333 Works

Established and potentially invasive fish of the Laurentian Great Lakes

Christopher Jerde, Andrew Mahon & Erin Grey
Environmental DNA (eDNA) metabarcoding has shown promise as a tool for estimating biodiversity and early detection of invasive species. In aquatic systems, advantages of this method include the ability to concurrently monitor biodiversity and detect incipient invasions simply through the collection and analysis of water samples. However, depending on the molecular markers chosen for a given study, reference libraries containing target sequences from present species may limit the usefulness of eDNA metabarcoding. To explore the...

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

BEDMAP3 - Ice thickness, bed and surface elevation for Antarctica - standardised shapefiles and geopackages

Peter Fretwell, Hamish Pritchard, Alice Fremand, Julien Bodart, A. Aitken, Jonathan Bamber, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, K Christianson, H Conway, Hugh Corr, X. Cui, D Damaske, V. Damn, R. Drews, G. Eagles, O. Eisen, H. Eisermann, F Ferraccioli, Rene Forsberg, S Franke … & A. Zirizzotti
We present here the Bedmap3 ice thickness, bed and surface elevation aggregated points and survey lines. The aggregated points consist of statistically-summarised shapefile points (centred on a continent-wide 500 m x 500 m grid) that reports the average values of Antarctic ice thickness, bed and surface elevation from the full-resolution survey data and information on their distribution. The points presented here correspond to the added points since the last release of Bedmap2. The data comes...

Regulatory Requirements of Banks and Arbitrage in the Post-Crisis Federal Funds Market

Rod Garratt & SOFIA PRIAZHKINA
This paper explains the nature of interest rates in the U.S. federal funds market after the 2007- 09 financial crisis. We build a model of the over-the-counter lending market that incorporates new aspects of the financial system: abundance of liquidity, different regulatory standards for banks, and arbitrage opportunities created by limited access to the facility granting interest on excess reserves. The model determines the equilibrium federal funds rate as a function of the policy rates...

Repercussions of Patrilocal Residence on Mothers’ Social Support Networks Among Tsimane Forager-Farmers

Sarah Alami, Edmond Seabright, Thomas S Kraft, Helen E Davis, Ann E Caldwell, Paul Hooper, Lisa McAllister, Sarah Mulville, Christopher Von Rueden, Benjamin Trumble, Jonathan Stieglitz, Michael Gurven & Hillard Kaplan
While it is commonly thought that patrilocality is associated with worse outcomes for women 27 and their children due to lower social support, few studies have examined whether the structure 28 of female social networks covaries with post-marital residence. Here we analyze scan sample 29 data collected among Tsimane forager-farmers. We compare the social groups and activity 30 partners of 181 women residing in the same community as their parents, their husband’s parents, 31 both...

Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing

Shuting Lin, Soojin Yi & Peng Qiu
Abstract The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with...

Data from: Exploitation and recovery of a sea urchin predator has implications for the resilience of southern California kelp forests

Scott L. Hamilton & Jennifer E. Caselle
Size-structured predator–prey interactions can be altered by the history of exploitation, if that exploitation is itself size-selective. For example, selective harvesting of larger sized predators can release prey populations in cases where only large individuals are capable of consuming a particular prey species. In this study, we examined how the history of exploitation and recovery (inside marine reserves and due to fisheries management) of California sheephead (Semicossyphus pulcher) has affected size-structured interactions with sea urchin...

Data from: The new bioinformatics: integrating ecological data from the gene to the biosphere

Matthew B. Jones, Mark P. Schildahuer, O. J. Reichman, Shawn Bowers, Mark P. Schildhauer & O.J. Reichman
Bioinformatics, the application of computational tools to the management and analysis of biological data, has stimulated rapid research advances in genomics through the development of data archives such as GenBank, and similar progress is just beginning within ecology. One reason for the belated adoption of informatics approaches in ecology is the breadth of ecologically pertinent data (from genes to the biosphere) and its highly heterogeneous nature. The variety of formats, logical structures, and sampling methods...

Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Paul F. Gugger, Makihiko Ikegami & Victoria L. Sork
Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated...

Data from: Lights out: the evolution of bacterial bioluminescence in Loliginidae

Frank E. Anderson, Alexis Bergman, Samantha H. Cheng, M. Sabrina Pankey & Tooraj Valinassab
Representatives of several metazoan clades engage in symbiotic interactions with bioluminescent bacteria, but the evolution and maintenance of these interactions remain poorly understood. Uroteuthis is a genus of loliginid squid (Cephalopoda: Loliginidae) characterized by paired ventral photophores (light organs) housing bioluminescent bacteria. While previous phylogenetic studies have suggested that Uroteuthis is closely related to Loliolus, a genus of non-bioluminescent species, this relationship remains unresolved. To illuminate Uroteuthis and Loliolus phylogeny and its implications for the...

Data from: Evolution of transcription networks in response to temporal fluctuations

Kyoungmin Roh, Farshad R. Pour Safaei, João P. Hespanha & Stephen R. Proulx
Organisms respond to changes in their environment over a wide range of biological and temporal scales. Such phenotypic plasticity can involve developmental, behavioral, physiological, and genetic shifts. The adaptive value of a plastic response is known to depend on the nature of the information that is available to the organism as well as the direct and indirect costs of the plastic response. We modeled the dynamic process of simple gene regulatory networks as they responded...

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: Nitrogen cycling and export in California chaparral: the role of climate in shaping ecosystem responses to fire

Erin J. Hanan, Christina Naomi Tague & Joshua P. Schimel
Climate change models predict that interannual rainfall variability will increase in California over the next several decades; these changes will likely influence how frequently California ecosystems burn and how they respond to fire. Fires uncouple N mobilization from uptake by destroying plant biomass and increasing nitrification. Following fire, autumn and winter rains can leach N into streams from slopes that have been denuded. The amount of N exported depends on how rapidly soil microbes metabolize...

Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR

Andrea J. Adams, John P. LaBonte, Morgan L. Ball, Kathryn L. Richards-Hrdlicka, Mary H. Toothman & Cheryl J. Briggs
Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR...

Data from: The Centennial Trends Greater Horn of Africa precipitation dataset

Chris C. Funk, Sharon E. Nicholson, Martin Landsfeld, Douglas Klotter, Pete Peterson & Laura Harrison
East Africa is a drought prone, food and water insecure region with a highly variable climate. This complexity makes rainfall estimation challenging, and this challenge is compounded by low rain gauge densities and inhomogeneous monitoring networks. The dearth of observations is particularly problematic over the past decade, since the number of records in globally accessible archives has fallen precipitously. This lack of data coincides with an increasing scientific and humanitarian need to place recent seasonal...

Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific

Mattias L. Johansson, Filipe Alberto, Daniel C. Reed, Peter T. Raimondi, Nelson C. Coelho, Mary A. Young, Patrick T. Drake, Christopher A. Edwards, Kyle Cavanaugh, Jorge Assis, Lydia B. Ladah, Tom W. Bell, James A. Coyer, David A. Siegel & Ester A. Serrão
At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific....

Data from: Bolstered physical defences under nutrient-enriched conditions may facilitate a secondary foundational algal species in the South Pacific

Sarah Joy Bittick, Rachel Joy Clausing, Caitlin Ryan Fong & Peggy Fong
1. Humans have a long history of changing species’ ranges and habitat distributions, making studies of the ecological processes that may facilitate these changes of key importance, particularly in cases where a primary foundation species is replaced by another, less desirable species. 2. We investigated the impact of nutrients and herbivory on Turbinaria ornata, a secondary foundational macroalga that depends on and likely competes with coral, the primary foundational community. T. ornata is also rapidly...

Data from: Adaptation to temporally fluctuating environments by the evolution of maternal effects

Snigdhadip Dey, Stephen R. Proulx & Henrique Teotonio
All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e., anticipatory maternal effects or transgenerational phenotypic plasticity) underlies adaptation to environments that fluctuate in a predictably alternating fashion over maternal-offspring generations. In contrast, randomizing maternal effects (i.e., diversifying and conservative bet-hedging), are expected to evolve in response to unpredictably fluctuating environments. Although maternal effects are common, evidence for their adaptive significance is equivocal since they can easily evolve...

Data from: Male mate choice via cuticular hydrocarbon pheromones drives reproductive isolation between Drosophila species

Michael P. Shahandeh, Alison Pischedda & Thomas L. Turner
Mate discrimination is a key mechanism restricting gene flow between species. While studied extensively with respect to female mate choice, mechanisms of male mate choice between species are far less studied. Thus, we have little knowledge of the relative frequency, importance, or overall contribution of male mate discrimination to reproductive isolation. In the present study, we estimated the relative contributions of male and female choice to reproductive isolation between Drosophila simulans and D. sechellia, and...

Data from: Abiotic and habitat drivers of tick vector abundance, diversity, phenology and human encounter risk in southern California

Andrew J. MacDonald
The distribution, abundance and seasonal activity of vector species, such as ticks and mosquitoes, are key determinants of vector-borne disease risk, and are strongly influenced by abiotic and habitat conditions. Despite the numerous species of tick vectors in the heavily populated North American West Coast, all but Ixodes pacificus, the primary vector of the Lyme disease spirochete, is poorly characterized with regard to seasonal activity patterns and fine scale drivers of distribution and abundance, particularly...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: Accounting for disturbance history in models: using remote sensing to constrain carbon and nitrogen pool spin‐up

Erin J. Hanan, Christina Tague, Janet Choate, Mingliang Liu, Crystal Kolden & Jennifer Adam
Disturbances such as wildfire, insect outbreaks, and forest clearing, play an important role in regulating carbon, nitrogen, and hydrologic fluxes in terrestrial watersheds. Evaluating how watersheds respond to disturbance requires understanding mechanisms that interact over multiple spatial and temporal scales. Simulation modeling is a powerful tool for bridging these scales; however, model projections are limited by uncertainties in the initial state of plant carbon and nitrogen stores. Watershed models typically use one of two methods...

Data from: Transcriptomics reveal transgenerational effects in purple sea urchin embryos: adult acclimation to upwelling conditions alters the response of their progeny to differential pCO2 levels

Juliet M. Wong, Kevin M. Johnson, Morgan W. Kelly & Gretchen E. Hofmann
Understanding the mechanisms with which organisms can respond to a rapidly changing ocean is an important research priority in marine sciences, especially in light of recent predictions regarding the pace of ocean change in the coming decades. Transgenerational effects, in which the experience of the parental generation can shape the phenotype of their offspring, may serve as such a mechanism. In this study, adult purple sea urchins, Strongylocentrotus purpuratus, were conditioned to regionally and ecologically...

Data from: Size, age, and habitat determine effectiveness of Palau's Marine Protected Areas

Alan M. Friedlander, Yimnang Golbuu, Enric Ballesteros, Jennifer E. Caselle, Marine Gouezo, Dawnette Olsudong & Enric Sala
Palau has a rich heritage of conservation that has evolved from the traditional moratoria on fishing, or "bul", to more western Marine Protected Areas (MPAs), while still retaining elements of customary management and tenure. In 2003, the Palau Protected Areas Network (PAN) was created to conserve Palau's unique biodiversity and culture, and is the country's mechanism for achieving the goals of the Micronesia Challenge (MC), an initiative to conserve ?30% of near-shore marine resources within...

Data from: Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution

Alastair R. Tanner, Dirk Fuchs, Inger E. Winkelmann, Thomas P. Gilbert, M. Sabrina Pankey, Angela M. Ribeiro, Kevin M. Kocot, Kenneth M. Halanych, Todd H. Oakley, Rute R. Da Fonseca, Davide Pisani, Jakob Vinther & M. Thomas P. Gilbert
Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution....

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