145 Works

Phenotype data, genotype input files, and scripts related to adaptation in wild house mice from Western North America

Kathleen Ferris, Andreas Chavez, Taichi Suzuki, Megan Phifer-Rixey, Ke Bi, Michael Nachman & Elizabeth Beckman
Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America....

Analyses on the fungus-farming termite, Macrotermes natalensis

Mark Harrison, Mireille Vassuer-Cognet, Sarah Seite, David Sillam-Dussès, Roland Lupoli, Alain Robert, Laure-Anne Poissonnier, Tom Van Dooren, Arnaud Lemainque, David Renault, Sebastien Acket, Muriel Andrieu, Jose Viscarra, Hei Sook Sul, Wilhelm De Beer & Erich Bornberg-Bauer
Kings and queens of eusocial termites can live for decades, while queens sustain a nearly maximal fertility. To investigate the molecular mechanisms underlying their long lifespan, we carried out transcriptomics, lipidomics and metabolomics in Macrotermes natalensis on sterile short-lived workers, long-lived kings and five stages spanning twenty years of adult queen maturation. Reproductives share gene expression differences from workers in agreement with a reduction of several aging-related processes, involving upregulation of DNA damage repair and...

Pierce's disease vector transmission-preference experiment on PdR1 resistant grapevines

Adam Zeilinger, Dylan Beal, Anne Sicard, Christopher Wallis, M. Andrew Walker & Rodrigo Almeida
Host defense against vector-borne plant pathogens is a critical component of integrated disease management. However, theory predicts that traits that confer tolerance or partial resistance can, under certain ecological conditions, enhance the spread of pathogens and spillover to more susceptible populations or cultivars. A key component driving such epidemic risk appears to be variation in host selection behavior of vectors based on infection status of the host. While recent theory has further emphasized the importance...

Data and supporting information from: Higher metabolic plasticity in temperate compared to tropical lizards suggests increased resilience to climate change

Baojun Sun, Caroline Williams, Teng Li, John Speakman, Zengguang Jin, Hongliang Lu, Laigao Luo & Weiguo Du
We investigate thermal acclimation of three species of Takydromus lizards distributed along a broad latitudinal gradient in China. The dataset are including metabolic rates, organ size, mitochondrial respiration, Cox activities, proteomic and metabolomic regulations of three Takydromus lizards after warm and cold acclimation in the laboratory. See details in related paper.

Data supporting: Synthesis of higher order feature codes through stimulus-specific supra-linear summation

Daniel Mossing, Evan Lyall & Hillel Adesnik
How cortical circuits build representations of complex objects is poorly understood. The massive dimensional expansion from the thalamus to the primary sensory cortex may enable sparse, comprehensive representations of higher order features to facilitate object identification. To generate such a code, cortical neurons must integrate broadly over space, yet simultaneously obtain sharp tuning to specific stimulus features. The logic of cortical integration that may synthesize such a sparse, high dimensional code for complex features is...

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

Jessen Bredeson, Jessica Lyons, Ibukun Oniyinde, Nneka Okereke, Olufisayo Kolade, Ikenna Nnabue, Nneka Okereke, Christian Nwadili, Eva Hribova, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey Barton, Anna Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie Egesi, Jonathan Featherston … & Daniel Rokhsar
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an ‘orphan crop.’ Here we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive...

Data from: Community-level responses of African carnivores to prescribed burning

Laura Gigliotti, Goncalo Curveira-Santos, Rob Slotow, Craig Sholto-Douglas, Lourens Swanepoel & David Jachowski
Fires are common in many ecosystems worldwide, and are frequently used as a management tool. Although the responses of herbivores to fire have been well-studied, the responses of carnivores to fire remain unclear. In particular, post-fire habitat changes, and the associated changes in prey availability, might affect the coexistence or competition of carnivore species within the larger carnivore community, but few studies have focused on how fires influence multiple carnivore species simultaneously. Using South African...

Photoionization and electron impact ionization frequencies in the dayside ionosphere of Mars, calculated from MAVEN in situ data

Robert Lillis
The following data set contains valid photoionization frequencies and electron impact ionization frequencies for the primary neutral species CO2, O, CO, N2, and Ar in the dayside ionosphere of Mars, calculated from MAVEN in situ data from November 1, 2014 until December 12, 2019. It also contains necessary ancillary data, including Time UTC, Mars season, solar zenith angle, spacecraft altitude, atmospheric pressure, normalized on attenuated CO2 photoionization frequency (as a proxy for solar activity), the...

Data for: Carnivore niche partitioning in a human landscape

Mauriel Rodriguez Curras, Emiliano Donadío, Arthur Middleton & Jonathan Pauli
To minimize competitive overlap, carnivores modify one of their critical niche axes: space, time, or resources. However, we currently lack rules for how carnivore communities operate in human-dominated landscapes. We simultaneously quantified overlap in the critical niche axes of a simple carnivore community – an apex carnivore (Puma concolor), a dominant meso-carnivore (Lycalopex culpaeus), and a subordinate meso-carnivore (L. griseus) – in a human-landscape featuring pastoralists and semi-domestic carnivores (i.e., dogs Canis familiaris). We found...

Data from: Temporal scale of habitat selection for large carnivores: Balancing energetics, risk and finding prey

Anna Nisi, Justin Suraci, Nathan Ranc, Laurence Frank, Alayne Oriol-Cotterill, Steven Ekwanga, Terrie Williams & Christopher Wilmers
1. When navigating heterogeneous landscapes, large carnivores must balance trade-offs between multiple goals, including minimizing energetic expenditure, maintaining access to hunting opportunities, and avoiding potential risk from humans. The relative importance of these goals in driving carnivore movement likely changes across temporal scales, but our understanding of these dynamics remains limited. 2. Here we quantified how drivers of movement and habitat selection changed with temporal grain for two large carnivore species living in human-dominated landscapes,...

Energy limitation or sensitive predators? Trophic and non-trophic impacts of wastewater pollution on stream food webs

Jordi-René Mor, Isabel Muñoz, Sergi Sabater, Lluís Zamora & Albert Ruhi
Impacts of environmental stressors on food webs are often difficult to predict because trophic levels can respond in divergent ways, and biotic interactions may dampen or amplify responses. Here we studied food-web level impacts of urban wastewater pollution, a widespread source of degradation that can alter stream food webs via top-down and bottom-up processes. We selected ten pairs of sampling locations (i.e., twenty sites total) in ten small-to-medium tributaries of the Ebro River (NE Iberian...

A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape

Emilie Richards
To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid...

Snowpack, precipitation, and temperature measurements at the Central Sierra Snow Laboratory for water years 1971 to 2019

Randall Osterhuber & Andrew Schwartz
The snowpack of the Sierra Nevada Mountains is an indispensable freshwater resource for large portions of western North America. The Central Sierra Snow Laboratory (CSSL) has had an intigral role in the measurement of snowfall and snowpack properties within the Sierra Nevada Mountains, and has worked to develop a physical understanding of the processes that govern snow since 1946. This dataset contains measurements of temperature, precipiation quantity, snowfall, and snowpack characteristics including 24-hour snowfall, snowpack...

Evolution of conserved noncoding sequences in Arabidopsis thaliana

Alan Yocca, Zefu Lu, Robert Schmitz, Michael Freeling & Patrick Edger
Recent pangenome studies have revealed that a large fraction (>20%) of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana...

Data for: Perceived risk structures the space use of competing carnivores

Mauriel Rodriguez Curras, Emiliano Donadio, Arthur Middleton & Jonathan Pauli
Competition structures ecological communities. In carnivorans, competitive interactions are disproportionately costly to subordinate carnivores who must account for risk of interspecific killing when foraging. Accordingly, missed opportunity costs for meso-carnivores imposed by risk can benefit the smallest-bodied competitors. However, the extent to which the risk perpetuates into spatial partitioning in hierarchically structured communities remains unknown. To determine how risk-avoidance behaviors shape the space-use of carnivore communities, we studied a simple community of carnivores in northern...

Nucleation and heterochromatin establishment in Drosophila miranda

Kevin Wei
Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established in vivo are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual Drosophila early embryos at precisely staged developmental time points.

Quantitative assessment of agricultural sustainability reveals divergent priorities among nations

Guolin Yao, Xin Zhang, Srishti Vishwakarma, Carole Dalin, Adam Komarek, David Kanter, Kyle Davis, Kimberly Pfeifer, Jing Zhao, Tan Zou, Paolo D'Odorico, Christian Folberth, Fernando Galeana Rodriguez, Jessica Fanzo, Lorenzo Rosa, William Dennison, Mark Musumba, Amy Heyman & Eric Davidson
Agriculture is fundamental to all three pillars of sustainability, environment, society, and economy. However, the definition of sustainable agriculture and capacities to measure it remain elusive. Independent and transparent measurements of national sustainability are needed to gauge progress, encourage accountability, and inform policy. Here, we developed a Sustainable Agriculture Matrix (SAM) to quantify national performance indicators in agriculture and to investigate the tradeoffs and synergies based on historical data for most countries of the world....

Phylogeny of the supertribe Nebriitae (Coleoptera: Carabidae) based on analyses of DNA sequence data

David H. Kavanaugh, David Maddison, W. Brian Simison, Sean D. Schoville, Joachim Schmidt, Arnaud Faille, Wendy Moore, James M. Pflug, Sophie L. Archambeault, Tinya Hoang & Jei-Ying Chen
The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK and wingless) and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI (“barcode” region) and COI (“Pat/Jer” region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted...

Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

Patrice Salomé & Sabeeha Merchant
The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a...

Supplementary table from: Spectrometry of Greta oto untreated and hexane treated clear wing regions and simulated reflectance spectra

Aaron Pomerantz
The wings of butterflies and moths (Lepidoptera) are typically covered with thousands of flat, overlapping scales that endow the wings with colorful patterns. Yet, numerous species of Lepidoptera have evolved highly transparent wings, which often possess scales of altered morphology and reduced size, and the presence of membrane surface nanostructures that dramatically reduce reflection. Optical properties and anti-reflective nanostructures have been characterized for several ‘clearwing’ Lepidoptera, but the developmental processes underlying wing transparency are unknown....

Data from: Patterns of fine-scale spatial genetic structure and pollen dispersal in giant sequoia (Sequoiadendron giganteum)

Rainbow DeSilva & Richard Dodd
Research Highlights: Patterns of dispersal shape the distribution and temporal development of genetic diversity both within and among populations. In an era of unprecedented environmental change, the maintenance of extant genetic diversity is crucial to population persistence. Background and Objectives: We investigate patterns of pollen dispersal and spatial genetic structure within populations of giant sequoia (Sequoiadendron giganteum). Materials and Methods: The leaf genotypes of established trees from twelve populations were used to estimate the extent...

Inferring core processes using stochastic models of the geodynamo

William Davis & Bruce Buffett
Recent studies have represented time variations in the Earth's axial magnetic dipole field as a stochastic process, which comprises both deterministic and random elements. To explore how these elements are affected by the style and vigor of convection in the core, as well as the core-mantle boundary conditions, we construct stochastic models from a set of numerical dynamo simulations at low Ekman numbers. The deterministic part of the stochastic model, the drift term, characterises the...

Change and persistence of hunting & dietary practices among Kadazandusun-Murut (KDM) bearded pig hunters in Sabah, Malaysia

David Kurz, Fiffy Saikim, Vanielie Justine, Jordan Bloem, Matthew Libassi, Matthew Luskin, Lauren Withey, Benoit Goossens, Justin Brashares & Matthew Potts
This dataset consists of 38 semi-structured interviews that we conducted with Kadazandusun-Murut (KDM) hunters in Sabah, Malaysian Borneo. The dataset is based on information shared during over 50 hours of time with the hunters. The data cover a variety of topics about the relationships between KDM hunters and bearded pigs, the favored game animal for this hunting group. We asked the hunters about their hunting and dietary practices, changes in hunting practices, and perceived changes...

Example measurements of electron energy and pitch angle distributions from Venus Express

Shaosui Xu, Rudy Frahm, Yingjuan Ma, Janet Luhmann & David Mitchell
Venus has negligible intrinsic magnetic fields to the first order, such that its ionosphere (the charged part of the atmosphere) interacts directly with the solar wind plasma and magnetic field. Therefore, magnetic connectivity to the ionosphere and/or solar wind is an important piece of information for understanding the near-Venus space environment and the Sun-Venus interaction. We utilize measurements from the Venus Express to determine magnetic connectivity, or magnetic topology, for the first time. We find...

Source code for StrVCTVRE: a supervised learning method to predict the pathogenicity of human genome structural variants

Andrew Sharo, Zhiqiang Hu, Shamil Sunyaev & Steven Brenner
Whole genome sequencing resolves many clinical cases where standard diagnostic methods have failed. However, at least half of these cases remain unresolved after whole genome sequencing. Structural variants (SVs; genomic variants larger than 50 base pairs) of uncertain significance are the genetic cause of a portion of these unresolved cases. As sequencing methods using long or linked reads become more accessible and SV detection algorithms improve, clinicians and researchers are gaining access to thousands of...

Registration Year

  • 2021
    145

Resource Types

  • Dataset
    145

Affiliations

  • University of California, Berkeley
    144
  • Laboratory for Atmospheric and Space Physics
    30
  • University of Orléans
    25
  • Goddard Space Flight Center
    5
  • University of Washington
    3
  • Stanford University
    3
  • Utah State University
    3
  • University of California, Davis
    3
  • National Research Institute for Agriculture, Food and Environment
    2
  • University of Pretoria
    2