125 Works

Data from: Neither philopatric nor panmictic: microsatellite and mtDNA evidence suggests lack of natal homing but limits to dispersal in Pacific lamprey

Erin K. Spice, Damon H. Goodman, Stewart B. Reid & Margaret F. Docker
Most species with lengthy migrations display some degree of natal homing; some (e.g., migratory birds and anadromous salmonids) show spectacular feats of homing. However, studies of the sea lamprey (Petromyzon marinus) indicate that this anadromous species locates spawning habitat based on pheromonal cues from larvae rather than through philopatry. Previous genetic studies in the anadromous Pacific lamprey (Entosphenus tridentatus) have both supported and rejected the hypothesis of natal homing. To resolve this, we used nine...

Data from: Genetic structure and the history of chub in the Alvord Basin

Christian T. Smith, Jennifer Von Bargen, Patrick W. DeHaan, Paul Scheerer & Michael H. Meeuwig
Knowledge of the distribution of genetic resources within and among taxa is prerequisite for development of management strategies which facilitate conservation of those resources. We used restriction-site associated DNA (RAD) sequencing to survey genetic variation in Alvord Chub and Borax Lake Chub from the Alvord Basin in southeastern Oregon and northern Nevada, USA. Our specific goals were to gain an understanding of the population genetic structure of Alvord Chub and the relationship between this species...

Data from: Quantifying the importance of geographic replication and representativeness when estimating demographic rates, using a coastal species as a case study

Christopher R. Field, Katharine J. Ruskin, Bri Benvenuti, Alyssa C. Borowske, Jonathan B. Cohen, Laura Garey, Thomas P. Hodgman, Rebecca A. Kern, Erin King, Alison R. Kocek, Adrienne I. Kovach, Kathleen M. O'Brien, Brian J. Olsen, Nancy Pau, Samuel G. Roberts, Emma Shelly, W. Gregory Shriver, Jennifer Walsh, Chris S. Elphick & Rebecca A. Longenecker
Demographic rates are rarely estimated over an entire species range, limiting empirical tests of ecological patterns and theories, and raising questions about the representativeness of studies that use data from a small part of a range. The uncertainty that results from using demographic rates from just a few sites is especially pervasive in population projections, which are critical for a wide range of questions in ecology and conservation. We developed a simple simulation to quantify...

Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation

Christopher H. Martin, Sebastian Hohna, Jacob E. Crawford, Bruce J. Turner, Emilie J. Richards & Lee H. Simons
Our recent estimation of the divergence time and isolation of Death Valley pupfishes, including the iconic Devil’s Hole pupfish (DHP), rewrote widespread assumptions about this group. These species were previously assumed to be relic populations isolated over millions of years; our genomic analyses indicated recent colonization of Devil’s Hole within the past 105–830 years and frequent gene flow among Death Valley populations [1]. These results understandably attracted substantial attention given the iconic battle for conservation...

Data from: Integrating encounter theory with decision analysis to evaluate collision risk and determine optimal protection zones for wildlife

Bradley J. Udell, Julien Martin, , Mathieu Bonneau, Holly Edwards, Timothy A. Gowan, Stacie K. Hardy, Eliezer Gurarie, Charles Calleson, Charles J. Deutsch, Robert J. Fletcher & Charles S. Calleson
1. Better understanding human-wildlife interactions and their links with management can help improve the design of wildlife protection zones. One important example is the problem of wildlife collisions with vehicles or human-built structures (e.g. power lines, wind farms). In fact, collisions between marine wildlife and watercraft are among the major threats faced by several endangered species of marine mammals. Natural resource managers are therefore interested in finding cost-effective solutions to mitigate these threats. 2. We...

Data from: Rarity does not limit genetic variation or preclude subpopulation structure in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis

Joshua G. Harrison, Matthew L. Forister, Stephanie R. Mcknight, Erin Nordin & Thomas L. Parchman
Premise of the study: Characteristics of rare taxa include small population sizes and limited geographical ranges. The genetic consequences of rarity are poorly understood for most taxa. A small geographical range could result in reduced opportunity for isolation by distance or environment, thereby limiting genetic structure and variation, but few studies explore genetic structure at small spatial scales with sufficient resolution to test this hypothesis. Moreover, few comparative genetic studies exist among infrataxa differing in...

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...

Dunlin subspecies exhibit regional segregation and high site fidelity along the East Asian−Australasian Flyway

Benjamin Lagassé, Richard Lanctot, Mark Barter, Stephen Brown, Chung-Yu Chiang, Chi-Yeung Choi, Yuri Gerasimov, Steve Kendall, Joseph Liebezeit, Konstantin Maslovsky, Alexander Matsyna, Ekaterina Matsyna, David Payer, Sarah Saalfeld, Yoshimitsu Shigeta, Ivan Tiunov, Pavel Tomkovich, Olga Valchuk & Michael Wunder
The degree that individuals migrate among particular breeding, migration, and wintering sites can have important implications for prioritizing conservation efforts. Four subspecies of Dunlin (Calidris alpina) migrate along the East Asian−Australasian Flyway (EAAF). Each subspecies has a distinct and well-defined breeding range, but their migration and winter ranges are poorly defined or unknown. We assessed the migratory connectivity of 3 of these subspecies by evaluating a dataset that encompasses 57 years (1960–2017), and comprises more...

Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular giant, Consolea (Opuntioideae)

Lucas Majure, Duniel Barrios, Edgardo Díaz, Bethany Zumwalde, Weston Testo & Vivian Negrón-Ortíz
Premise: The Caribbean islands are renowned for their small size but high species diversity, and cacti make up a fascinating component of seasonally dry tropical forest (SDTF) there. Consolea consist of nine species of dioecious, hummingbird pollinated trees endemic to the West Indies, which form a conspicuous element of the SDTF. Several species are threatened by anthropogenic disturbance, disease, sea-level rise and invasive species, and are of conservation concern. However, no comprehensive phylogeny yet exists...

Habitat openness and edge avoidance predict saltmarsh sparrow abundance better than habitat area

Hallie Marshall, Erik Blomberg, Valerie Watson, Meaghan Conway, Jonathan Cohen, Maureen Correll, Chris Elphick, Thomas Hodgman, Alison Kocek, Adrienne Kovach, W. Gregory Shriver, Whitney Wiest & Brian Olsen
The Saltmarsh Sparrow (Ammospiza caudacuta) is a tidal marsh bird facing rapid population decline throughout its range, largely caused by degradation and loss of breeding habitat. Thus there is a need to preserve tidal marshes in the northeastern United States, but to do so requires an understanding of the habitat features that support robust populations. Previous studies have shown Saltmarsh Sparrow abundance increases with marsh size, but in similar bird species, area sensitivity is more...

Data from: Effects of arthropod inquilines on growth and reproductive effort among metacommunities of the purple pitcher plant (Sarracenia purpurea var. montana)

Rebecca Hale, Elise Powell, Leila Beikmohamadi & Mara Alexander
Many plant species harbor communities of symbionts that release nutrients used by their host plants. However, the importance of these nutrients to plant growth and reproductive effort is not well understood. Here, we evaluate the relationship between the communities that colonize pitcher plant phytotelmata and the pitcher plants’ vegetative growth and flower production to better understand the symbiotic role played by phytotelma communities. We focus on the mountain variety purple pitcher plant (Sarracenia purpurea var....

Data from: Intrapopulation differences in polar bear movement and step selection patterns

Ryan Wilson, Michelle St Martin, Eric Regehr & Karyn Rode
Background: The spatial ecology of individuals often varies within a population or species. Identifying how individuals in different classes interact with their environment can lead to a better understanding of population responses to human activities and environmental change and improve population estimates. Most inferences about polar bear (Ursus maritimus) spatial ecology are based on data from adult females due to morphological constraints on applying satellite radio collars to other classes of bears. Recent studies, however,...

Evaluation of the Impacts of Radio-Marking Devices on Feral Horses and Burros in a Captive Setting

Kathryn A. Schoenecker, Sarah R. B. King & Gail H. Collins
Radio-collars and other radio-marking devices have been invaluable tools for wildlife managers for >40 years. These marking devices have improved our understanding of wildlife spatial ecology and demographic parameters and provided new data facilitating model development for species conservation and management. Although these tools have been used on virtually all North American ungulates, their deployment on feral horses (Equus ferus caballus) or burros (E. asinus) has been limited. To determine if radio-collars and radio-tags could...

Project Report NOAA Ship Hi‘ialakai, Project HA-15-01, Leg 1

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PIFSC project report ; Project HA-15-01

Data from: Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird

Charles B. Van Rees, J. Michael Reed, Robert E. Wilson, Jared G. Underwood & Sarah A. Sonsthagen
Anthropogenic alterations to landscape structure and composition can have significant impacts on biodiversity, potentially leading to species extinctions. Population-level impacts of landscape change are mediated by animal behaviors, in particular dispersal behavior. Little is known about the dispersal habits of rails (Rallidae) due to their cryptic behavior and tendency to occupy densely vegetated habitats. The effects of landscape structure on the movement behavior of waterbirds in general are poorly studied due to their reputation for...

Data from: A comparison of pedigree- and genetic-based measures for identifying inbreeding depression in the critically endangered Attwater’s Prairie-chicken

Susan C. Hammerly, Michael E. Morrow & Jeff A. Johnson
The primary goal of captive breeding programs for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study both pedigree-...

Data from: Demographic and spatiotemporal patterns of avian influenza infection at the continental scale, and in relation to annual life cycle of a migratory host

Rodolfo Nallar, Zsuzsanna Papp, Tasha Epp, Frederick A. Leighton, Seth R. Swafford, Thomas J. DeLiberto, Robert J. Dusek, Hon S. Ip, Jeffrey Hall, Johannes Berhane, Samantha E. J. Gibbs, Catherine Soos & Yohannes Berhane
Since the spread of highly pathogenic avian influenza (HPAI) H5N1 in the eastern hemisphere, numerous surveillance programs and studies have been undertaken to detect the occurrence, distribution, or spread of avian influenza viruses (AIV) in wild bird populations worldwide. To identify demographic determinants and spatiotemporal patterns of AIV infection in long distance migratory waterfowl in North America, we fitted generalized linear models with binominal distribution to analyze results from 13,574 blue-winged teal (Anas discors, BWTE)...

Plasma metabolite indices are robust to extrinsic variation and useful indicators of foraging habitat quality in Lesser Scaup (Aythya affinis)

Eric Smith, Michael Anteau, Heath Hagy & Christopher Jacques
This dataset contains plasma lipid metabolite values collected from Lesser Scaup (Aythya affinis) during spring migration (March 2016 and 2017) as described in the paper "Smith, E.J., M.J. Anteau, H. M. Hagy and C.N. Jacques (2021). Plasma metabolite indices are robust to extrinsic variation and useful indicators of foraging habitat quality in Lesser Scaup (Aythya affinis). Ornithology. In press." The experiment investigates the use of plasma metabolites beta-hydroxybutyrate (BOHB) and triglyceride (TRIG) as predictors of...

Supplementary materials: Monitoring recovery of overgrazed lichen communities on Hagemeister Island, southwestern Alaska

Patrick Walsh & Trevor Goward
Understanding the recovery rate of overgrazed lichen communities has value to mangers of lands in northern regions. We describe lichen community composition and present recovery rate measurements for a 12-year period following overgrazing by reindeer (Rangifer tarandus) on Hagemeister Island, Alaska. Reindeer were removed from the island in 1993 following overgrazing and average total lichen biomass increased from 504.2 kg/ha (SD 205.4) in 2003 to 795.3 (SD 489.6) in 2015. We estimate time to recovery...

Lesser Yellowlegs location data describing the occurrence of birds within harvest zones in the Caribbean and South America

Laura A. McDuffie, Katherine S. Christie, Autumn-Lynn Harrison, Audrey R. Taylor, Brad A. Andres, Benoit Laliberte & James A. Johnson
Shorebirds have experienced a precipitous reduction in abundance over the past four decades. While some threats to shorebirds are widespread (e.g. habitat alteration), others are regional and may affect specific populations. Lesser Yellowlegs (Tringa flavipes) are long-distance migrants that breed across the North American boreal biome and have declined in abundance by 60-80% since the 1970s. The documented harvest of Lesser Yellowlegs in the Caribbean and northeastern South America during southward migration is a possible...

Genetic variation in sea otters (Enhydra lutris) from the North Pacific with relevance to the threatened Southwest Alaska distinct population segment

Blair Flannery, Ora Russ, Michelle St. Martin, William Beatty, Kristin Worman, Joel Garlich-Miller, Varena Gill, Patrick Lemons, Daniel Monson, Kimberly Kloecker, Daniel Esler & John Wenburg
For the sea otter (Enhydra lutris), genetic population structure is an area of research that has not received significant attention, especially in Southwest Alaska where that distinct population segment has been listed as threatened since 2005 pursuant to the U.S. Endangered Species Act. In this study, 501 samples from 14 locations from Prince William Sound, Alaska to the Commander Islands in Russia were analyzed for variation at 13 microsatellite loci. Our results indicate a high...

Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium

Jesse Conklin, Yvonne Verkuil, Phil Battley, Chris Hassell, Job Ten Horn, James Johnson, Pavel Tomkovich, Allan Baker, Theunis Piersma & Michaël Fontaine
Present-day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, Calidris canutus, is an arctic-breeding, long-distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual-cycle phenology, in a global distribution thought to have arisen just since the Last Glacial Maximum (LGM). We used nextRAD sequencing of 10,881 single-nucleotide...

Data from: Using citizen-science observations to understand long-term trends in common and Pacific loon populations in urbanized Southcentral Alaska

Laura A. McDuffie, Julie C. Hagelin, Marian L. Snively, Grey W. Pendleton & Audrey R. Taylor
For over 30 years, the Alaska Loon Watch (1985−1999) and the Alaska Loon and Grebe Watch (2000−2015) engaged citizen scientist participants to record over 10,000 observations of common Gavia immer and Pacific loons Gavia pacifia at 346 lakes in five sub-regions of Southcentral Alaska. We used generalized linear mixed models to estimate long-term trends in adult loon counts and chick survival and examined environmental variables associated with loon abundance. Adult common loon counts increased in...

Data from: Diabolical survival in Death Valley: recent pupfish colonization, gene flow, and genetic assimilation in the smallest species range on earth

Christopher Martin, Jacob Crawford, Bruce Turner, Lee Simons, Jacob E. Crawford & Christopher H. Martin
One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 U.S. Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of...

Data from: A generalizable energetics-based model of avian migration to facilitate continental-scale waterbird conservation

Eric V. Lonsdorf, Wayne E. Thogmartin, Sarah Jacobi, Kevin Aagaard, Jorge Coppen, Amélie Davis, Timothy Fox, Patricia Heglund, Rex Johnson, Malcolm T. Jones, Kevin Kenow, James E. Lyons, Kirsten Luke, Shannon Still & Brian Tavernia
Conserving migratory birds is made especially difficult because of movement among spatially disparate locations across the annual cycle. In light of challenges presented by the scale and ecology of migratory birds, successful conservation requires integrating objectives, management, and monitoring across scales, from local management units to ecoregional and flyway administrative boundaries. We present an integrated approach using a spatially explicit energetic-based mechanistic bird migration model useful to conservation decision-making across disparate scales and locations. This...

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