103 Works

Data from: Where and how to restore in a changing world: a demographic-based assessment of resilience

Loralee Larios, Lauren M. Hallett & Katharine N. Suding
Managers are increasingly looking to apply concepts of resilience to better anticipate and understand conservation and restoration in a changing environment. In this study, we explore how information on demography (recruitment, growth and survival) and competitive effects in different environments and with different starting species abundances can be used to better understand resilience. We use observational and experimental data to better understand dynamics between native Stipa pulchra and exotic Avena barbata and fatua, grasses characteristic...

Data from: Experimental evolution of the Caenorhabditis elegans sex determination pathway

Christopher H. Chandler, Genna Elise Chadderdon, Patrick C. Phillips, Ian Dworkin & Fredric J. Janzen
Sex determination is a critical developmental decision with major ecological and evolutionary consequences, yet a large variety of sex determination mechanisms exist and we have a poor understanding of how they evolve. Theoretical and empirical work suggest that compensatory adaptations to mutations in genes involved in sex determination may play a role in the evolution of these pathways. Here, we directly address this problem using experimental evolution in Caenorhabditis elegans lines fixed for a pair...

Data from: Alongshore variation in barnacle populations is determined by surfzone hydrodynamics

Alan L. Shanks, Steven G. Morgan, Jamie MacMahan, Ad J.H.M. Reniers & Ad J. H. M. Reniers
Larvae in the coastal ocean are transported toward shore by a variety of mechanisms. Crossing the surf zone is the last step in a shoreward migration and surf zones may act as semipermeable barriers altering delivery of larvae to the shore. We related variation in the structure of intertidal barnacle populations to surfzone width (surfzone hydrodynamics proxy), wave height, alongshore wind stress (upwelling proxy), solar radiation, and latitude at 40 rocky intertidal sites from San...

Data from: Ecological history of a long-lived conifer in a disjunct population

Erin M. Herring, Daniel G. Gavin, Solomon Z. Dobrowski, Matias Fernandez & Feng Sheng Hu
1. In northern Idaho (USA), more than 100 vascular plant species are disjunct <200 km from their main distribution along the Pacific Northwest coast. It remains unclear whether most species within this interior forest disjunction, including Tsuga mertensiana, survived the last glacial period in a north-Idaho refugium or whether these species colonized the region via long-distance dispersal during the Holocene. 2. Sediment cores were extracted from three mid- to high-elevation lakes within T. mertensiana dominated...

Data from: A phylogenetic analysis of egg size, clutch size, spawning mode, adult body size, and latitude in reef fishes

Katja Kasimatis & Cynthia Riginos
Theoretical treatments of egg size in fishes suggest that constraints on reproductive output should create trade-offs between the size and number of eggs produced per spawn. For marine reef fishes, the observation of distinct reproductive care strategies (demersal guarding, egg scattering, and pelagic spawning) has additionally prompted speculation that these strategies reflect alternative fitness optima with selection on egg size differing by reproductive mode and perhaps latitude. Here, we aggregate data from 278 reef fish...

Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Morris Goodman, Kirstin N. Sterner, M. Munirul Islam, Monica Uddin, Chet C. Sherwood, Patrick R. Hof, Zhuo-Cheng Hou, Leonard Lipovich, Hui Jia, Lawrence I. Grossman, Derek E. Wildman, M. Islam & Z. C. Hou
Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains...

Data from: Increases and decreases in marine disease reports in an era of global change

Allison M. Tracy, Madeline L. Pielmeier, Reyn M. Yoshioka, Scott F. Heron & C. Drew Harvell
Outbreaks of marine infectious diseases have caused widespread mass mortalities, but the lack of baseline data has precluded evaluating whether disease is increasing or decreasing in the ocean. We use an established literature proxy method from Ward and Lafferty (2004) to analyze a 44-year global record of normalized disease reports from 1970 to 2013. Major marine hosts are combined into nine taxonomic groups, from seagrasses to marine mammals, to assess disease swings, defined as positive...

Data from: Black abalone (Haliotis cracherodii) population structure shifts through deep time: Management implications for southern California's northern Channel Islands

Hannah Haas, Todd J. Braje, Matthew S. Edwards, Jon M. Erlandson & Steven G. Whitaker
For over 10,000 years, black abalone (Haliotis cracherodii) were an important resource in southern California, first for coastal Native Americans, then beginning in the nineteenth century, as one of the state's first commercial shellfisheries. By 1993, after years of heavy fishing, rising sea surface temperatures (SST), and the spread of withering syndrome (WS), black abalone populations declined dramatically, resulting in the closure of the Alta California fishery. After nearly 25 years of management and recovery...

Data from: Natural and experimental evolution of sexual conflict within Caenorhabditis nematodes

Michael F. Palopoli, Colin Peden, Caitlin Woo, Ken Akiha, Megan Ary, Lori Cruze, Jennifer L. Anderson & Patrick C. Phillips
Background: Although males and females need one another in order to reproduce, they often have different reproductive interests, which can lead to conflict between the sexes. The intensity and frequency of male-male competition for fertilization opportunities is thought to be an important contributor to this conflict. The nematode genus Caenorhabditis provides an opportunity to test this hypothesis because the frequency of males varies widely among species with different mating systems. Results: We find evidence that...

Data from: Rapid identification of major histocompatibility complex class I haplotypes using deep sequencing in an endangered Old World monkey

Noah D. Simons, Maria Jose Ruiz-Lopez, Colin A. Chapman, Tony L. Goldberg, Julie A. Karl, Roger W. Wiseman, Patrick S. Bohn, David H. O'Connor & Nelson Ting
Immunogenetic data from wild primate populations have been difficult to obtain, due to logistic and methodological constraints. We applied a well-characterized deep sequencing method for MHC I typing, developed for macaques, to a population of wild red colobus to assess the feasibility of identifying MHC I-A/B haplotypes. Ten individuals produced sufficient data from blood and tissue samples to assign haplotypes. Eighty-two sequences were classified as red colobus MHC I alleles distributed across six MHC I...

Data from: Evidence of linked selection on the Z chromosome of hybridizing hummingbirds

C. J. Battey
Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/sasin/calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence...

Germination and epiphytic seed fungi on Festuca roemeri and Danthonia californica

Bitty Roy, Hunter C. Mackin & Tiffany E Thornton
Demographic studies measure drivers of plant fecundity such as seed production and survival, but few address environmental drivers of seed viability, such as germination and dormancy. Variation in climate and seed type may both directly and indirectly alter seed germination via altered fungal pathogen abundance. We examined seed germination and microbial communities of seeds of Danthonia californica, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and Festuca roemeri, which are solely chasmogamous. Seed...

Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction

Hannah Wellman, Rita Austin, Nihan Dagtas, Madonna Moss, Torben Rick & Courtney Hofman
Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus....

Dynamics of gaze control during prey capture in freely moving mice

Angie Michaiel, Elliott Abe & Cristopher Niell
Most studies of visual processing are conducted under head- and gaze-restricted conditions. While this provides experimental control, it radically limits the natural exploration of the visual world which is typically achieved through directed eye, head, and body movements. As such, less is known about how animals naturally sample the external visual world to acquire relevant visual information in natural contexts. To determine how mice target their gaze and sample the visual world during natural behavior,...

Climate manipulations differentially affect plant population dynamics within versus beyond northern range limits

Paul Reed, Megan Peterson, Laurel Pfeifer-Meister, William Morris, Daniel Doak, Bitty Roy, Bart Johnson, Graham Bailes & Aaron Nelson
Predicting species’ range shifts under future climate is a central goal of conservation ecology. Studying populations within and beyond multiple species’ current ranges can help identify whether demographic responses to climate change exhibit directionality, indicative of range shifts, and whether responses are uniform across a suite of species. We quantified the demographic responses of six native perennial prairie species planted within and, for two species, beyond their northern range limits to a three-year experimental manipulation...

Introduced annuals mediate climate-driven community change in Mediterranean prairies of the Pacific Northwest, USA

Paul Reed, Laurel Pfeifer-Meister, Bitty Roy, Bart Johnson, Graham Bailes, Aaron Nelson & Scott Bridgham
Aim: How climate change will alter plant functional group composition is a critical question given the well-recognized effects of plant functional groups on ecosystem services. While climate can have direct effects on different functional groups, indirect effects mediated through changes in biotic interactions have the potential to amplify or counteract direct climatic effects. As a result, identifying the underlying causes for climate effects on plant communities is important to conservation and restoration initiatives. Location: Western...

Data from: Genetic variation for outcrossing among Caenorhabditis elegans isolates

Henrique Teotonio, Diogo Manoel & Patrick C. Phillips
The evolution of breeding systems results from the existence of genetic variation and selective forces favoring different outcrossing rates. In this study we determine the extent of genetic variation for characters directly related to outcrossing, such as male frequency, male mating ability, and male reproductive success, in several wild isolates of the nematode Caenorhabditis elegans. This species is characterized by an androdioecious breeding system in which males occur with hermaphrodites that can either self-fertilize or...

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

Julian Catchen, Angel Amores & Susan Bassham
The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional,...

Latitudinal gradients in population growth do not reflect demographic responses to climate

Megan Peterson, Graham Bailes, Lauren Hendricks, Laurel Pfeifer-Meister, Paul Reed, Scott Bridgham, Bart Johnson, Robert Shriver, Ellen Waddle, Hannah Wroton, Daniel Doak, Bitty Roy & William Morris
Spatial gradients in population growth, such as across latitudinal or elevational gradients, are often assumed to primarily be driven by variation in climate, and are frequently used to infer species’ responses to climate change. Here, we use a novel demographic, mixed model approach to dissect the contributions of climate variables vs. other latitudinal or local site effects on spatiotemporal variation in population performance in three perennial bunchgrasses. For all three species, we find that performance...

Data from: Phylogeographic estimation and simulation of global diffusive dispersal

Stilianos Louca
The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2-dimensional plane, however the accuracy of these methods deteriorates substantially when dispersal occurs at global scales because Spherical Brownian Motion (SBM) differs from planar Brownian Motion. No statistical method exists for estimating SBM diffusion coefficients from a...

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

Aryn Wilder, Stephen Palumbi, David Conover & Nina Overgaard Therkildsen
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome-wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity...

Data from: Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

Sean Stankowski, James M. Sobel & Matthew A. Streisfeld
A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially explicit framework, but has not been used...

Data from: MycoDB, a global database of plant response to mycorrhizal fungi

V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook G. Milligan, John C. Moore, , Bridget Piculell, Blake Ramsby … & Jason D. Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...

Data from: Variation in ecophysiological traits might contribute to ecogeographic isolation and divergence between parapatric ecotypes of Mimulus aurantiacus

James M. Sobel, Sean Stankowski & Matthew A. Streisfeld
Many forms of reproductive isolation contribute to speciation, and early acting barriers may be especially important, because they have the first opportunity to limit gene flow. Ecogeographic isolation occurs when intrinsic traits of taxa contribute to disjunct geographic distributions, reducing the frequency of inter‐taxon mating. Characterizing this form of isolation requires knowledge of both the geographic arrangement of suitable habitats in nature and the identification of phenotypes involved in shaping geographic distributions. In Mimulus aurantiacus,...

Data from: Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

Natalie L. Rosser, Luke Thomas, Sean Stankowski, Zoe T. Richards, W. Jason Kennington & Michael S. Johnson
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC. Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it...

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