Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...
Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidisAllison Q. Byrne, Andrew P. Rothstein, Thomas J. Poorten, Jesse Erens, Matthew L. Settles & Erica Bree Rosenblum
One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity...
Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approachWilliam A. Freyman, Sebastian Höhna & William A Freyman
Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and...
Differential seed dispersal, in which selfed and outcrossed seeds possess different dispersal propensities, represents a potentially important individual-level association. A variety of traits can mediate differential seed dispersal, including inflorescence and seed size variation. However, how natural selection shapes such associations is poorly known. Here, we developed theoretical models for the evolution of mating system and differential seed dispersal in metapopulations, incorporating heterogeneous pollination, dispersal cost, cost of outcrossing, and environment-dependent inbreeding depression. We considered...
Data from: Phenotypic and genotypic variation across a stable white-eye (Zosterops sp.) hybrid zone in central South AfricaGraeme Oatley, Dawie H. De Swardt, Rick J. Nuttal, Timothy M. Crowe & Rauri C.K. Bowie
The interbreeding of two species after a period of separation (secondary contact) most often results in stable areas of hybridization or tension zones characterized by selection against hybrid individuals. Three plumage forms of Zosterops meet and interbreed in central South Africa. Here we examine how phenotypic measures (biometric and plumage) and genotypic markers (mitochondrial and nuclear DNA) change through a putative hybrid zone located in the area where the ranges of the Orange River white-eye...
Data from: Floral resource availability from groundcover promotes bee abundance in coffee agroecosystemsKaleigh Fisher, David J. Gonthier, Katherine K. Ennis & Ivette Perfecto
Patterns of bee abundance and diversity across different spatial scales have received thorough research consideration. However, the impact of short and long term temporal resource availability on biodiversity has been less explored. This is highly relevant in tropical agricultural systems for pollinators, as many foraging periods of pollinators extend beyond flowering of any single crop species. In this study, we sought to understand how bee communities in tropical agroecosystems changed between seasons, and if short...
Data from: High throughput functional genomics identifies modulators of TCE metabolite genotoxicity and candidate susceptibility genesVanessa Y. De La Rosa, Jonathan Asfaha, Michael Fasullo, Alex Loguinov, Peng Li, Lee E. Moore, Nathaniel Rothman, Jun Nakamura, James A. Swenberg, Ghislaine Scelo, Luoping Zhang, Martyn T. Smith & Chris D. Vulpe
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites....
Contact networks are fundamental to the transmission of infection and host sex often affects the acquisition and progression of infection. However, the epidemiological impacts of sex-related variation in animal contact networks have rarely been investigated. We test the hypothesis that sex-biases in infection are related to variation in multilayer contact networks structured by sex in a population of European badgers Meles meles naturally infected with Mycobacterium bovis. Our key results are that male-male and between-sex...
Although genetic diversity within a population is suggested to improve population-level fitness and productivity, the existence of these effects is controversial because empirical evidence for an ecological effect of genetic diversity and the underlying mechanisms is scarce and incomplete. Here, we show that the natural single-gene behavioural polymorphism (Rover and sitter) in Drosophila melanogaster has a positive effect on population fitness. Our simple numerical model predicted that the fitness of a polymorphic population would be...
In metropolitan regions made up of multiple independent jurisdictions, adaptation to increased coastal flooding due to sea level rise requires coordinated strategic planning of physical and organizational approaches. To better understand specific choices for sea level rise adaptation we examined potential costs to raise current protective infrastructure to future water levels. This data further explores our cost data at the county scale in an attempt to better characterize the region’s counties by their relative capacity...
A subset of Californian vascular plant species recognized by Baldwin et al. (2017), corresponding to to the “large and intermediate-sized genera” studied by Stebbins & Major (1965)Bruce G. Baldwin, Andrew H. Thornhill, William A. Freyman, David D. Ackerly, Matthew M. Kling, Naia Morueta-Holme & Brent D. Mishler
Column one includes 2356 Californian vascular plant species recognized by Baldwin et al. (2017 Amer. J. Bot.), and column 2 includes their correspondence to the “large and intermediate-sized genera” studied by Stebbins & Major (1965 Ecol. Monogr.). These 2356 species represent 44.8% of the 5257 species examined by Baldwin et al. (2017) and include only the species that conform to the generic concepts of Stebbins & Major, which sometimes differ from revised generic concepts in...
Master spatial file for native California vascular plants used by Baldwin et al. (2017 Amer. J. Bot.)Bruce G. Baldwin, Andrew H. Thornhill, William A. Freyman, David. D. Ackerly, Matthew M. Kling, Naia Morueta-Holme & Brent D. Mishler
Georeferenced locality information of all Californian native vascular plant species from herbarium specimens obtained from five different online sources in August 2015: (1) the Consortium of California Herbaria (CCH, http://ucjeps.berkeley.edu/consortium/), (2) the Consortium of Pacific Northwest Herbaria (http://www.pnwherbaria.org), (3) Australia’s Virtual Herbarium (avh.chah.org.au), (4) Canadensys (http://www.canadensys.net), and (5) the Global Biodiversity Information Facility (http://www.gbif.org). Data were carefully cleaned as described in Baldwin et al. 2017, and this final data set contains 1,383,762 occurrences.
Experimental and Supplementary Data for The Roles of Impact and Inertia in the Failure of a Shoelace KnotChristopher Daily-Diamond, Christine Gregg & Oliver O'Reilly
Raw experimental data gathered during impulsive forcing of a shoelace knot on a pendulum apparatus, in various orientations, with corresponding data summary sheets. Also included are two supplementary video files of treadmill and pendulum tests.
Slab Ocean forcing file and model output for \"Seasonal Transitions and the Westerly Jet in the Holocene East Asian Summer Monsoon\"Wenwen Kong, Leif Swenson & John Chiang
This dataset contains slab ocean forcing file and key model outputs from CAM5 simulations used in: Kong, W., L.M. Swenson, and J.C.H. Chiang, Seasonal Transitions and the Westerly Jet in the Holocene East Asian Summer Monsoon. Journal of Climate, doi:10.1175/JCLI-D-16-0087.1 link
The surrogate bio-volume and topography spatial dataset of Wax Lake Delta
Master spatial file for for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)Andrew Thornhill, Bruce Baldwin, William Freyman, Sonia Nosratinia, Matthew Kling, Naia Morueta-Holme, Thomas Madsen, David Ackerly, Brent Mishler & Andrew Thornhill
Georeferenced locality information for 1083 OTUs assembled from all Californian native vascular plant records from herbarium specimens obtained from five different online sources in August 2015: (1) the Consortium of California Herbaria (CCH, http://ucjeps.berkeley.edu/consortium/), (2) the Consortium of Pacific Northwest Herbaria (http://www.pnwherbaria.org), (3) Australia’s Virtual Herbarium (avh.chah.org.au), (4) Canadensys (http://www.canadensys.net), and (5) the Global Biodiversity Information Facility (http://www.gbif.org). Data were carefully cleaned as described in Baldwin et al. 2017, and combined into OTUs as described...
This datafile contains fluorescence indices and the results of a parallel factor analysis (PARAFAC) performed on samples collected within the Salmon Creek Watershed in Sonoma County, Califonia. Please see Woelfle-Erskine et al. (2017) for site location details. The present dataset is provided in support of Larsen and Woelfle-Erskine (in review). The purpose of this dataset was to develop a fluorescent fingerprint for purposes of differentiating between surface water, groundwater, and hyporheic water.
This datafile contains results of 222Rn analysis of samples collected within the Salmon Creek Watershed in Sonoma County, Califonia. Please see Woelfle-Erskine et al. (2017) for site location details. The present dataset is provided in support of Larsen and Woelfle-Erskine (in review).The purpose of this dataset was to determine relative ages of water samples.Data were collected in 2016 in the Fay Creek and Tannery Creek watersheds, both second-order tributaries of Salmon Creek.For further information, please...
The zip file contains field line tracing results from a MHD simulation, which are used to create Figure 3 of manuscript #2017GL075831, titled as "High-altitude closed magnetic loops at Mars observed by MAVEN".
In metropolitan regions made up of multiple independent jurisdictions, adaptation to increased coastal flooding due to sea level rise requires coordinated strategic planning of physical and organizational approaches. To better understand specific choices for sea level rise adaptation we examined potential costs to raise current protective infrastructure to future water levels.
Data from: Tree-growth is more sensitive than species distributions to recent changes in climate and acidic deposition in the northeastern United StatesJay W. Wason, Martin Dovciak, Colin M. Beier & John J. Battles
Tree-growth responses to environmental change could provide early detection of shifts in forest composition and help facilitate ecosystem management and conservation. We studied forest tree responses to recent trends in climate and acidic deposition using analyses of tree rings and long-term climate, deposition and forest plot data along an elevational climatic gradient in the northeastern United States. We analyzed how (a) individual growth of dominant species (Picea rubens, Abies balsamea), and (b) spatial distributions of...
Data from: The seasonal climate niche predicts phenology and distribution of an ephemeral annual plant, Mollugo verticillataJoe Hereford, Johanna Schmitt & David D. Ackerly
1.Many short-lived species complete their life cycles during brief seasonal windows of favorable environmental conditions. Such species may persist in the face of climate warming by migration to track their seasonal climate niche in space and/or by phenological shifts to track favorable conditions in time within the year. To describe the seasonal climate niche of the short-lived annual Mollugo verticillata in California, we used data from herbarium specimens and historic climate records to estimate environmental...
Data from: Trapped within the city: Integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanizationAndré Lourenço, David Álvarez, Ian J. Wang & Guillermo Velo-Antón
Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders...
A novel weed has recently emerged, causing serious agronomic damage in one of the most important maize-growing regions of Western Europe, the Northern Provinces of Spain. The weed has morphological similarities to a wild relative of maize and has generally been referred to as teosinte. However, the identity, origin or genetic composition of ‘Spanish teosinte’ was unknown. Here, we present a genome-wide analysis of single-nucleotide polymorphism (SNP) data for Spanish teosinte, sympatric populations of cultivated...
Data from: Population genetic and field ecological analyses return similar estimates of dispersal over space and time in an endangered amphibianIan J. Wang & H. Bradley Shaffer
The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field ecological studies. However, empirical assessments of the concordance between direct field ecological and indirect population genetic studies...
University of California, Berkeley82
University of California System10
University of Colorado Boulder4
University of Washington3
The University of Texas at Austin3
University of Michigan-Ann Arbor3
University of North Carolina3
Australian National University3
California Academy of Sciences3
University of Florida3