101 Works

Data from: Climate structures genetic variation across a species' elevation range: a test of range limits hypotheses

Jason P. Sexton, Matthew B. Hufford, Ashley Bateman, David B. Lowry, Harald Meimberg, Sharon Y. Strauss, Kevin J. Rice & Ashley C.Bateman
Gene flow may influence the formation of species range limits, yet little is known about the patterns of gene flow with respect to environmental gradients or proximity to range limits. With rapid environmental change it is especially important to understand patterns of gene flow to inform conservation efforts. Here we investigate the species range of the selfing, annual plant, Mimulus laciniatus, in the California Sierra Nevada. We assessed genetic variation, gene flow, and population abundance...

Data from: Unlinked Mendelian inheritance of red and black pigmentation in snakes: implications for Batesian mimicry

Alison R. Davis Rabosky, Christian L. Cox & Daniel L. Rabosky
Identifying the genetic basis of mimetic signals is critical to understanding both the origin and dynamics of mimicry over time. For species not amenable to large laboratory breeding studies, widespread color polymorphism across natural populations offers a powerful way to assess the relative likelihood of different genetic systems given observed phenotypic frequencies. We classified color phenotype for 2,175 ground snakes (Sonora semiannulata) across the continental United States to analyze morph ratios and test among competing...

Data from: Populations of aspen (Populus tremuloides Michx.) with different evolutionary histories differ in their climate occupancy

Burke T. Greer, Christopher Still, Glenn T. Howe, Christina Tague & Dar A. Roberts
Quaking aspens (Populus tremuloides Michx.) are found in diverse habitats throughout North America. While the biogeography of aspens' distribution has been documented, the drivers of the phenotypic diversity of aspen are still being explored. In our study, we examined differences in climate between northern and southwestern populations of aspen, finding large-scale differences between the populations. Our results suggest that northern and southwestern populations live in distinct climates and support the inclusion of genetic and phenotypic...

Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification

Sean Harrington, Tod W. Reeder, S. Harrington & T. W. Reeder
The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth–death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the...

Data from: Fine with heat, problems with water: microclimate alters water loss in a thermally adapted insular lizard

Anat Belasen, Kinsey Brock, Binbin Li, Dimitra Chremou, Efstratios Valakos, Panayiotis Pafilis, Barry Sinervo & Johannes Foufopoulos
Global change, including habitat isolation and climate change, has both short- and long-term impacts on wildlife populations. For example, genetic drift and inbreeding result in genetic impoverishment in small, isolated populations, while species undergo range shifts or adaptive phenotypic change in response to shifts in environmental temperatures. In this study, we utilize a model system in which Holocene landscape changes have occurred to examine long-term effects of population isolation. To examine how isolation may constrain...

Data from: Seed predation has the potential to drive a rare plant to extinction

Helen M. Kurkjian, Sydney K. Carothers & Erik S. Jules
1. Pre-dispersal seed predation is sometimes considered unlikely to dramatically affect plant population growth because plants are generally expected to produce more seeds than there are safe sites for germination. Lupinus constancei is a rare herb of limited distribution, with fewer than 400 reproductive individuals restricted to a single square kilometre of north-western California, USA. In addition to the vulnerability resulting from its extremely small population size, L. constancei faces heavy seed predation by small...

Data from: Sequencing improves our ability to study threatened migratory species: genetic population assignment in California's Central Valley Chinook salmon

Mariah H. Meek, Melinda R. Baerwald, Molly R. Stephens, Alisha Goodbla, Michael R. Miller, Katharine M. H. Tomalty & Bernie May
Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large-scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single-nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled...

Data from: Macroevolution of perfume signalling in orchid bees

Marjorie G. Weber, Lukasz Mitko, Thomas Eltz & Santiago R. Ramírez
Theory predicts that both stabilising selection and diversifying selection jointly contribute to the evolution of sexual signalling traits by (1) maintaining the integrity of communication signals within species and (2) promoting the diversification of traits among lineages. However, for many important signalling traits, little is known about whether these dynamics translate into predictable macroevolutionary signatures. Here, we test for macroevolutionary patterns consistent with sexual signalling theory in the perfume signals of neotropical orchid bees, a...

Data from: Seed set variation in wild Clarkia populations: teasing apart the effects of seasonal resource depletion, pollen quality, and pollen quantity

Alisa A. Hove, Susan J. Mazer & Christopher T. Ivey
In habitats where resource availability declines during the growing season, selection may favor early-flowering individuals. Under such ephemerally favorable conditions, late-blooming species (and individuals) may be particularly vulnerable to resource limitation of seed production. In California, a region prone to seasonal drought, members of the annual genus Clarkia are among the last to flower in the spring. We compared pollen limitation (PL) of seed set and outcrossing rates between early- and late-flowering individuals in two...

Data from: Stimulation-based control of dynamic brain networks

Sarah Feldt Muldoon, Fabio Pasqualetti, Shi Gu, Matthew Cieslak, Scott T. Grafton, Jean M. Vettel & Danielle S. Bassett
The ability to modulate brain states using targeted stimulation is increasingly being employed to treat neurological disorders and to enhance human performance. Despite the growing interest in brain stimulation as a form of neuromodulation, much remains unknown about the network-level impact of these focal perturbations. To study the system wide impact of regional stimulation, we employ a data-driven computational model of nonlinear brain dynamics to systematically explore the effects of targeted stimulation. Validating predictions from...

Data from: Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations

Nicolas J. Rawlence, Catherine J. Collins, Christian N. K. Anderson, Justin J. Maxwell, Ian W. G. Smith, Bruce C. Robertson, Michael Knapp, Katherine Ann Horsburgh, Jo-Ann L. Stanton, R. Paul Scofield, Alan J. D. Tennyson, Elizabeth A. Matisoo-Smith & Jonathan M. Waters
While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450–1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within...

Data from: The evolution of reproductive diversity in Afrobatrachia: a phylogenetic comparative analysis of an extensive radiation of African frogs

Daniel M. Portik & David C. Blackburn
The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water...

Data from: Gene duplication and divergence produce divergent MHC genotypes without disassortative mating

Donald C. Dearborn, Andrea B. Gager, Andrew G. McArthur, Morgan E. Gilmour, Elena Mandzhukova & Robert A. Mauck
Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defence, which in turn can select for MHC-disassortative mate choice. However, many species lack this expected pattern of MHC-disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus-specific primers for high-throughput sequencing of two expressed MHC Class...

Data from: Community functional trait composition at the continental scale: the effects of non-ecological processes

A. Michelle Lawing, Jussi T. Eronen, Jessica L. Blois, Catherine H. Graham & P. David Polly
Ecological communities and their response to environmental gradients are increasingly being described by measures of trait composition at the community level – the trait-based approach. Whether ecological or non-ecological processes influence trait composition between communities has been debated. Understanding the processes that influence trait composition is important for reconstructing paleoenvironmental conditions from fossil deposits and for understanding changes in community functionality through time. Here, we assess the influence of ecological and non-ecological processes on the...

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: Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis

Lani U. Gleason & Ronald S. Burton
The balance between natural selection, gene flow and genetic drift is difficult to resolve in marine invertebrates with extensive dispersal and fluctuating population sizes. The intertidal snail Chlorostoma funebralis has planktonic larvae and previous work using mtDNA polymorphism reported no genetic population structure. Nevertheless, recent studies have documented differences in thermal tolerance and transcriptomic responses to heat stress between northern and southern California, USA, populations. To gain insight into the dynamics influencing adaptive divergence, we...

Data from: Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities

Amanda C. Hollowell, John U. Regus, David Turissini, Kelsey A. Gano-Cohen, Roxanne Bantay, Andrew Bernardo, Devora Moore, Jonathan Pham & Joel L. Sachs
Root nodule forming rhizobia exhibit a bipartite lifestyle, replicating in soil and also within plant cells where they fix nitrogen for legume hosts. Host control models posit that legume hosts act as a predominant selective force on rhizobia, but few studies have examined rhizobial fitness in natural populations. Here, we genotyped and phenotyped Bradyrhizobium isolates across >800km of the native Acmispon strigosus host range. We sequenced chromosomal genes expressed under free-living conditions and accessory symbiosis...

Data from: A generalizable energetics-based model of avian migration to facilitate continental-scale waterbird conservation

Eric V. Lonsdorf, Wayne E. Thogmartin, Sarah Jacobi, Kevin Aagaard, Jorge Coppen, Amélie Davis, Timothy Fox, Patricia Heglund, Rex Johnson, Malcolm T. Jones, Kevin Kenow, James E. Lyons, Kirsten Luke, Shannon Still & Brian Tavernia
Conserving migratory birds is made especially difficult because of movement among spatially disparate locations across the annual cycle. In light of challenges presented by the scale and ecology of migratory birds, successful conservation requires integrating objectives, management, and monitoring across scales, from local management units to ecoregional and flyway administrative boundaries. We present an integrated approach using a spatially explicit energetic-based mechanistic bird migration model useful to conservation decision-making across disparate scales and locations. This...

Data from: Trans-species variation in Dmrt1 is associated with sex determination in four European tree-frog species

Alan Brelsford, Christophe Dufresnes & Nicolas Perrin
Empirical studies on the relative roles of occasional XY recombination versus sex-chromosome turnover in preventing sex-chromosome differentiation may shed light on the evolutionary forces acting on sex-determination systems. Signatures of XY recombination are difficult to distinguish from those of homologous transitions (i.e., transitions in sex-determination systems that keep sex-chromosome identity): both models predict X and Y alleles at sex-linked genes to cluster by species. However, the XY-recombination model specifically predicts the reverse pattern (clustering by...

Data from: Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard, Carlia amax

Sally Potter, Jason G. Bragg, Benjamin M. Peter, Ke Bi & Craig Moritz
High-throughput sequencing approaches offer opportunities to better understand the evolutionary processes driving diversification, particularly in nonmodel organisms. In particular, the 100–1000's of loci that can now be sequenced are providing unprecedented power in population, speciation and phylogenetic studies. Here, we apply an exon capture approach to generate >99% complete sequence and SNP data across >2000 loci from a tropical skink, Carlia amax, and exploit these data to identify divergent lineages and infer their relationships and...

Data from: Effects of sea ice cover on satellite-detected primary production in the Arctic Ocean

Mati Kahru, Zhongping Lee, Brian Greg Mitchell, Cynthia D. Nevison & B. Greg Mitchell
The influence of decreasing Arctic sea ice on net primary production (NPP) in the Arctic Ocean has been considered in multiple publications but is not well constrained owing to the potentially large errors in satellite algorithms. In particular, the Arctic Ocean is rich in coloured dissolved organic matter (CDOM) that interferes in the detection of chlorophyll a concentration of the standard algorithm, which is the primary input to NPP models. We used the quasi-analytic algorithm...

Data from: Cooperative interactions between different classes of disordered proteins play a functional role in the nuclear pore complex of Baker's yeast

David E. Ando, Ajay Gopinathan & David Ando
Nucleocytoplasmic transport is highly selective, efficient, and is regulated by a poorly understood mechanism involving hundreds of disordered FG nucleoporin proteins (FG nups) lining the inside wall of the nuclear pore complex (NPC). Previous research has concluded that FG nups in Baker's yeast (S. cerevisiae) are present in a bimodal distribution, with the ``Forest Model'' classifying FG nups as either di-block polymer like ``trees'' or single-block polymer like ``shrubs''. Using a combination of coarse-grained modeling...

Data from: Audience affects decision-making in a marmoset communication network

Camille R. Toarmino, Lauren Wong & Cory T. Miller
An audience can have a profound effect on the dynamics of communicative interactions. As a result, non-human primates often adjust their social decision-making strategies depending on the audience composition at a given time. Here we sought to test how the unique vocal behaviour of multiple audience members affected decisions to communicate. To address this issue, we developed a novel experimental paradigm in which common marmosets directly interacted with multiple ‘virtual monkeys’ (VMs), each of whom...

Data from: Biotic and abiotic variables influencing plant litter breakdown in streams: a global study

Luz Boyero, Richard Pearson, Cang Hui, Mark Gessner, Javier Perez, Markos Alexandrou, Manuel Graça, Bradley Cardinale, Ricardo Albariño, M. Arunachalam, Leon Barmuta, Andrew Boulton, Andreas Bruder, Marcos Callisto, Eric Chauvet, Russell Death, David Dudgeon, Andrea Encalada, Veronica Ferreira, Ricardo Figueroa, Alex Flecker, Gonçalves Jr., Jose Francisco, Julie Helson, Tomoya Iwata, Tajang Jinggut … & Catherine Yule
Plant litter breakdown is a key ecological process in terrestrial and freshwater ecosystems. Streams and rivers, in particular, have high rates of carbon dioxide evasion and they contribute substantially to global carbon fluxes. However, there is little information available on the relative roles of different drivers of plant litter breakdown in fresh waters, particularly at large scales. We present a global-scale study of litter breakdown in streams to compare the roles of biotic, climatic and...

Data from: A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and blasticidin S

Anthony L. Shiver, Hendrik Osadnik, George Kritikos, Bo Li, Nevan Krogan, Athanasios Typas & Carol A. Gross
Fighting antibiotic resistance requires a deeper understanding of the genetic factors that determine the antibiotic susceptibility of bacteria. Here we describe a chemical-genomic screen in Escherichia coli K-12 that was designed to discover new aspects of antibiotic resistance by focusing on a set of 26 antibiotics and other stresses with poorly characterized mode-of-action and determinants of resistance. We show that the screen identifies new resistance determinants for these antibiotics including a common signature from two...

Registration Year

  • 2016
    101

Resource Types

  • Dataset
    101

Affiliations

  • University of California System
    101
  • University of California, Davis
    6
  • Australian National University
    5
  • University of Georgia
    4
  • San Diego State University
    4
  • University of California, Los Angeles
    4
  • University of Michigan–Ann Arbor
    3
  • University of Florida
    3
  • California Polytechnic State University
    2
  • University of Washington
    2
  • Utah State University
    2
  • Princeton University
    2
  • Swiss Federal Institute of Aquatic Science and Technology
    2
  • Duke University
    2
  • University of North Carolina at Chapel Hill
    2