197 Works

Cold call: the acoustic repertoire of Ross Sea killer whales (Orcinus orca, Type C) in McMurdo Sound, Antarctica

Rebecca Wellard, Robert Pitman, John Durban & Christine Erbe
Killer whales (Orcinus orca) are top marine predators occurring globally. In Antarctic waters, five ecotypes have been described, with Type C being the smallest form of killer whale known. Acoustic recordings of nine encounters of Type C killer whales were collected in 2012 and 2013 in McMurdo Sound, Ross Sea. In a combined 3.5 hours of recordings, 6386 killer whale vocalisations were detected and graded based on their signal-to-noise ratio. Spectrograms of the highest-quality calls...

An animal without a mitochondrial genome: the salmon parasite Henneguya salminicola (Cnidaria: Myxozoa)

Dorothée Huchon, Dayana Yahalomi, Stephen D. Atkinson, Moran Neuhof, E. Sally Chang, Hervé Philippe, Paulyn Cartwright & Jerri L. Bartholomew
Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no...

Data for Runups of unusual size: rogueness and variability of swash

Gabriel García-Medina, H. Tuba Ozkan-Haller, Peter Ruggiero, Robert A. Homan & Chuan Li
This repository item contains the files needed to reproduce the results reported in the published work entitled "Runups of unusual size: rogueness and variability of swash" in the Journal of Geophysical Research. As described in the publication, the results described within it pertain to simulations of wave runup for various configurations of beaches using various idealized surface gravity wave conditions. All discussed results pertain to a model-generated data set using the publically-available code "funwavec" for...

Sitticine jumping spiders: phylogeny, classification and chromosomes (Araneae: Salticidae: Sitticini)

Wayne Maddison, David Maddison, Shahan Derkarabetian & Marshal Hedin
We review the systematics of sitticine jumping spiders, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribe Aillutticina (a group of 5 Neotropical genera)...

Spectral data for quaking aspen (Populus tremuloides) clones of different ploidy levels

B. Blonder, B.J. Graae, B. Greer, M. Haagsma, K. Helsen, R.E. Kapás, H. Pai, J. Rieksta, D. Sapena, C.J. Still & R. Strimbeck
Data comprise measurements of spectral reflectance for quaking aspen (Populus tremuloides Michx.) trees at a range of sites in southwestern Colorado near the town of Crested Butte. Spectra were measured in three different ways: hyperspectral measurements of leaves, hyperspectral measurements of bark, and multispectral measurements of canopies. The first two measurements were made using a handheld spectrometer, while the latter were made via airborne imaging from an unmanned aerial system. In addition to these reflectance...

Data from: Recurrent mutualism breakdown events in a legume rhizobia metapopulation

Joel Sachs, Kelsey Gano-Cohen, Camille Wendlandt, Khadija Al Moussawi, Peter Stokes, Kenjiro Quides, Alexandra Weisberg & Jeff Chang
Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating Bradyrhizobium spp. that associate with the native legume Acmispon strigosus. We quantified mutualism traits of 85 Bradyrhizobium...

Data from: Big fishery, big data, and little crabs: using genomic methods to examine the seasonal recruitment patterns of early life stage Dungeness crab (Cancer magister) in the California current ecosystem

Elizabeth Lee
The California Current Ecosystem (CCE) is a dynamic marine ecosystem from which many socioeconomically important fisheries species are harvested. Here, a genotypingby-sequencing (GBS) approach was used to examine genomic variation in an early life stage (megalopae) of the Dungeness crab (Cancer magister), which constitutes the most valuable single-species commercial fishery in the CCE. Variation in abundance and timing of megalopae recruitment has been extensively studied for over two decades in Coos Bay, Oregon, United States....

Independent losses of the Hypoxia-Inducible Factor (HIF) pathway within Crustacea

Allie Graham & Felipe Barreto
Metazoans respond to hypoxic stress via the Hypoxia Inducible Factor (HIF) pathway, a mechanism thought to be extremely conserved due to its importance in monitoring cellular oxygen levels and regulating responses to hypoxia. However, recent work revealed that key members of the HIF pathway have been lost in specific lineages (a tardigrade and a copepod), suggesting alternative mechanisms have evolved but are still undescribed. Using genomic and transcriptomic data from 70 different species across 12...

A framework for mapping the distribution of seabirds by integrating tracking, demography and phenology

Ana P. B. Carneiro, Elizabeth J. Pearmain, Steffen Oppel, Thomas A. Clay, Richard A. Phillips, Anne-Sophie Bonnet-Lebrun, Ross M. Wanless, Edward Abraham, Yvan Richard, Joel Rice, Jonathan Handley, Tammy E. Davies, Ben J. Dilley, Peter G. Ryan, Cleo Small, Javier Arata, John P. Y. Arnould, Elizabeth Bell, Leandro Bugoni, Letizia Campioni, Paulo Catry, Jaimie Cleeland, Lorna Deppe, Graeme Elliott, Amanda Freeman … & Maria P. Dias
1. The identification of geographic areas where the densities of animals are highest across their annual cycles is a crucial step in conservation planning. In marine environments, however, it can be particularly difficult to map the distribution of species, and the methods used are usually biased towards adults, neglecting the distribution of other life-history stages even though they can represent a substantial proportion of the total population. 2. Here we develop a methodological framework for...

Sex identification PCR-RFLP assay tested in eight species of Sebastes rockfish

Felix Vaux, Hannah M. Aycock, Sandra Bohn, Leif K. Rasmuson & Kathleen G. O'Malley
Files for 'Sex identification PCR-RFLP assay tested in eight species of Sebastes rockfish'. Files include a sampling spreadsheet for eight species of Sebastes rockfish, and a .fasta file of DNA sequences for a male and female from each species for the Sch.182255-210250 locus.

Data from: Removal of cattle accelerates tropical dry forests succession in Northwestern Mexico

Leonel Lopez-Toledo, Abdieel Quisehuatl-Medina, Joshua Averet & Bryan Endress
Domestic livestock influence patterns of secondary succession across forest ecosystems. However, the effects of cattle on the regeneration of tropical dry forests (TDF) in Mexico are poorly understood, largely because it is difficult to locate forests that are not grazed by cattle or other livestock. We describe changes in forest composition and structure along a successional chronosequence of TDF stands with and without cattle (chronic grazing or exclusion from grazing for ~8 yr). Forest stands...

Multi-dimensional biodiversity hotspots and the future of taxonomic, ecological, and phylogenetic diversity: a case study of North American rodents

Tara Smiley, Pascal Title, Miriam Zelditch & Rebecca Terry
Aim: We investigate geographic patterns across taxonomic, ecological, and phylogenetic diversity to test for spatial (in)congruency and identify aggregate diversity hotspots in relation to present land-use and future climate. Simulating extinctions of imperiled species, we demonstrate where losses across diversity dimensions and geography are predicted. Location: North America Time period: Present-day, future Major taxa studied: Rodentia Methods: Using geographic range maps for rodent species, we quantified spatial patterns for eleven dimensions of diversity: taxonomic (species,...

Data from: Community-based wildlife management area supports similar mammal species richness and densities compared to a national park

Christian Kiffner, Seth Thomas, Talia Speaker, Victoria O’Connor, Paige Schwarz, John Kioko & Bernard Kissui
Community-based conservation models have been widely implemented across Africa to improve wildlife conservation and livelihoods of rural communities. In Tanzania, communities can set aside land and formally register it as Wildlife Management Area (WMA), which allows them to generate revenue via consumptive or non-consumptive utilization of wildlife. The key, yet often untested, assumption of this model is that economic benefits accrued from wildlife motivate sustainable management of wildlife. To test the ecological effectiveness (here defined...

Data from: Multiple innate antibacterial immune defense elements are correlated in diverse ungulate species

Brian Dugovich, Lucie Crane, Benji Alcantar, Brianna Beechler, Brian Dolan & Anna Jolles
In this study, we aimed to evaluate to what extent different assays of innate immunity reveal similar patterns of variation across ungulate species. We compared several measures of innate antibacterial immune function across seven different ungulate species using blood samples obtained from captive animals maintained in a zoological park. We measured mRNA expression of two receptors involved in innate pathogen detection, toll-like receptors 2 and 5 (TLR2 and 5), the bactericidal capacity of plasma, as...

Phylogenetic relatedness among Cladosporium leaf endophytes predicts their ability to reduce the severity of a poplar leaf rust disease

Edward Barge
More closely related organisms are expected to function more similarly than distantly related organisms due to shared ancestry and functional trait heritability. However, there have been few tests of this hypothesis for fungal leaf endophytes, which can modify host plant disease severity by a variety of mechanisms. We tested whether phylogenetic relatedness within Cladosporium, a genus including many common fungal leaf endophyte species, predicts endophyte effects on cottonwood leaf rust disease severity caused by Melampsora...

Species delimitation, classical taxonomy, and genome skimming: a review of the ground beetle genus Lionepha (Coleoptera: Carabidae)

David Maddison & John Sproul
The western North American genus Lionepha is shown to contain at least 11 species through a combination of eight-gene species delimitation analyses and morphological study. In order to confirm the names of several species, we sequence DNA of primary types of several names, including a LeConte lectotype collected in the 1850s, using next-generation sequencing. We examine chromosomes of eight species, and show that all have 12 pairs of autosomes and an X0/XX sex-chromosome system. The...

Data from: The landscape genetic signature of pollination by trapliners: evidence from the tropical herb, Heliconia tortuosa

Felipe Torres-Vanegas, Adam S. Hadley, Urs G. Kormann, F. Andrew Jones, Matthew G. Betts & Helene H. Wagner
Animal-mediated pollination is essential for the maintenance of plant reproduction, especially in tropical ecosystems, where pollination networks have been thought to have highly generalized structures. However, accumulating evidence suggests that not all floral visitors provide equally effective pollination services, potentially reducing the number of realized pollinators and increasing the cryptic specialization of pollination networks. Thus, there is a need to understand how different functional groups of pollinators influence pollination success. Here we examined whether patterns...

Data from: Deer-mediated ecosystem service vs. disservice depends on forest management intensity

Thomas D. Stokely & Matthew G. Betts
MANUSCRIPT ABSTRACT As global terrestrial biodiversity declines via land-use intensification, society has placed increasing value on non-commercial species as providers of ecosystem services. Yet, many deer species and non-crop plants are perceived negatively when they decrease crop productivity, leading to reduced economic gains and human-wildlife conflict. We hypothesized that deer provide an ecosystem service in forest plantations by controlling competition and promoting crop-tree growth, although the effects of herbivory may depend on forest management intensity....

Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands

Caitlin Wells, Philip Lavretsky, Michael Sorenson, Jeffrey Peters, Jeffrey DaCosta, Stephen Turnbull, Kimberly Uyehara, Christopher Malachowski, Bruce Dugger, John Eadie & Andrew Engilis
Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation...

Revisiting the origin of octoploid strawberry

Aaron Liston, Na Wei, Jacob Tennessen, Jumin Li, Ming Dong & Ashman Tia-Lynn
The cultivated strawberry (Fragaria ×ananassa) is an octoploid, and the identity of its four subgenomes has long been a mystery. In their recent strawberry genome publication, Edger et al. present a novel hypothesis: each subgenome originated from a different extant diploid progenitor, and the hexaploid species Fragaria moschata was a direct ancestor. We reanalyzed the four octoploid subgenomes in a phylogenomic context and our results support only two extant diploids progenitors; we also found no...

Social status, forest disturbance, and Barred Owls shape long-term trends in breeding dispersal distance of Northern Spotted Owls

Julianna Jenkins, Damon Lesmeister, Eric Forsman, Katie Dugger, Steven Ackers, L. Steven Andrews, Chris McCafferty, M. Shane Pruett, Janice Reid, Stan Sovern, Rob Horn, Scott Gremel, J. David Wiens & Zhiqiang Yang
Dispersal among breeding sites in territorial animals (i.e. breeding dispersal) is driven by numerous selection pressures, including competition and spatiotemporal variation in habitat quality. The scale and trend of dispersal movements over time may signal changing conditions within the population or on the landscape. We examined 2,158 breeding dispersal events from 694 male and 608 female individually-marked Northern Spotted Owls (Strix occidentalis caurina) monitored over 28 years on seven study areas to assess the relative...

Origin and adaptive radiation of the exceptional and threatened bembidiine beetle fauna of St Helena (Coleoptera: Carabidae)

David Maddison, John Sproul & Howard Mendel
The central peaks of the isolated island of St Helena (in the south Atlantic Ocean) are home to an extraordinary set of ground beetles of the tribe Bembidiini, and belong to three endemic genus-group taxa. These beetles are strikingly different in overall body form from the many bembidiines found elsewhere in the world. At least some of the St Helena species are likely extinct, and all are threatened by habitat destruction and invasive species. Through...

Data from: Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Felix Vaux, Leif K. Rasmuson, Lisa A. Kautzi, Polly S. Rankin, Matthew T.O. Blume, Kelly A. Lawrence, Sandra Bohn & Kathleen G. O’Malley
Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50 km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed...

Data from: Comparative knowledge, attitudes, and practices regarding anthrax, brucellosis, and rabies in three districts of northern Tanzania

Christian Kiffner, Michelle Latzer, Ruby Vise, Hayley Benson, Elizabeth Hammon & John Kioko
Background Knowledge, attitudes, and practices (KAP) surveys regarding zoonotic diseases are crucial to understanding the extent of knowledge among citizens and for guiding health-related education programs. Method Employing a structured questionnaire, we interviewed residents (n=388) in three districts of northern Tanzania (Karatu n=128, Monduli n=114, Babati n=146) to assess knowledge, attitudes and reported practices regarding three zoonotic diseases that occur in the region (anthrax, brucellosis, and rabies). We used generalized linear mixed effects models and...

Data from: Species identification and likely catch time period of whale bones from South Georgia

Angela L. Sremba, Anthony R. Martin, C. Scott Baker & C. Scott Baker
Skeletal remains of baleen whales killed during the onset of 20th century commercial whaling lie scattered across the shores and abandoned whaling stations of the subantarctic island of South Georgia. Here we report on genetic species identification of whale bones collected from South Georgia using standard historical DNA protocols. We amplified and sequenced short fragments of the mitochondrial DNA (mtDNA) control region from 281 available bone samples. Of these, 231 provided mtDNA sequences of sufficient...

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  • Oregon State University
  • University of Washington
  • University of Georgia
  • University of California System
  • United States Department of Agriculture
  • Utah State University
  • University of Auckland
  • University of Kansas
  • University of Michigan–Ann Arbor
  • University of Minnesota
  • University of Pittsburgh
  • Southwest Fisheries Science Center
  • Purdue University West Lafayette
  • University of Sydney
  • University of California, Davis