191 Works

Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Irina Smolina, Spyros Kollias, Marloes Poortvliet, Torkel Nielsen, Penelope Lindeque, Claudia Castellani, Eva Møller, Leocadio Blanco-Bercial & Galice Hoarau
Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear...

Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

Nora Mitchell, Paul O. Lewis, Emily Moriarty Lemmon, Alan R. Lemmon & Kent E. Holsinger
PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for...

Data from: Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments

Parrish C. Brady, Alexander A. Gilerson, George W. Kattawar, James M. Sullivan, Michael S. Twardowski, Heidi M. Dierssen, Meng Gao, Kort Travis, Robert I. Etheredge, Alberto Tonizzo, Amir Ibrahim, Carlos Carrizo, Yalong Gu, Brandon J. Russell, Kathryn Mislinski, Shulei Zhao & Molly E. Cummings
Despite appearing featureless to our eyes, the open ocean is a highly variable environment for polarization-sensitive viewers. Dynamic visual backgrounds coupled with predator encounters from all possible directions make this habitat one of the most challenging for camouflage. We tested open-ocean crypsis in nature by collecting more than 1500 videopolarimetry measurements from live fish from distinct habitats under a variety of viewing conditions. Open-ocean fish species exhibited camouflage that was superior to that of both...

Data from: Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?

Timothy E. Moore, Carl D. Schlichting, Matthew E. Aiello-Lammens, Kerri Mocko & Cynthia S. Jones
Functional traits in closely related lineages are expected to vary similarly along common environmental gradients due to shared evolutionary and biogeographic history, or legacy effects, and due to biophysical tradeoffs in construction. We test these predictions in Pelargonium, a relatively recent evolutionary radiation. Bayesian phylogenetic mixed effects models assessed, at the subclade level, associations between plant height, leaf area, leaf nitrogen content and leaf mass per area (LMA), and five environmental variables capturing temperature and...

Data from: The use of a mercury biosensor to evaluate the bioavailability of mercury-thiol complexes and mechanisms of mercury uptake in bacteria

Udonna Ndu, Tamar Barkay, Robert P. Mason, Amina Traore Schartup, Radwan Al-Farawati, Jie Liu & John R. Reinfelder
As mercury (Hg) biosensors are sensitive to only intracellular Hg, they are useful in the investigation of Hg uptake mechanisms and the effects of speciation on Hg bioavailability to microbes. In this study, bacterial biosensors were used to evaluate the roles that several transporters such as the glutathione, cystine/cysteine, and Mer transporters play in the uptake of Hg from Hg-thiol complexes by comparing uptake rates in strains with functioning transport systems to strains where these...

Data from: Transitions between phases of genomic differentiation during stick-insect speciation

Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A. Comeault, Timothy E. Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R. Dennis, Clarissa F. De Carvalho, Rebecca J. Safran, Cristina P. Sandoval, Jeff Feder, Regine Gries, Bernard J. Crespi, Gerhard Gries, Zach Gompert & Patrik Nosil
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

Data from: Molecular species-delimitation methods recover most song-delimited cicada species in the European Cicadetta montana complex

Elizabeth Wade, Thomas Hertach, Matija Gogala, Tomi Trilar, Chris Simon & E. J. Wade
Molecular species delimitation is increasingly being used to discover and inform illuminate species level diversity and a number of methods have been developed. Here we compare the ability of two molecular species delimitation methods to recover song-delimited species in the Cicadetta montana cryptic species complex throughout Europe. Recent bioacoustics studies of male calling songs (pre-mating reproductive barriers) have revealed cryptic species diversity in this complex. Maximum likelihood and Bayesian phylogenetic analyses were used to analyze...

Data from: Contrasting the ecological and taxonomic consequences of extinction

Max Christie, Steven M. Holland & Andrew M. Bush
Extinction in the fossil record is most often measured by the percentage of taxa (species, genera, families, etc.) that go extinct in a certain time interval. This is a measure of taxonomic loss, but previous work has indicated that taxonomic loss may be decoupled from the ecological effects of an extinction. To understand the role extinction plays in ecological change, extinction should also be measured in terms of loss of functional diversity. This study tests...

Data from: Day/night upper thermal limits differ within Ectatomma ruidum ant colonies

Annika S. Nelson, Trey Scott, Maciej Barczyk, Terrence P. McGlynn, Arian Avalos, Elizabeth Clifton, Amlan Das, Andreia Figueiredo, Laura L. Figueroa, Mark Janowiecki, Sarah Pahlke, Jignasha D. Rana & Sean O'Donnell
In the tropics, daily temperature fluctuations can pose physiological challenges for ectothermic organisms, and upper thermal limits may affect foraging activity over the course of the day. Variation in upper thermal limits can occur among and within species, and for social insects such as ants, within colonies. Within colonies, upper thermal limits may differ among individuals or change for an individual throughout the day. Daytime foragers of the Neotropical ant Ectatomma ruidum have higher critical...

Data from: The ‘Last Hurrah of the Reigning Darwinulocopines’? Ostracoda (Arthropoda, Crustacea) from the Lower Jurassic Moenave Formation, Arizona and Utah, USA

Lucas S. Antonietto, Lisa E. Park Bousch, Celina A. Suarez, Andrew R.C. Milner & James I. Kirkland
An ostracod fauna is described from lacustrine sediments of the Hettangian, Lower Jurassic Whitmore Point Member of the Moenave Formation. The Moenave is well known for its rich, Late Triassic?–Early Jurassic fossil record, which includes fossil fishes, stromatolites, ostracods, spinicaudatans and a diverse ichnofauna of invertebrates and vertebrates. Four ostracod species, all belonging to the suborder Darwinulocopina, were recovered from these sediments: Suchonellina globosa, Suchonellina stricta, Whipplella? sp. 1 and Whipplella? sp. 2. The diversity...

Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.

Hilary A. McManus, Karolina Fučíková, Paul O. Lewis, Louise A. Lewis & Kenneth G. Karol
Premise of the study: Phylogenomic analyses across the green algae are resolving relationships at the class, order and family levels, and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. Methods: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired...

Data from: Quantifying the importance of geographic replication and representativeness when estimating demographic rates, using a coastal species as a case study

Christopher R. Field, Katharine J. Ruskin, Bri Benvenuti, Alyssa C. Borowske, Jonathan B. Cohen, Laura Garey, Thomas P. Hodgman, Rebecca A. Kern, Erin King, Alison R. Kocek, Adrienne I. Kovach, Kathleen M. O'Brien, Brian J. Olsen, Nancy Pau, Samuel G. Roberts, Emma Shelly, W. Gregory Shriver, Jennifer Walsh, Chris S. Elphick & Rebecca A. Longenecker
Demographic rates are rarely estimated over an entire species range, limiting empirical tests of ecological patterns and theories, and raising questions about the representativeness of studies that use data from a small part of a range. The uncertainty that results from using demographic rates from just a few sites is especially pervasive in population projections, which are critical for a wide range of questions in ecology and conservation. We developed a simple simulation to quantify...

Data from: Subspecies delineation amid phenotypic, geographic, and genetic discordance in a songbird

Jennifer Walsh, Irby J. Lovette, Virginia Winder, Chris S. Elphick, Brian J. Olsen, W. Gregory Shriver, Adrienne I. Kovach & Gregory Shriver
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to...

Data from: Resolving the Northern Hemisphere source region for the long-distance dispersal event that gave rise to the South American endemic dung moss Tetraplodon fuegianus

Lily Lewis, Elisabeth M. Biersma, Sarah B. Carey, Kent Holsinger, Stuart F. McDaniel, Ricardo Rozzi, Bernard Goffinet & Lily R. Lewis
Premise of the study—American bipolar plant distributions characterize taxa at various taxonomic ranks but are most common in the bryophytes at infraspecific and infrageneric levels. A previous study on the bipolar disjunction in the dung moss genus Tetraplodon found that direct long-distance dispersal from North to South in the Miocene - Pleistocene accounted for the origin of the Southern American endemic Tetraplodon fuegianus, congruent with other molecular studies on bipolar bryophytes. The previous study, however,...

Data from: The effects of model choice and mitigating bias on the ribosomal tree of life

Erica Lasek-Nesselquist & Johann Peter Gogarten
Deep-level relationships within Bacteria, Archaea, and Eukarya as well as the relationships of these three domains to each other require resolution. The ribosomal machinery, universal to all cellular life, represents a protein repertoire resistant to horizontal gene transfer, which provides a largely congruent signal necessary for reconstructing a tree suitable as a backbone for life’s reticulate history. Here, we generate a ribosomal tree of life from a robust taxonomic sampling of Bacteria, Archaea, and Eukarya...

Data from: Climate change impacts on bumblebees converge across continents

Jeremy T. Kerr, Alana Pindar, Paul Galpern, Laurence Packer, Stuart M. Roberts, Pierre Rasmont, Oliver Schweiger, Sheila R. Colla, Leif L. Richardson, David L. Wagner, Lawrence F. Gall, Derek S. Sikes & Alberto Pantoja
For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long-term observations across Europe and North America over 110 years, we tested for climate change–related range shifts in bumblebee species across the full extents of their latitudinal and thermal limits and movements along elevation gradients. We found cross-continentally consistent trends in failures to track warming through time at species’ northern...

Data from: Sensory drive does not explain reproductive character displacement of male acoustic signals in the Upland Chorus Frog (Pseudacris feriarum)

Emily Claire Moriarty Lemmon, Jessica Ribado, John H. Malone & Emily Moriarty Lemmon
Biotic and abiotic factors have been proposed to explain patterns of reproductive character displacement, but which factor is most important to character displacement of acoustic signals is not clear. Male vocalizations of the frog Pseudacris feriarum are known to undergo reproductive character displacement in areas of sympatry with P. brimleyi and P. nigrita. Despite evidence for reinforcement as an important mechanism, local adaptation via sensory drive might explain this pattern because Pseudacris breed in different...

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

Data from: Moth body size increases with elevation along a complete tropical elevational gradient for two hyperdiverse clades

Gunnar Brehm, Dirk Zeuss & Robert K. Colwell
The body size of an animal is probably its most important functional trait. For arthropods, environmental drivers of body size variation are still poorly documented and understood, especially in tropical regions. We use a unique dataset for two species-rich, phylogenetically independent moth taxa (Lepidoptera: Geometridae; Arctiinae), collected along an extensive tropical elevational gradient in Costa Rica, to investigate the correlates and possible causes of body-size variation. We studied 15,047 specimens (794 species) of Geometridae and...

Data from: Spatially heterogeneous impact of climate change on small mammals of montane California

Kevin C. Rowe, Karen M. C. Rowe, Morgan W. Tingley, Michelle S. Koo, James L. Patton, Christopher J. Conroy, John D. Perrine, Steven R. Beissinger & Craig Moritz
Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one...

Leaf margins in a deciduous lineage from the Greater Cape Floristic Region track climate in unexpected directions

Henry Frye, Kerri Mocko, Timothy Moore, Carl Schlichting & Cynthia Jones
Premise of the study: The functional significance of leaf margins has long been debated. In this study we explore influences of climate, leaf lobing, woodiness, and shared evolutionary history on two leaf margin traits within the genus Pelargonium. Methods: Leaves from 454 populations of Pelargonium (161 species) were collected in the Greater Cape Floristic Region and scored for tooth presence/absence and degree of lobing. Tooth density (number of teeth per interior perimeter distance) was measured...

Habitat openness and edge avoidance predict saltmarsh sparrow abundance better than habitat area

Hallie Marshall, Erik Blomberg, Valerie Watson, Meaghan Conway, Jonathan Cohen, Maureen Correll, Chris Elphick, Thomas Hodgman, Alison Kocek, Adrienne Kovach, W. Gregory Shriver, Whitney Wiest & Brian Olsen
The Saltmarsh Sparrow (Ammospiza caudacuta) is a tidal marsh bird facing rapid population decline throughout its range, largely caused by degradation and loss of breeding habitat. Thus there is a need to preserve tidal marshes in the northeastern United States, but to do so requires an understanding of the habitat features that support robust populations. Previous studies have shown Saltmarsh Sparrow abundance increases with marsh size, but in similar bird species, area sensitivity is more...

Data from: Testing models of reciprocal relations between social influence and integration in STEM across the college years

Paul Hernandez, V. Bede Agocha, Lauren Carney, Mica Estrada, Sharon Lee, David Loomis, Michelle Williams & Crystal Park
The present study tests predictions from the Tripartite Integration Model of Social Influences (TIMSI) concerning processes linking social interactions to social integration into science, technology, engineering, and mathematics (STEM) communities and careers. Students from historically overrepresented groups in STEM were followed from their senior year of high school through their senior year in college. Based on TIMSI, we hypothesized that interactions with social influence agents (operationalized as mentor network diversity, faculty mentor support, and research...

High-resolution CONUS-wide downscaled rainfall estimates (HRCDRE)

Stergios Emmanouil, Andreas Langousis, Efthymios I. Nikolopoulos & Emmanouil N. Anagnostou
The spatiotemporal character of rainfall is particularly important for hydrologic modeling, as well as hydroclimatic risk estimation and impact assessment. Existing atmospheric reanalysis datasets offer extensive record lengths and global coverage, but usually their spatial resolution is coarse for distributed hydrologic simulations at small spatial scales. On the other hand, the temporal coverage of high-resolution radar-based rainfall estimates can be rather short for risk applications. To address these shortcomings, we simultaneously bias-correct and downscale a...

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  • University of Connecticut
  • The University of Texas at Austin
  • Duke University
  • Columbia University
  • The Institute for Bird Populations
  • University of California Los Angeles
  • Lund University
  • University of Minnesota
  • University of Maine
  • United States Department of Agriculture