42 Works

Data from: A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna

Henrik Krehenwinkel, Maxene Graze, Dennis Roedder, Tanaka Kazuhiro, Yuki G. Baba, Christoph Muster, Gabriele Uhl & Kazuhiro Tanaka
Aim: The phylogeographical history of wide-ranging Palaearctic species is not well understood. Here, we present a range-wide phylogeographical study of the wasp spider, Argiope bruennichi (Scopoli, 1772), a highly dispersive and widely distributed Palaearctic species. We aim to identify glacial refugia and patterns of interglacial gene flow across the Palaearctic. Location: Palaearctic region, including the Azores, Madeira, Europe, North Africa and Asia. Methods: We conduct a range-wide phylogeographical survey. Our study is based on nuclear...

Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Victor C. Mason, Gang Li, Patrick Minx, Jurgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L. Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen & William J. Murphy
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal...

Data from: Morphological identification and single-cell genomics of marine diplonemids

Ryan M. R. Gawryluk, Javier Del Campo, Noriko Okamoto, Jurgen F. H. Strassert, Julius Lukes, Thomas A. Richards, Alexandra Z. Worden, Alyson E. Santoro & Patrick J. Keeling
Recent global surveys of marine biodiversity have revealed that a group of organisms known as “marine diplonemids” constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago [2 and 3], their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids,...

Data from: Ants exhibit asymmetric hybridization in a mosaic hybrid zone

Jessica Purcell, Sacha Zahnd, Anouk Athanasiades, Rebecca Türler, Michel Chapuisat & Alan Brelsford
Research on hybridization between species provides unparalleled insights into the pre- and post-zygotic isolating mechanisms that drive speciation. In social organisms, colony-level incompatibilities may provide additional reproductive barriers not present in solitary species, and hybrid zones offer an opportunity to identify these barriers. Here, we use genotyping-by-sequencing to sequence hundreds of markers in a hybrid zone between two socially polymorphic ant species, Formica selysi and Formica cinerea. We characterize the zone, determine the frequency of...

Data from: Herbivore size matters for productivity-richness relationships in African savannas

Deron E. Burkepile, Richard W. S. Fynn, Dave I. Thompson, Nathan P. Lemoine, Sally E. Koerner, Stephanie Eby, Nicole Hagenah, Kevin R. Wilcox, Scott L. Collins, Kevin P. Kirkman, Alan K. Knapp & Melinda D. Smith
1.Productivity and herbivory often interact to shape plant community composition and species richness with levels of production mediating the impact of herbivory. Yet, differences in herbivore traits such as size, feeding guild, and dietary requirements may result in different impacts of diverse herbivore guilds across productivity gradients. 2.We used size-selective herbivore exclosures to separate the effects of herbivory by larger herbivores, such as elephant, Burchell's zebra, and blue wildebeest from those of medium/smaller herbivores, such...

Data from: Post-fire recovery in coastal sage scrub: seed rain and community trajectory

Erin Conlisk, Rebecca Swab, Alejandra Martínez-Berdeja & Matthew P. Daugherty
Disturbance is a primary mechanism structuring ecological communities. However, human activity has the potential to alter the frequency and intensity of natural disturbance regimes, with subsequent effects on ecosystem processes. In Southern California, human development has led to increased fire frequency close to urban areas that can form a positive feedback with invasive plant spread. Understanding how abiotic and biotic factors structure post-fire plant communities is a critical component of post-fire management and restoration. In...

Data from: Modeling effects of nonbreeders on population growth estimates

Aline M. Lee, Jane M. Reid & Steven R. Beissinger
Adult individuals that do not breed in a given year occur in a wide range of natural populations. However, such nonbreeders are often ignored in theoretical and empirical population studies, limiting our knowledge of how nonbreeders affect realized and estimated population dynamics and potentially impeding projection of deterministic and stochastic population growth rates. We present and analyse a general modelling framework for systems where breeders and nonbreeders differ in key demographic rates, incorporating different forms...

Data from: Neuroendocrine profiles associated with discrete behavioural variation in Symphodus ocellatus, a species with male alternative reproductive tactics

Bridget M. Nugent, Kelly A. Stiver, Suzanne H. Alonzo & Hans A. Hofmann
The molecular mechanisms underlying phenotypic plasticity are not well understood. Identifying mechanisms underlying alternative reproductive tactics (ARTs) in species for which the behavioural and fitness consequences of this variation are well characterized provides an opportunity to integrate evolutionary and mechanistic understanding of the maintenance of variation within populations. In the ocellated wrasse Symphodus ocellatus, the behavioural phenotypes of three distinct male morphs (sneakers, satellites and nesting males), which arise from a single genome, have been...

Data from: Invading Africa: a novel transoceanic dispersal by a New World ant parasitoid

Elizabeth A. Murray & John M. Heraty
Aim: An ant parasitoid wasp genus (Eucharitidae: Kapala) common in the New World exhibits the intriguing pattern of having one species distributed widely across tropical Africa and Madagascar. The unusual distribution prompted an investigation of the age, origins and diversification of the Afrotropical Kapala species. We evaluate a previous hypothesis that the species was anthropogenically introduced. Location: Africa and Madagascar and the Neotropics. Methods: Numerous forms of evidence are incorporated to explain the origin of...

Data from: Social selection parapatry in Afrotropical sunbirds

Jay P. McEntee, Joshua V. Peñalba, Chacha Werema, Elia Mulungu, Maneno Mbilinyi, David Moyer, Louis Hansen, Jon Fjeldså & Rauri C. K. Bowie
The extent of range overlap of incipient and recent species depends on the type and magnitude of phenotypic divergence that separates them, and the consequences of phenotypic divergence on their interactions. Signal divergence by social selection likely initiates many speciation events, but may yield niche-conserved lineages predisposed to limit each others’ ranges via ecological competition. Here we examine this neglected aspect of social selection speciation theory in relation to the discovery of a non-ecotonal species...

Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

James Starrett, Shahan Derkarabetian, Marshal Hedin, , John E. McCormack, Brant C. Faircloth & Robert W. Bryson
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic...

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: Do thermoregulatory costs limit altitude distributions of Andean forest birds?

Gustavo A. Londono, Mark A. Chappell, Jill E. Jankowski & Scott K. Robinson
Along tropical mountains, species often occupy narrow altitude ranges. Numerous biotic and abiotic factors have been proposed as determinants of altitude occupancy. We measured several aspects of thermal physiology of 215 bird species across a 2·6-km altitude gradient in the Peruvian Andes. We predicted that highland species would show adaptation to the colder high-altitude climate and that energy costs of thermoregulation might limit upslope dispersal of lowland natives. We found reductions in thermal conductance, body...

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...

Data from: Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

İsmail K. Sağlam, Jason Baumsteiger, Matt J. Smith, Javier Linares-Casenave, Andrew L. Nichols, Sean M. O'Rourke & Michael R. Miller
The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m2 pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an...

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: 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: 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: 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: 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: 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: 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: 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: 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...

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