42 Works

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: Comparing the responses of bryophytes and short-statured vascular plants to climate shifts and eutrophication

Risto Virtanen, Anu Eskelinen & Susan Harrison
Few experimental studies have tested how abundance and diversity of grassland bryophytes respond to global environmental changes such as climate shifts and eutrophication. Because bryophytes in grasslands are low-statured, and because plant height is a key functional trait governing plant responses to resource gradients, their responses to these factors could resemble those of better-studied small vascular plants. Alternatively, traits unique to bryophytes could lead to qualitatively different responses than those of small vascular plants. In...

Data from: An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

Daniel M. Portik, Lydia L. Smith & Ke Bi
Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron–exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic...

Data from: Spatiotemporal patterns of duck nest density and predation risk: a multi-scale analysis of 18 years and more than 10 000 nests

Kevin Ringelman, John M. Eadie, Joshua T. Ackerman, Andy Sih, Daniel L. Loughman, Gregory S. Yarris, Shaun L. Oldenburger, M. Robert McLandress, Kevin M. Ringelman & Andrew Sih
Many avian species are behaviorally-plastic in selecting nest sites, and may shift to new locations or habitats following an unsuccessful breeding attempt. If there is predictable spatial variation in predation risk, the process of many individuals using prior experience to adaptively change nest sites may scale up to create shifting patterns of nest density at a population level. We used 18 years of waterfowl nesting data to assess whether there were areas of consistently high...

Data from: Population structure of a vector-borne plant parasite

Kelsey M. Yule, Jennifer A. H. Koop, Nicolas M. Alexandre, Lauren R. Johnston & Noah K. Whiteman
Parasites are among the most diverse groups of life on Earth, yet complex natural histories often preclude studies of their speciation processes. The biology of parasitic plants facilitates in situ collection of data on both genetic structure and the mechanisms responsible for that structure. Here, we studied the role of mating, dispersal and establishment in host race formation of a parasitic plant. We investigated the population genetics of a vector-borne desert mistletoe (Phoradendron californicum) across...

Data from: Climate constrains lake community and ecosystem responses to introduced predators

Celia C. Symons & Jonathan B. Shurin
Human activities have resulted in rising temperatures and the introduction or extirpation of top predators worldwide. Both processes generate cascading impacts throughout food webs and can jeopardize important ecosystem services. We examined the impact of fish stocking on communities and ecosystems in California mountain lakes across an elevation (temperature and dissolved organic carbon) gradient to determine how trophic cascades and ecosystem function vary with climate. Here, we show that the impact of fish on the...

Data from: Plumage genes and little else distinguish the genomes of hybridizing warblers

David P. L. Toews, Scott A. Taylor, Rachel Vallender, Alan Brelsford, Bronwyn G. Butcher, Philipp W. Messer & Irby J. Lovette
When related taxa hybridize extensively, their genomes may become increasingly homogenized over time. This mixing via hybridization creates conservation challenges when it reduces genetic or phenotypic diversity and when it endangers previously distinct species via genetic swamping [ 1 ]. However, hybridization also facilitates admixture mapping of traits that distinguish each species and the associated genes that maintain distinctiveness despite ongoing gene flow [ 2 ]. We address these dual aspects of hybridization in the...

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: 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: Local adaptation of fish consumers alters primary production through changes in algal community composition and diversity

Ron D. Bassar, Brynne L. Bryan, Michael C. Marshall, Catherine M. Pringle, David N. Reznick, Joseph Travis & Ronald D. Bassar
Ecological research has focused on understanding how changes in consumer abundance affect community structure and ecosystem processes. However, there is increasing evidence that evolutionary changes in consumers can also alter community structure and ecosystem processes. Typically, the effects of consumer phenotype on communities and ecosystem processes are measured as net effects that integrate numerous ecological pathways. Here, we analyze new data from experimental manipulations of Trinidadian guppy Poecilia reticulata presence, density and phenotype to examine...

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

Sean Harrington & Tod 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: The genetic architecture of novel trophic specialists: higher effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation

Christopher H. Martin, Priscilla A. Erickson & Craig T. Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining...

Data from: Extensive genetic diversity among populations of the malaria mosquito Anopheles moucheti revealed by population genomics

Caroline Fouet, Colince Kamdem, Stephanie Gamez & Bradley J. White
Malaria vectors are exposed to intense selective pressures due to large-scale intervention programs that are underway in most African countries. One of the current priorities is therefore to clearly assess the adaptive potential of Anopheline populations, which is critical to understand and anticipate the response mosquitoes can elicit against such adaptive challenges. The development of genomic resources that will empower robust examinations of evolutionary changes in all vectors including currently understudied species is an inevitable...

Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

Michael R. May, Sebastian Hoehna & Brian R. Moore
The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching...

Data from: Calling in sick: impacts of fever on intra-urban human mobility

T. Alex Perkins, Valerie A. Paz-Soldan, Steven T. Stoddard, Amy C. Morrison, Brett M. Forshey, Kanya C. Long, Eric S. Halsey, Tadeusz J. Kochel, John P. Elder, Uriel Kitron, Thomas W. Scott & Gonzalo M. Vazquez-Prokopec
Pathogens inflict a wide variety of disease manifestations on their hosts, yet the impacts of disease on the behaviour of infected hosts are rarely studied empirically and are seldom accounted for in mathematical models of transmission dynamics. We explored the potential impacts of one of the most common disease manifestations, fever, on a key determinant of pathogen transmission, host mobility, in residents of the Amazonian city of Iquitos, Peru. We did so by comparing two...

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...

Registration Year

  • 2016
    42

Resource Types

  • Dataset
    42

Affiliations

  • University of California System
    42
  • University of California, Berkeley
    7
  • San Diego State University
    4
  • University of California, Riverside
    4
  • University of California, Davis
    4
  • University of Florida
    3
  • University of North Carolina
    2
  • The University of Texas at Arlington
    2
  • University of Lausanne
    2
  • Australian National University
    2