must be perceptible by receivers. Here, we document...

Data from: CHIIMP: an automated high-throughput microsatellite genotyping approach reveals greater allelic diversity in wild chimpanzees

Hannah J. Barbian, Andrew Jesse Connell, Alexa N. Avitto, Ronnie M. Russell, Andrew G. Smith, Madhurima S. Gundlapally, Alexander L. Shazad, Yingying Li, Frederic Bibollet-Ruche, Emily E. Wroblewski, Deus Mjungu, Elizabeth V. Lonsdorf, Fiona A. Stewart, Alexander K. Piel, Anne E. Pusey, Paul M. Sharp & Beatrice H. Hahn
Short tandem repeats (STRs), also known as microsatellites, are commonly used to non-invasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park,...

Data from: Seed traits, not density or distance from parent, determine seed predation and establishment in an Afrotropical forest

Cooper Rosin & John R. Poulsen
Seed predators drive patterns in seed mortality and seedling establishment and are posited to contribute to the maintenance of plant species diversity through several mechanisms. Negative density dependence and spatially-restricted recruitment are apparently widespread in Neotropical forests, but are little studied in Afrotropical forests, where generalist vertebrates may contribute more to seed mortality than do specialized invertebrates and fungi. We experimentally assessed the roles of seed density and distance from the parent tree for ten...

Data from: Exposure to predators does not lead to the evolution of larger brains in experimental populations of threespine stickleback

Kieran Samuk, Jan Xue, Diana Jessie Rennison & Diana J. Rennision
Natural selection is often invoked to explain differences in brain size among vertebrates. However, the particular agents of selection that shape brain size variation remain obscure. Recent studies suggest that predators may select for larger brains because increased cognitive and sensory abilities allow prey to better elude predators. Yet, there is little direct evidence that exposure to predators causes the evolution of larger brains in prey species. We experimentally tested this prediction by exposing families...

Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

Kristina M. Cammen, Thomas F. Schultz, W. Don Bowen, Michael O. Hammill, Wendy B. Puryear, Jonathan Runstadler, Frederick W. Wenzel, Stephanie A. Wood & Michael Kinnison
Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed...

Data from: A comprehensive analysis of autocorrelation and bias in home range estimation

Michael J. Noonan, Marlee A. Tucker, Christen H. Fleming, Tom S. Akre, Susan C. Alberts, Abdullahi H. Ali, Jeanne Altmann, Pamela C. Antunes, Jerrold L. Belant, Dean Beyer, Niels Blaum, Katrin Böhning-Gaese, , Rogerio De Paula Cunha, Jasja Dekker, Jonathan Drescher-Lehman, Nina Farwig, Claudia Fichtel, Christina Fischer, Adam T. Ford, Jacob R. Goheen, René Janssen, Florian Jeltsch, Matthew Kauffman, Peter M. Kappeler … & Justin M. Calabrese
Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of...

Data from: Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception

Robert R. Fitak, Lorian E. Schweikert, Benjamin R. Wheeler, David A. Ernst, Kenneth J. Lohmann & Sonke Johnsen
The ability to perceive Earth’s magnetic field, or magnetoreception, exists in numerous animals. Although the mechanism underlying magnetoreception has not been clearly established in any species, in salmonid fish it is hypothesized to occur by means of crystals of magnetite associated with nervous tissue such as the brain, olfactory organ, or retina. In this study, rainbow trout (Oncorhynchus mykiss) were exposed to a brief magnetic pulse known to disrupt magnetic orientation behavior in several animals....

Data from: Don’t throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

Emilie J. Richards, Jelmer W. Poelstra & Christopher H. Martin
Genomic data has revealed complex histories of colonization and repeated gene flow previously unrecognized in some of the most celebrated examples of sympatric speciation and radiation. However, much of the evidence for secondary gene flow into these radiations comes from summary statistics calculated from sparse genomic sampling without knowledge of which specific genomic regions introgressed. This tells us little about how gene flow potentially influenced sympatric diversification. Here we investigated whole genomes of Barombi Mbo...

Data from: The role of diversification in the continental scale community assembly of the American oaks (Quercus)

Jeannine Cavender-Bares, Shan Kothari, José Eduardo Meireles, Matthew A. Kaproth, Paul S. Manos & Andrew L. Hipp
Premise of the study: Evolutionary and biogeographic history, including past environmental change and diversification processes, are likely to have influenced the expansion, migration, and extinction of populations, creating evolutionary legacy effects that influence regional species pools and the composition of communities. We consider the consequences of the diversification process in shaping trait evolution and assembly of oak-dominated communities throughout the continental U.S. Methods: Within the US oaks, we tested for phylogenetic and functional trait patterns...

Data from: High-throughput sequencing of the T-cell receptor beta chain gene distinguishes two subgroups of cutaneous T-cell lymphoma

Jie Wang, Bryan Rea, Paul Haun, Ryan Emerson, Ilan Kirsch & Adam Bagg
HTS of the TCR beta chain distinguishes two subgroups of CTCLT-cell repertoire characterization data are provided herein as a supplement to: High-Throughput Sequencing of the T-cell receptor beta chain gene distinguishes two subgroups of cutaneous T-cell lymphoma By Jie Wang, MD, Bryan Rea, MD, Paul Haun, MD, Ryan Emerson, PhD, Ilan Kirsch, MD, and Adam Bagg, MD

Data from: A test of the eavesdropping avoidance hypothesis as an explanation for the structure of low amplitude aggressive signals in the song sparrow

Joseph M. Niederhauser, Adrienne L. DuBois, William A. Searcy, Stephen Nowicki & Rindy C. Anderson
Low amplitude signals function in private exchanges of information between signalers and nearby receivers. The eavesdropping avoidance hypothesis proposes that selection favors quiet threat signals in order to avoid the costs of eavesdroppers. If true, then selection should favor other acoustic traits in addition to low amplitude that lead to quiet signals transmitting less effectively through the environment compared to broadcast signals. The “warbled” soft songs of male song sparrows differ from “crystallized” soft songs...

Data from: Genome-wide analysis of SNPs is consistent with no domestic dog ancestry in the endangered Mexican wolf (Canis lupus baileyi)

Robert R. Fitak, Sarah E. Rinkevich & Melanie Culver
The Mexican gray wolf (Canis lupus baileyi) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in three separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from three, two, and two founders, respectively. These lineages were merged in 1995 to increase the available genetic variation,...

Data from: Costs of injury for scent signalling in a strepsirrhine primate

Rachel L. Harris, Marylène Boulet, Kathleen E. Grogan & Christine M. Drea
Honesty is crucial in animal communication when signallers are conveying information about their condition. Condition dependence implies a cost to signal production; yet, evidence of such cost is scarce. We examined the effects of naturally occurring injury on the quality and salience of olfactory signals in ring-tailed lemurs (Lemur catta). Over a decade, we collected genital secretions from 23 (13 male, 10 female) adults across 34 unique injuries, owing primarily to intra-group fights. Using gas...

Data from: Interbirth intervals in wild baboons: environmental predictors and hormonal correlates

Laurence R. Gesquiere, Jeanne Altmann, Elizabeth A. Archie & Susan C. Alberts
Objectives: Interbirth intervals (IBIs) are a key metric of female reproductive success; understanding how they are regulated by environmental, social, and demographic factors can provide insight into sources of variance in female fitness. Materials and Methods: Using 36 years of reproductive data on 490 IBIs for 160 wild female baboons, we identified sources of variance in the duration of IBIs and of their component phases: postpartum amenorrhea (PPA), sexual cycling, and pregnancy. We also examined...

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: Urbanization and anticoagulant poisons promote immune dysfunction in bobcats

Laurel E.K. Serieys, Amanda J. Lea, Marta Epeldegui, Tiffany C. Armenta, Joanne Moriarty, Sue Vandewoude, Scott Carver, Janet Foley, Robert K. Wayne, Seth P.D. Riley, Christel H. Uittenbogaart, Laurel E. K. Serieys & Seth P. D. Riley
Understanding how human activities influence immune response to environmental stressors can support biodiversity conservation across increasingly urbanizing landscapes. We studied a bobcat (Lynx rufus) population in urban southern California that experienced a rapid population decline from 2002–2005 due to notoedric mange. Because anticoagulant rodenticide (AR) exposure was an underlying complication in mange deaths, we aimed to understand sublethal contributions of urbanization and ARs on 65 biochemical markers of immune and organ function. Variance in immunological...

Data from: Herbivory enhances the resistance of mangrove forest to cordgrass invasion

Yihui Zhang, Hanyu Meng, Yi Wang & Qiang He
The biotic resistance hypothesis proposes that biotic interactions, such as competition and herbivory, resist the establishment and spread of non-native species. The relative and interactive role of competition and herbivory in resisting plant invasions, however, remains poorly understood. We investigated the interactive role of competition and herbivory (by the native rodent Rattus losea) in resisting Spartina alterniflora (cordgrass) invasions into mangrove forests. In southern China, although exotic cordgrass numerically dominates intertidal mudflats and open gaps...

Data from: Costs and benefits of non-random seed release for long distance dispersal in wind-dispersed plant species

Jelle Treep, Monique De Jager, Leandra S. Kuiper, Tomer Duman, Gabriel G. Katul & Merel B. Soons
The dispersal ability of plants is a major factor driving ecological responses to global change. In wind-dispersed plant species, non-random seed release in relation to wind speeds has been identified as a major determinant of dispersal distances. However, little information is available about the costs and benefits of non-random abscission and the consequences of timing for dispersal distances. We asked: 1) To what extent is non-random abscission able to promote long-distance dispersal and what is...

Registration Year

  • 2018
    54

Resource Types

  • Dataset
    54

Affiliations

  • Duke University
    54
  • Princeton University
    4
  • University of North Carolina
    4
  • University of British Columbia
    4
  • University of Pennsylvania
    3
  • University of Washington
    3
  • University of Pretoria
    3
  • Field Museum of Natural History
    3
  • University of Minnesota
    3
  • University of California, Davis
    3