26 Works

Data from: Exploring visual plasticity: dietary carotenoids can change color vision in guppies (Poecilia reticulata)

Benjamin A. Sandkam, Kerry A. Deere-Machemer, Ashley M. Johnson, Gregory F. Grether, F. Helen Rodd & Rebecca C. Fuller
Differences in color vision can play a key role in an organism’s ability to perceive and interact with the environment across a broad range of taxa. Recently, species have been shown to vary in color vision across populations as a result of differences in regulatory sequence and/or plasticity of opsin gene expression. For decades, biologists have been intrigued by among-population variation in color-based mate preferences of female Trinidadian guppies. We proposed that some of this...

Data from: Can plan recommendations improve the coverage decisions of vulnerable populations in health insurance marketplaces?

Andrew J. Barnes, Yaniv Hanoch & Thomas Rice
Objective: The Affordable Care Act’s marketplaces present an important opportunity for expanding coverage but consumers face enormous challenges in navigating through enrollment and re-enrollment. We tested the effectiveness of a behaviorally informed policy tool—plan recommendations—in improving marketplace decisions. Study Setting: Data were gathered from a community sample of 656 lower-income, minority, rural residents of Virginia. Study Design: We conducted an incentive-compatible, computer-based experiment using a hypothetical marketplace like the one consumers face in the federally-facilitated...

Data from: Mechanisms of resilience: empirically quantified positive feedbacks produce alternate stable states dynamics in a model of a tropical reef

Ranjan Muthukrishnan, James O. Lloyd-Smith & Peggy Fong
Alternate stable states (ASS) theory is a dominant conceptual framework for understanding processes that support resilience of ecological communities in the face of multiple anthropogenic disturbances. For decades, coral reefs have been cited as a classic example of ASS, yet this position remains highly controversial, largely because convincing empirical evaluations have been elusive. Using a combination of empirical measurements of positive feedback processes and simulation modelling, we assessed ASS in coral reefs of the Eastern...

Data from: 1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

Michael Worobey, Thomas D. Watts, Richard A. McKay, Marc A. Suchard, Timothy Granade, Dirk E. Teuwen, Beryl A. Koblin, Walid Heneine, Philippe Lemey & Harold W. Jaffe
The emergence of HIV-1 group M subtype B in North American men who have sex with men was a key turning point in the HIV/AIDS pandemic. Phylogenetic studies have suggested cryptic subtype B circulation in the United States (US) throughout the 1970s1, 2 and an even older presence in the Caribbean2. However, these temporal and geographical inferences, based upon partial HIV-1 genomes that postdate the recognition of AIDS in 1981, remain contentious3, 4 and the...

Data from: Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area

John F. Benson, Peter J. Mahoney, Jeff A. Sikich, Laurel E.K. Serieys, John P. Pollinger, Holly B. Ernest, Seth P.D. Riley, Laurel E. K. Serieys & Seth P. D. Riley
The extinction vortex is a theoretical model describing the process by which extinction risk is elevated in small, isolated populations owing to interactions between environmental, demographic, and genetic factors. However, empirical demonstrations of these interactions have been elusive. We modelled the dynamics of a small mountain lion population isolated by anthropogenic barriers in greater Los Angeles, California, to evaluate the influence of demographic, genetic, and landscape factors on extinction probability. The population exhibited strong survival...

Data from: Bolstered physical defences under nutrient-enriched conditions may facilitate a secondary foundational algal species in the South Pacific

Sarah Joy Bittick, Rachel Joy Clausing, Caitlin Ryan Fong & Peggy Fong
1. Humans have a long history of changing species’ ranges and habitat distributions, making studies of the ecological processes that may facilitate these changes of key importance, particularly in cases where a primary foundation species is replaced by another, less desirable species. 2. We investigated the impact of nutrients and herbivory on Turbinaria ornata, a secondary foundational macroalga that depends on and likely competes with coral, the primary foundational community. T. ornata is also rapidly...

Data from: The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

Paul M. Hime, Scott Hotaling, Richard E. Grewelle, Eric M. O'Neill, S. Randal Voss, H. Bradley Shaffer & David W. Weisrock
Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence datasets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large datasets is time consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of...

Data from: Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study

Greer A. Dolby, Ryan Hechinger, Ryan A. Ellingson, Lloyd T. Findley, Julio Lorda & David K. Jacobs
Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the LGM (approx. 20 kya), when sea level was approximately 130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions...

Data from: Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

Richard C. Harrington, Brant C. Faircloth, Ron I. Eytan, W. Leo Smith, Thomas J. Near, Michael E. Alfaro & Matt Friedman
Background: Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have yielded a polyphyletic or only weakly supported flatfish clade. Lack of resolution for flatfish relationships has been...

Data from: Admixture mapping identifies introgressed genomic regions in North American canids

Bridgett M. VonHoldt, Roland W. Kays, John P. Pollinger & Robert K. Wayne
Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years...

Data from: Adaptive evolution of a derived radius morphology in manakins (Aves, Pipridae) to support acrobatic display behavior

Anthony R. Friscia, Gloria D. Sanin, Willow R. Lindsay, Lainy B. Day, Barney A. Schlinger, Josh Tan, Matthew J. Fuxjager & Anthony Friscia
The morphology of the avian skeleton is often studied in the context of adaptations for powered flight. The effects of other evolutionary forces, such as sexual selection, on avian skeletal design are unclear, even though birds produce diverse behaviors that undoubtedly require a variety of osteological modifications. Here, we investigate this issue in a family of passerine birds called manakins (Pipridae), which have evolved physically unusual and elaborate courtship displays. We report that, in species...

Data from: Genome sequencing highlights the dynamic early history of dogs

Adam H. Freedman, Ilan Gronau, Rena M. Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Pedro M. Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Holly Beale, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi G. Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D. Bustamante, Timothy T. Harkins … & John Novembre
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow....

Data from: Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients

Paul F. Gugger, Sorel Fitz-Gibbon, Matteo Pellegrini & Victoria L. Sork
DNA methylation in plants affects transposon silencing, transcriptional regulation and thus phenotypic variation. One unanswered question is whether DNA methylation could be involved in local adaptation of plant populations to their environments. If methylation alters phenotypes to improve plant response to the environment, then methylation sites or the genes that affect them could be a target of natural selection. Using reduced-representation bisulphite sequencing (RRBS) data, we assessed whether climate is associated with variation in DNA...

Data from: Behavioral hypervolumes of predator groups and predator-predator interactions shape prey survival rates and selection on prey behavior

Jonathan N. Pruitt, Kimberley Howell, Shaniqua Gladney, Yusan Yang, James L. L. Lichtenstein, Michelle Elise Spicer, Sebastian A. Echeverri & Noa Pinter-Wollman
Predator-prey interactions often vary on the basis of the traits of the individual predators and prey involved. Here we examine whether the multidimensional behavioral diversity of predator groups shapes prey mortality rates and selection on prey behavior. We ran individual sea stars (Pisaster ochraceus) through three behavioral assays to characterize individuals’ behavioral phenotype along three axes. We then created groups that varied in the volume of behavioral space that they occupied. We further manipulated the...

Eurasian pollen data from 21 kiloannum to the present

A. Binney. H., A. Lozhkin, P Anderson, A. Andreev, E. Bezrukova, T. Blyakharchuk, V. Jankovska, I. Khazhina, S. Krivonogov, K. Kremenetski, E. Novenko, N. Ryabogina, N. Solovieva & V. Zernitzkaya
This dataset contains fossil and modern pollen data collated during a workshop held in the UK in 2008 as part of the NERC (Quantifying and Understanding the Earth System) QUEST programme. The 96 sampling sites are located from 24°E (western Ukraine and Belarus) to easternmost Siberia, and lie north of latitude 40°N. The sample ages range from 21ka to present and are assigned to 1,000 year time slices. The dataset has been checked for consistent...

Data from: Microbial consortia controlling biogenic gas formation in the Qaidam Basin of western China

Yanhua Shuai, Shuichang Zhang, Stephen E. Grasby, Weiguo Hou, Zhuoheng Chen, Ling Huang, Mingqing Kui, Yirui Xu & Yang Wang
Knowledge of what controls the activity of subsurface microbial communities is critical for assessing and managing biogenic methane resources. In this study, 19 formation waters and five gas samples were collected at depths of 800 to 1900 m from Quaternary biogenic gas fields of the Qaidam Basin, China. The formation waters were brines with chloride (Cl) concentrations from 1200 to 2700 mM. Bacterial 16S rRNA gene copies ranged from 3.75 × 104 to 2.23 ×...

Data from: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

Yehudit Hasin-Brumshtein, Arshad H. Khan, Farhad Hormozdiari, Calvin Pan, Brian W. Parks, Vladislav A. Petyuk, Paul D. Piehowski, Anneke Brümmer, Matteo Pellegrini, Xinshu Xiao, Eleazar Eskin, Richard D. Smith, Aldons J. Lusis & Desmond J. Smith
Previous studies had shown that integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic...

Data from: Epidemiological models to control the spread of information in marine mammals

Zachary A. Schakner, Michael G. Buhnerkempe, Mathew J. Tennis, Robert J. Stansell, Bjorn K. Van Der Leeuw, James O. Lloyd-Smith & Daniel T. Blumstein
Socially transmitted wildlife behaviours that create human–wildlife conflict are an emerging problem for conservation efforts, but also provide a unique opportunity to apply principles of infectious disease control to wildlife management. As an example, California sea lions (Zalophus californianus) have learned to exploit concentrations of migratory adult salmonids below the fish ladders at Bonneville Dam, impeding endangered salmonid recovery. Proliferation of this foraging behaviour in the sea lion population has resulted in a controversial culling...

Data from: Behavioural hypervolumes of spider communities predict community performance and disbandment

Jonathan N. Pruitt, Daniel I. Bolnick, Andrew Sih, Nicholas DiRienzo & Noa Pinter-Wollman
Trait-based ecology argues that an understanding of the traits of interactors can enhance the predictability of ecological outcomes. We examine here whether the multidimensional behavioural-trait diversity of communities influences community performance and stability in situ. We created experimental communities of web-building spiders, each with an identical species composition. Communities contained one individual of each of five different species. Prior to establishing these communities in the field, we examined three behavioural traits for each individual spider....

Data from: Meta-analysis reveals that hydraulic traits explain cross-species patterns of drought-induced tree mortality across the globe

William R. L. Anderegg, Tamir Klein, Megan Bartlett, Lawren Sack, Adam F. A. Pellegrini, Brendan Choat & Steven Jansen
Drought-induced tree mortality has been observed globally and is expected to increase under climate change scenarios, with large potential consequences for the terrestrial carbon sink. Predicting mortality across species is crucial for assessing the effects of climate extremes on forest community biodiversity, composition, and carbon sequestration. However, the physiological traits associated with elevated risk of mortality in diverse ecosystems remain unknown, although these traits could greatly improve understanding and prediction of tree mortality in forests....

Data from: Maintenance of age in human neurons generated by microRNA-based neuronal conversion of fibroblasts

Christine J. Huh, Bo Zhang, Matheus Victor, Sonika Dahiya, Luis F. Z. Batista, Steve Horvath, Andrew S. Yoo, Matheus B Victor & Luis FZ Batista
Aging is a major risk factor in many forms of late-onset neurodegenerative disorders. The ability to recapitulate age-related characteristics of human neurons in culture will offer unprecedented opportunities to study the biological processes underlying neuronal aging. Here, we show that using a recently demonstrated microRNA-based cellular reprogramming approach, human fibroblasts from postnatal to near centenarian donors can be efficiently converted into neurons that maintain multiple age-associated signatures. Application of an epigenetic biomarker of aging (referred...

Data from: A quantitative electrophysiological biomarker of duplication 15q11.2-q13.1 syndrome

Joel Frohlich, Damla Senturk, Vidya Saravanapandian, Peyman Golshani, Lawrence T. Reiter, Raman Sankar, Ronald Thibert, Charlotte Distefano, Scott Huberty, Edwin H. Cook & Shafali S. Jeste
Background: Duplications of 15q11.2-q13.1 (Dup15q syndrome) are highly penetrant for autism spectrum disorder (ASD). A distinct electrophysiological (EEG) pattern characterized by excessive activity in the beta band has been noted in clinical reports. We asked whether EEG power in the beta band, as well as in other frequency bands, distinguished children with Dup15q syndrome from those with non-syndromic ASD and then examined the clinical correlates of this electrophysiological biomarker in Dup15q syndrome. Methods: In the...

Data from: Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

Matthew D. McGee, Brant C. Faircloth, Samuel R. Borstein, Jimmy Zheng, Christopher Darrin Hulsey, Peter C. Wainwright & Michael E. Alfaro
Decoupling of the upper jaw bones—jaw kinesis—is a distinctive feature of the ray-finned fishes, but it is not clear how the innovation is related to the extraordinary diversity of feeding behaviours and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well known for its ecological and functional diversity—African rift lake cichlids. We sequenced ultraconserved elements to generate a phylogenomic tree of the Lake Tanganyika and Lake...

Data from: How the zebra got its stripes: a problem with too many solutions

Brenda Larison, Ryan J. Harrigan, Henri A. Thomassen, Daniel I. Rubenstein, Alec M. Chan-Golston, Elizabeth Li & Thomas B. Smith
The adaptive significance of zebra stripes has thus far eluded understanding. Many explanations have been suggested, including social cohesion, thermoregulation, predation evasion and avoidance of biting flies. Identifying the associations between phenotypic and environmental factors is essential for testing these hypotheses and substantiating existing experimental evidence. Plains zebra striping pattern varies regionally, from heavy black and white striping over the entire body in some areas to reduced stripe coverage with thinner and lighter stripes in...

Data from: Dietary breadth is positively correlated with venom complexity in cone snails

Mark A. Phuong, Gusti N. Mahardika & Michael E. Alfaro
Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e.,...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of California Los Angeles
  • Princeton University
  • University of Pittsburgh
  • University of Arizona
  • University of California, Davis
  • University of Tennessee Health Science Center
  • University of Kansas
  • Massachusetts General Hospital
  • Estación Biológica de Doñana
  • Plymouth University