59 Works

Data from: Individual marking of soft-bodied subtidal invertebrates in situ - a novel staining technique applied to the giant plumose anemone Metridium farcimen (Tilesius, 1809)

Christopher D. Wells & Kenneth P. Sebens
The ability to recognize individuals and track growth over time is crucial to population dynamics research as well as studies of animal behavior. Invertebrates are particularly difficult to track as they often molt, have regenerative capabilities, or lack hard parts to attach markers. We tested, in laboratory and field studies, a new way of marking sea anemones (order Actiniaria) by injection of three vital stains (i.e., neutral red, methylene blue, and fluorescein). Neutral red and...

Data from: Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

Cristian B. Canales-Aguirre, Lisa W. Seeb, James E. Seeb, Maria I. Cadiz, Selim S. Musleh, Ivan Arismendi, Gonzalo Gajardo, Ricardo Galleguillos & Daniel Gomez-Uchida
Different pathways of propagation and dispersal of non-native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile’s largest producer of...

Data from: 2D or Not 2D? Testing the utility of 2D vs. 3D landmark data in geometric morphometrics of the sculpin subfamily Oligocottinae (Pisces; Cottoidea)

Thaddaeus J. Buser, Brian L. Sidlauskas & Adam P. Summers
We contrast 2D vs. 3D landmark‐based geometric morphometrics in the fish subfamily Oligocottinae by using 3D landmarks from CT‐generated models and comparing the morphospace of the 3D landmarks to one based on 2D landmarks from images. The 2D and 3D shape variables capture common patterns across taxa, such that the pairwise Procrustes distances among taxa correspond and the trends captured by principal component analysis are similar in the xy plane. We use the two sets...

Data from: A phylogenomic perspective on the biogeography of skinks in the Plestiodon brevirostris group inferred from target enrichment of ultraconserved elements

, Charles W. Linkem, Carlos J. Pavón-Vázquez, Adrián Nieto-Montes De Oca, John Klicka, John E. McCormack & Robert W. Bryson
Aim: The aim of our study was to reconstruct ancestral geographic distributions from time-calibrated phylogenies generated from phylogenomic data to answer three broad questions about the biogeography of skinks in the Plestiodon brevirostris group: (1) Are biogeographic patterns correlated with the formation of the Trans-Mexican Volcanic Belt? (2) Do different methods of phylogenetic estimation result in different topologies? If so, (3) are biogeographic reconstructions impacted by the use of different phylogenetic trees? Location: Mexico. Methods:...

Data from: A major shift in diversification rate helps explain macroevolutionary patterns in primate species diversity

Jessica H. Arbour & Sharlene E. Santana
Primates represent one of the most species rich, wide ranging and ecologically diverse clades of mammals. What major macroevolutionary factors have driven their diversification and contributed to the modern distribution of primate species remains widely debated. We employed phylogenetic comparative methods to examine the role of clade age and evolutionary rate heterogeneity in the modern distribution of species diversity of Primates. Primate diversification has accelerated since its origin, with decreased extinction leading to a shift...

Data from: Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

Morten T. Limborg, Wesley A. Larson, Lisa W. Seeb & James E. Seeb
A whole-genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalysed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD because gene duplicates (i.e., paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both...

Data for allometric equations of Chrysolepis sempervirens, Cornus sericea, Corylus cornuta ssp. californica, and Leucothoe davisiae.

James A. Lutz, J. A. Freund, A. J. Larson, M. E. Swanson, T. J. Furniss, K. M. L. Becker, E. M. Blomdahl, C. A. Cansier, S. J. Germain & S. M. A. Jeronimo
This data set includes measurements of 40 stems of Chrysolepis sempervirens (Kellogg) Hjelmq. (bush chinquapin), 41 stems of Cornus sericea L. (redosier dogwood), 50 stems of Corylus cornuta Marsh. ssp. californica (A. DC.) E. Murray, and 40 stems of Leucothoe davisiae Torrey (Sierra laurel), as reported in Lutz et al. (2014, 2017). Nomenclature follows Flora of North America (1993+).

Data from: Morphological and functional maturity of the oral jaws covary with offspring size in Trinidadian guppies

Terry R. Dial, Luz Patricia Hernandez & Elizabeth L. Brainerd
Large size of individual offspring is routinely selected for in highly competitive environments, such as in low-predation populations of the Trinidadian guppy (Poecilia reticulata). Large guppy offspring outcompete their smaller conspecifics, but the functional mechanisms underlying this advantage are unknown. We measured jaw kinematics during benthic feeding and cranial musculoskeletal morphologies in neonates and juveniles from five populations of Trinidadian guppy and found that both kinematics and morphologies vary substantially with neonatal size. Rotation at...

Data from: The oceanic biological pump: rapid carbon transfer to depth at continental margins during winter

Laurenz Thomsen, Jacopo Aguzzi, Corrado Costa, Fabio De Leo, Andrea Ogston & Autun Purser
The oceanic biological pump is responsible for the important transfer of CO2-C as POC “Particulate Organic Carbon” to the deep sea. It plays a decisive role in the Earth’s carbon cycle and significant effort is spent to quantify its strength. In this study we used synchronized daily time-series data of surface chlorophyll-a concentrations from the NASA’s MODIS satellite in combination with hourly to daily observations from sea surface buoys and from an Internet Operated Vehicle...

Data from: Microbiome sharing between children, livestock and household surfaces in western Kenya

Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Ceclia Noecher, Ohad Manor, Sarah Hilton, Samuel M. Thmbi, Clayton Onyango, Gemina Garland-Lewis, Douglas R. Call, M. Kariuki Njenga, Judith N. Wasserheit, Jennifer A. Zambriski, Judd L. Walson, Guy H. Palmer, Joel Montgomery, Elhanan Borenstein, Richard Omore, Peter M. Rabinowitz, Samuel M. Thumbi & Cecilia Noecker
The gut microbiome community structure and development are associated with several health outcomes in young children. To determine the household influences of gut microbiome structure, we assessed microbial sharing within households in western Kenya by sequencing 16S rRNA libraries of fecal samples from children and cattle, cloacal swabs from chickens, and swabs of household surfaces. Among the 156 households studied, children within the same household significantly shared their gut microbiome with each other, although we...

Data from: The function and organization of the motor system controlling flight maneuvers in flies

Theodore H. Lindsay, Anne Sustar, Michael H. Dickinson, Theodore Lindsay & Michael Dickinson
Animals face the daunting task of controlling their limbs using a small set of highly constrained actuators. This problem is particularly demanding for insects such as Drosophila, which must adjust wing motion for both quick voluntary maneuvers and slow compensatory reflexes using only a dozen pairs of muscles. To identify strategies by which animals execute precise actions using sparse motor networks, we imaged the activity of a complete ensemble of wing control muscles in intact,...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

Wesley Loftie-Eaton, Kelsie Bashford, Hannah Quinn, Kieran Dong, Jack Millstein, Samuel Hunter, Maureen K. Thomason, Houra Merrikh, Jose M. Ponciano & Eva M. Top
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms, and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multi-drug resistance plasmid RP4, determined plasmid persistence and cost using a joint...

Data from: Hemiparasites can transmit indirect effects from their host plants to herbivores

Nathan L. Haan, Jonathan D. Bakker & M. Deane Bowers
Parasitic plants can serve as critical intermediaries between their hosts and other organisms; however these relationships are not well understood. To investigate the relative importance of plant traits in such interactions, we studied the role of the root hemiparasite, Castilleja levisecta (Orobanchaceae), as a mediator of interactions between the host plants it parasitizes and the lepidopteran herbivore Euphydryas editha (Nymphalidae), whose caterpillars feed on Castilleja and sequester iridoid glycosides from it. We tested whether the...

Data from: Genetic mapping of molar size relations identifies inhibitory locus for third molars in mice

Nicolas Navarro & A. Murat Maga
Molar size in Mammals shows considerable disparity and exhibits variation similar to that predicted by the Inhibitory Cascade model. The importance of such developmental systems in favoring evolutionary trajectories is also underlined by the fact that this model can predict macroevolutionary patterns. Using backcross mice, we mapped QTL for molar sizes controlling for their sequential development. Genetic controls for upper and lower molars appear somewhat similar, and regions containing genes implied in dental defects drive...

Data from: Caenorhabditis elegans genes affecting interindividual variation in life-span biomarker gene expression

Alexander Mendenhall, Matthew M. Crane, Patricia M. Tedesco, Thomas E. Johnson & Roger Brent
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior...

Data from: Range contraction and increasing isolation of a polar bear subpopulation in an era of sea-ice loss

Kristin L. Laidre, Erik W. Born, Stephen N. Atkinson, Øystein Wiig, Liselotte W. Andersen, Nicholas J. Lunn, Markus Dyck, Eric V. Regehr, Richard McGovern & Patrick Heagerty
Climate change is expected to result in range shifts and habitat fragmentation for many species. In the Arctic, loss of sea ice will reduce barriers to dispersal or eliminate movement corridors, resulting in increased connectivity or geographic isolation with sweeping implications for conservation. We used satellite telemetry, data from individually marked animals (research and harvest), and microsatellite genetic data to examine changes in geographic range, emigration, and interpopulation connectivity of the Baffin Bay (BB) polar...

Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Christopher Blair, & Robert W. Bryson
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods...

Data from: Graphics for relatedness research

Iván Galván-Femenía, Jan Graffelman & Carles Barceló-I-Vidal
Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article is to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS and IBD based allele sharing studies are considered. Furthermore, we...

Data from: A descending neuron correlated with the rapid steering maneuvers of flying Drosophila

Bettina Schnell, Ivo G. Ros & Michael H. Dickinson
To navigate through the world, animals must stabilize their path against disturbances and change direction to avoid obstacles and to search for resources. Locomotion is thus guided by sensory cues but also depends on intrinsic processes, such as motivation and physiological state. Flies, for example, turn with the direction of large-field rotatory motion, an optomotor reflex that is thought to help them fly straight. Occasionally, however, they execute fast turns, called body saccades, either spontaneously...

Salmon Creek Organic Geochemistry Chemometric Data

Laurel Larsen & Cleo Woelfle-Erskine
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.

Salmon Creek radon data

Laurel Larsen & Cleo Woelfle-Erskine
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...

Data from: Clearing muddied waters: capture of environmental DNA from turbid waters

Kelly E. Williams, Antoinette J. Piaggio & Kathryn P. Huyvaert
Understanding the differences in efficiencies of various methods to concentrate, extract, and amplify environmental DNA (eDNA) is vital for best performance of eDNA detection. Aquatic systems vary in characteristics such as turbidity, eDNA concentration, and inhibitor load, thus affecting eDNA capture efficiency. Application of eDNA techniques to the detection of terrestrial invasive or endangered species may require sampling at intermittent water sources that are used for drinking and cooling; these water bodies may often be...

Data from: Neural evidence supports a dual sensory-motor role for insect wings

Brandon Pratt, Tanvi Deora, Thomas Mohren, Tom Daniel & Thomas Daniel
Flying insects use feedback from various sensory modalities including vision and mechanosensation to navigate through their environment. The rapid speed of mechanosensory information acquisition and processing compensates for the slower processing times associated with vision, particularly under low light conditions. While halteres in dipteran species are well known to provide such information for flight control, less is understood about the mechanosensory roles of their evolutionary antecedent, wings. The features that wing mechanosensory neurons (campaniform sensilla)...

Data from: Species discrimination of co-occurring small fossil mammals: a case study of the Cretaceous-Paleogene multituberculate genus Mesodma

Stephanie M. Smith & Gregory P. Wilson
The mammalian fossil record is largely composed of isolated teeth and tooth-bearing elements. In vertebrate microfossil assemblages with closely related, co-occurring species of mammals, it can be difficult to identify isolated teeth to species level because morphological differences among species may be slight and based on a single tooth position. Here we investigate the utility of the allegedly diagnostic lower fourth premolar (p4) for species-level identification in the genus Mesodma (Multituberculata, Neoplagiaulacidae). We conducted linear...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Washington
  • University of Montana
  • Oregon State University
  • University of California, Berkeley
  • United States Department of Agriculture
  • Fred Hutchinson Cancer Research Center
  • University of Pennsylvania
  • Burke Museum of Natural History and Culture
  • Occidental College
  • University of Colorado Boulder