38 Works

Data from: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America

Katherine Silliman
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent...

Data from: Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

John M. Jumper, Nabil F. Faruk, Karl F. Freed & Tobin R. Sosnick
An ongoing challenge in protein chemistry is to identify the underlying interaction energies that capture protein dynamics. The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assumption that detailed force fields are typically well-parameterized, obtaining a significant fraction of possible accuracy. We re-examine this trade-off in the more realistic regime in which parameterization is a greater source of error than the level of detail in the force field. To...

Data from: Morphology of the petrosal and stapes of Borealestes (Mammaliaformes, Docodonta) from the Middle Jurassic of Skye, Scotland

Elsa Panciroli, Julia A. Schultz & Zhe-Xi Luo
\We describe, in unprecedented detail, the petrosals and stapes of the docodont Borealestes from the Middle Jurassic of Scotland, using high resolution μCT and phase‐contrast synchrotron imaging. We describe the inner ear endocast and the vascularized interior structure of the petrosal, and provide the first endocranial view of a docodontan petrosal. Our study confirms some similarities in petrosal and stapedial morphology with the better known Haldanodon of the Late Jurassic of Portugal, including: (1) the...

Data from: Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal

Choongwon Jeong, David B. Witonsky, Buddha Basnyat, Maniraj Neupane, Cynthia M. Beall, Geoff Childs, Sienna R. Craig, John Novembre & Anna Di Rienzo
Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting selective sweeps and polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. We performed genome-wide association analysis and tests for polygenic adaptations which showed evidence of positive selection...

Data from: Testing the adaptive hypothesis of Batesian mimicry among hybridizing North American admiral butterflies

Evan Breaux Kristiansen, Susan D. Finkbeiner, Ryan Isaac Hill, Louis Prusa & Sean Patrick Mullen
Batesian mimicry is characterized by phenotypic convergence between an unpalatable model and a palatable mimic. However, because convergent evolution may arise via alternative evolutionary mechanisms, putative examples of Batesian mimicry must be rigorously tested. Here we used artificial butterfly facsimiles (N=4000) to test the prediction that 1) palatable Limenitis lorquini butterflies should experience reduced predation when in sympatry with their putative model, Adelpha californica, 2) protection from predation on L. lorquini should erode outside of...

Data from: Does batrachotoxin autoresistance co-evolve with toxicity in Phyllobates poison-dart frogs?

Roberto Márquez, Valeria Ramírez-Castañeda & Adolfo Amézquita
Toxicity is widespread among living organisms, and evolves as a multimodal phenotype. Part of this phenotype is the ability to avoid self-intoxication (autoresistance). Evolving toxin resistance can involve fitness tradeoffs, so autoresistance is often expected to evolve gradually and in tandem with toxicity, resulting in a correlation between the degrees of toxicity and autoresistance among toxic populations. We investigate this correlation in Phyllobates poison frogs, notorious for secreting batrachotoxin (BTX), a potent neurotoxin that targets...

Data from: Diversity-dependent evolutionary rates in early Paleozoic zooplankton

Michael Foote, Roger A. Cooper, James S. Crampton & Peter M. Sadler
The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here we analyse the species-level fossil record of early Paleozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and...

Data from: Systemic thyroid hormone status during levothyroxine therapy in hypothyroidism: a systematic review and meta-analysis

Elizabeth A. McAninch, Kumar B. Rajan, Corinne H. Miller & Antonio C. Bianco
CONTEXT: The standard of care for overt hypothyroidism is levothyroxine at doses that normalize serum TSH levels. Whether this approach universally restores thyroid hormone signaling is unknown. OBJECTIVE: To review studies of overt hypothyroidism in which participants were treated with levothyroxine to normalize serum TSH levels and measured other objective markers of thyroid hormone signaling. DESIGN: Databases were searched for studies that reported objective markers of thyroid hormone signaling (serum low-density lipoprotein (LDL), total cholesterol...

Data from: Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models

Luis Felipe V. Ferrão, Romario G. Ferrão, Maria Amelia G. Ferrão, Aymbiré Fonseca, Peter Carbonetto, Matthew Stephens & Antonio A.F Garcia
Genomic selection have been proposed as the standard method to predict breeding values in animal and plant breeding. Although some crops have benefited from this methodology, studies in Coffea are still emerging. To date, there have been no studies of how well genomic prediction models work across populations and environments for different complex traits in coffee. Considering that predictive models are based on biological and statistical assumptions, it is expected that their performance vary depending...

Data from: Positive correlations between pre- and post-copulatory sexual traits in warblers

K. Supriya, Trevor D. Price & Melissah Rowe
Theoretical models predict that investment in pre-copulatory and post-copulatory sexually selected traits should trade-off. At the macroevolutionary scale, the majority of studies to date have focused on male weaponry as the target of pre-copulatory sexual selection, but the trade-off should equally apply to traits used to attract females, such as bird song and plumage. We studied the Old World leaf warblers (Phylloscopidae), a group of socially monogamous songbirds that experience relatively high levels of sperm...

Data from: Pattern and process in hominin brain size evolution are scale-dependent

Andrew Du, Andrew M. Zipkin, Kevin G. Hatala, Elizabeth Renner, Jennifer L. Baker, Serena Bianchi, Kallista H. Bernal & Bernard A. Wood
A large brain is a defining feature of modern humans, yet there is no consensus regarding the patterns, rates, and processes involved in hominin brain size evolution. We use a reliable proxy for brain size in fossils, endocranial volume (ECV), to better understand how brain size evolved at both clade- and lineage-level scales. For the hominin clade overall, the dominant signal is consistent with a gradual increase in brain size. This gradual trend appears to...

Data from: Oldest known multituberculate stapes suggests an asymmetric bicrural pattern as ancestral for Multituberculata

Julia A. Schultz, Irina Ruf & Thomas Martin
Middle ear ossicles (malleus, incus, stapes) are known only for few multituberculate taxa, and three different stapedial morphotypes have been suggested: (1) slender, columelliform and microperforate, (2) robust and rod-like, and (3) bicrural. Reinvestigation of Upper Jurassic (Kimmeridgian) mammalian petrosals from the Guimarota coal mine in central Portugal (Western Europe) revealed an asymmetric bicrural stapes (ABS) in the paulchoffatiid Pseudobolodon oreas. The middle ear bones displaced inside the osseous vestibule were detected by a microCT...

Data from: Geographic patterns of song variation in four species of Malurus fairy-wrens

David D. Yandell, Wesley M. Hochachka, Stephen Pruett-Jones, Michael S. Webster & Emma I. Greig
Geographic variation in song is widespread among birds, particularly in species that learn vocalizations. The relationship between geographic distance and song variation is likely related to the degree of isolation between populations. To assess this effect of geographic isolation on song divergence, we examined patterns of geographic song variation in four species of Australian fairy-wrens (Malurus), two with suspected histories of geographic isolation and two without. Song variation in all four species was consistent with...

Data from: Testing for human impacts in the mismatch of living and dead ostracode assemblages at nested spatial scales in subtropical lakes from the Bahamian archipelago

Andrew V. Michelson, Susan M. Kidwell, Lisa E. Park Boush & Jeanine L. Ash
Naturally time-averaged accumulations of skeletal remains – death assemblages – provide reliable, albeit temporally coarse, information on the species composition and structure of communities in diverse settings, and their mismatch with local living communities usually signals recent human-driven ecological change. Here, we present the first test of live-dead mismatch as an indicator of human stress using ostracodes. On three islands along a gradient of human population density in the Bahamas, we compared the similarity of...

Data from: Song recognition and heterospecific associations between two fairy-wren species (Maluridae)

Allison E. Johnson, Christina Masco & Stephen Pruett-Jones
Although heterospecific associations beneficial to one or both species involved (e.g. commensalisms or mutualisms) are common, it is generally assumed that interactions between species are transient and not particular to individuals. However, long-term interactions between individuals of different species do occur. In such heterospecific social groups, discrimination between heterospecific individuals may be beneficial, allowing individuals to direct beneficial or aggressive behaviors towards appropriate targets. Here we describe heterospecific groups composed of splendid and variegated fairy-wrens...

Data from: Determining the genetic basis of anthracycline-cardiotoxicity by response QTL mapping in induced cardiomyocytes

David A. Knowles, Courtney K. Burrows, John D. Blischak, Kristen M. Patterson, Daniel J. Serie, Nadine Norton, Carole Ober, Jonathan K. Pritchard & Yoav Gilad
Anthracycline-induced cardiotoxicity (ACT) is a key limiting factor in setting optimal chemotherapy regimes, with almost half of patients expected to develop congestive heart failure given high doses. However, the genetic basis of sensitivity to anthracyclines remains unclear. We created a panel of iPSC-derived cardiomyocytes from 45 individuals and performed RNA-seq after 24h exposure to varying doxorubicin dosages. The transcriptomic response is substantial: the majority of genes are differentially expressed and over 6000 genes show evidence...

Data from: Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

Joy Bergelson, Jana Mittelstrass & Matthew W. Horton
Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence...

Data from: Adaptive developmental plasticity in rhesus macaques: the serotonin transporter gene interacts with maternal care to affect juvenile social behaviour

Jesus E. Madrid, Tara M. Mandalaywala, Sean P. Coyne, Jamie Ahloy-Dallaire, Joseph P. Garner, Christina S. Barr, Dario Maestripieri & Karen J. Parker
Research has increasingly highlighted the role that developmental plasticity-the ability of a particular genotype to produce variable phenotypes in response to different early environments-plays as an adaptive mechanism. One of the most widely studied genetic contributors to developmental plasticity in humans and rhesus macaques is a serotonin transporter gene-linked polymorphic region (5-HTTLPR), which determines transcriptional efficiency of the serotonin transporter gene in-vitro and modifies the availability of synaptic serotonin in these species. A majority of...

Data from: Temporal scale of environmental correlations affects ecological synchrony

Robert A. Desharnais, Daniel C. Reuman, Robert F. Costantino & Joel E. Cohen
Population densities of a species, measured in different locations are often correlated over time, a phenomenon referred to as synchrony. Synchrony results from dispersal of individuals among locations and spatially correlated environmental variation, among other causes. Synchrony is often measured by a correlation coefficient. However, synchrony can vary with timescale. We demonstrate theoretically and experimentally that the timescale-specificity of environmental correlation affects the overall magnitude and timescale-specificity of synchrony, and that these effects are modified...

Measuring impostor phenomenon among health sciences librarians

Jill Barr-Walker, Michelle B. Bass, Debra A. Werner & Liz Kellermeyer
This dataset contains Appendices A-J corresponding to the article "Measuring impostor phenomenon among health sciences librarians". Objective: Impostor phenomenon, also known as impostor syndrome, is the inability to internalize accomplishments while experiencing the fear of being exposed as a fraud. Previous work has examined impostor phenomenon among academic college and research librarians, but health sciences librarians, who are often asked to be experts in medical subject areas with minimal training or education in these areas,...

Data from: Male competition drives song divergence along an ecological gradient in an avian ring species

Elizabeth S.C. Scordato & Elizabeth S. C. Scordato
Sexual selection operates via female choice and male competition, which can act independently, in concert, or in opposition. Female choice is typically considered the stronger selective force, but how these two processes interact to shape phenotypic divergence is poorly understood. I tested the hypothesis that variation in sexual selection in different habitats drives song divergence in the greenish warbler ring species. I evaluated the strength, direction, and targets of female choice and male competition in...

Data from: Ice-VII inclusions in diamonds: evidence for aqueous fluid in Earth’s deep mantle

Oliver Tschauner, Shichun Huang, Eran Greenberg, Vitali B. Prakapenka, Chi Ma, George R. Rossman, Andy H. Shen, Dongzhou Zhang, Matthew Newville, Antonio Lanzirotti & Kimberly Tait
Water-rich regions in Earth’s deeper mantle are suspected to play a key role in the global water budget and the mobility of heat-generating elements. We show that ice-VII occurs as inclusions in natural diamond and serves as an indicator for such water-rich regions. Ice-VII, the residue of aqueous fluid present during growth of diamond, crystallizes upon ascent of the host diamonds but remains at pressures as high as 24 gigapascals; it is now recognized as...

Data from: Frequency-dependence shapes the adaptive landscape of imperfect Batesian mimicry

Susan D. Finkbeiner, Patricio A. Salazar, Sofia Nogales, Cassidi E. Rush, Adriana D. Briscoe, Ryan I. Hill, Marcus R. Kronforst, Keith R. Willmott & Sean P. Mullen
Despite more than a century of biological research on the evolution and maintenance of mimetic signals, the relative frequencies of models and mimics necessary to establish and maintain Batesian mimicry in natural populations remains understudied. Here we investigate the frequency-dependent dynamics of imperfect Batesian mimicry, using predation experiments involving artificial butterfly models. We use two geographically distinct populations of Adelpha butterflies that vary in their relative frequencies of a putatively defended model (Adelpha iphiclus) and...

Data from: Female mate choice is a reproductive isolating barrier in Heliconius butterflies

Laura Southcott & Marcus R. Kronforst
In sexually reproducing organisms, speciation involves the evolution of reproductive isolating mechanisms that decrease gene flow. Premating reproductive isolation, often the result of mate choice, is a major obstacle to gene flow between species because it acts earlier in the life cycle than other isolating barriers. While female choice is often considered the default mode in animal species, research in the butterfly genus Heliconius, a frequent subject of speciation studies, has focused on male mate...

Data from: Coevolution-based inference of amino acid interactions underlying protein function

Victor H Salinas & Rama Ranganathan
Protein function arises from a poorly understood pattern of energetic interactions between amino acid residues. Sequence-based strategies for deducing this pattern have been proposed, but lack of benchmark data has limited experimental verification. Here, we extend deep-mutation technologies to enable measurement of many thousands of pairwise amino acid couplings in several homologs of a protein family – a deep coupling scan (DCS). The data show that cooperative interactions between residues are loaded in a sparse,...

Registration Year

  • 2018
    38

Resource Types

  • Dataset
    38

Affiliations

  • University of Chicago
    38
  • Stanford University
    3
  • New York University
    2
  • University of Zurich
    2
  • Harvard University
    2
  • University of Nebraska - Lincoln
    2
  • California Institute of Technology
    2
  • University of the Pacific
    2
  • Boston University
    2
  • University of Kansas
    1