78 Works

Data from: How climate extremes—not means—define a species' geographic range boundary via a demographic tipping point

Heather J. Lynch, Marc Rhainds, Justin M. Calabrese, Stephen Cantrell, Chris Cosner & William F. Fagan
Species’ geographic range limits interest biologists and resource managers alike; however, scientists lack strong mechanistic understanding of the factors that set geographic range limits in the field, especially for animals. There exists a clear need for detailed case studies that link mechanisms to spatial dynamics and boundaries because such mechanisms allow us to predict whether climate change is likely to change a species’ geographic range and, if so, how abundance in marginal populations compares to...

Assessing changes in genomic divergence following a century of human mediated secondary contact among wild and captive-bred ducks

Philip Lavretsky, Nancy Rotzel McInerney, Jonathon Mohl, Joshua Brown, Helen James, Kevin McCracken & Robert Fleischer
Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used world-wide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary time scales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America, and two domestic mallard-types (i.e., known game-farm mallards and feral Khaki Campbell’s). We show...

Data from: Parallel evolution of gene classes, but not genes: evidence from Hawai’ian honeycreeper populations exposed to avian malaria

Loren Cassin-Sackett, Taylor E. Callicrate & Robert C. Fleischer
Adaptation in nature is ubiquitous, yet characterizing its genomic basis is difficult because population demographics cause correlations with non-adaptive loci. Introduction events provide opportunities to observe adaptation over known spatial and temporal scales, facilitating the identification of genes involved in adaptation. The pathogen causing avian malaria, Plasmodium relictum, was introduced to Hawai’i in the 1930s and elicited extinctions and precipitous population declines in native honeycreepers. After a sharp initial population decline, the Hawai’i ‘amakihi (Chlorodrepanis...

Data from: Detecting slow introgression of invasive alleles in an extensively restocked game bird

Ines Sanchez-Donoso, Jisca Huisman, Jorge Echegaray, Manel Puigcerver, José Domingo Rodríguez-Teijeiro, Frank Hailer & Carles Vilà
Interbreeding of two species in the wild implies introgression of alleles from one species into the other only when admixed individuals survive and successfully backcross with the parental species. Consequently, estimating the proportion of first generation hybrids in a population may not inform about the evolutionary impact of hybridization. Samples obtained over a long time span may offer a more accurate view of the spreading of introgressed alleles in a species’ gene pool. Common quail...

Data from: Measures of effective population size in sea otters reveal special considerations for wide-ranging species

Roderick B. Gagne, M. Timothy Tinker, Kyle D. Gustafson, Katherine Ralls, Larson Shawn, L. Max Tarjan, Melissa A. Miller & Holly B. Ernest
Conservation genetic techniques and considerations of the evolutionary potential of a species are increasingly being applied to species conservation. For example, effective population size (Ne) estimates are useful for determining the conservation status of species, yet accurate estimates of current Ne remain difficult to obtain. The effective population size can contribute to setting federal delisting criteria, as was done for the southern sea otter (Enhydra lutris nereis). After being hunted to near extinction during the...

Data from: Two-species occupancy modeling accounting for species misidentification and nondetection

Thierry Chambert, Evan H. Campbell Grant, David A. W. Miller, James D. Nichols, Kevin P. Mulder & Adrianne B. Brand
1.In occupancy studies, species misidentification can lead to false positive detections, which can cause severe estimator biases. Currently, all models that account for false positive errors only consider omnibus sources of false detections and are limited to single species occupancy. 2.However, false detections for a given species often occur because of the misidentification with another, closely-related species. To exploit this explicit source of false positive detection error, we develop a two-species occupancy model that accounts...

Cattle and wild vertebrate habitat use in a long-term exclosure experiment

Harry Wells
1. Cattle and other livestock graze more than a quarter of the world’s terrestrial area and are widely regarded to be drivers of global biodiversity declines. Studies often compare the effects of livestock presence/absence but, to our knowledge, no studies have tested for interactive effects between large wild herbivores and livestock at varying stocking rates on small-bodied wild vertebrates. 2. We investigated the effects of cattle stocking rates (none/moderate/high) on the diversity of wildlife 0.05-1000...

Data from: Islands within an island: repeated adaptive divergence in a single population

Kathryn M. Langin, T. Scott Sillett, W. Chris Funk, Scott A. Morrison, Michelle A. Desrosiers & Cameron K. Ghalambor
Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially-replicated patterns of phenotypic divergence within a bird species endemic to 250 km2 Santa Cruz Island, California, USA. Island scrub-jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak...

Data from: A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird

Sara Kaiser, Scott A. Taylor, Nancy Chen, Scott Sillett, Eliana R. Bondra, Michael Webster, Sara A. Kaiser & T. Scott Sillett
Single-nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations of SNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120 SNP markers from a transcriptome assembled using RNA-sequencing of a songbird with the most common...

Data from: Mitogenomes and relatedness do not predict frequency of tool-use by sea otters

Kathy Ralls, Nancy Rotzel McInerney, Roderick B. Gagne, Holly B. Ernest, M. Tim Tinker, Jessica Fujii, Jesus Maldonado & Katherine Ralls
Many ecological aspects of tool-use in sea otters are similar to those in Indo-Pacific bottlenose dolphins. Within an area, most tool-using dolphins share a single mitochondrial haplotype and are more related to each other than to the population as a whole. We asked whether sea otters in California showed similar genetic patterns by sequencing mitogenomes of 43 otters and genotyping 154 otters at 38 microsatellite loci. There were six variable sites in the mitogenome that...

Data from: The impact of even-aged and uneven-aged forest management on regional biodiversity of multiple taxa in European beech forests

Peter Schall, Martin M. Gossner, Steffi Heinrichs, Markus Fischer, Steffen Boch, Daniel Prati, Kirsten Jung, Vanessa Baumgartner, Stefan Blaser, Stefan Böhm, Francois Buscot, Rolf Daniel, Kezia Goldmann, Kirstin Kaiser, Tiemo Kahl, Markus Lange, Jörg Müller, Jörg Overmann, Swen C. Renner, Ernst-Detlef Schulze, Johannes Sikorski, Marco Tschapka, Manfred Türke, Wolfgang W. Weisser, Bernd Wemheuer … & Kristin Kaiser
For managed temperate forests, conservationists and policymakers favour fine-grained uneven-aged management over more traditional coarse-grained even-aged management, based on the assumption that within-stand habitat heterogeneity enhances biodiversity. There is, however, little empirical evidence to support this assumption. We investigated for the first time how differently grained forest management systems affect the biodiversity of multiple above- and below-ground taxa across spatial scales. We sampled 15 taxa of animals, plants, fungi and bacteria within the largest contiguous...

Data from: Drivers of site fidelity in ungulates

Thomas Morrison, Jerod Merkel, J. Grant Hopcraft, Ellen Aikens, Jeffrey Beck, Randall Boone, Alyson Courtemanch, Samantha Dwinnell, Sue Fairbanks, Brad Griffith, Arthur Middleton, Kevin Monteith, Brendan Oates, Louise Riotte-Lambert, Hall Sawyer, Kurt Smith, Jared Stabach, Kaitlyn Taylor & Matthew Kauffman
While the tendency to return to previously visited locations – termed ‘site fidelity’ – is common in animals, the cause of this behaviour is not well understood. One hypothesis is that site fidelity is shaped by an animal’s environment, such that animals living in landscapes with predictable resources have stronger site fidelity. Site fidelity may also be conditional on the success of animals’ recent visits to that location, and it may become stronger with age...

Correcting parentage relationships in the endangered California condor: Improving mean kinship estimates for conservation management

Brigid M. Moran, Steven M. Thomas, Jessica M. Judson, Asako Navarro, Heidi Davis, Lindsay Sidak-Loftis, Marisa Korody, Michael Mace, Katherine Ralls, Taylor Callicrate, Oliver A. Ryder, Leona G. Chemnick & Cynthia C. Steiner
Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. Over the past three decades, the San Diego Zoo has performed long-term genetic studies in support of the recovery program for the critically endangered California condor (Gymnogyps californianus). This work has included sex determination of hatchlings and parentage confirmation using microsatellite genotyping. This paper describes...

Data from: Body size shifts influence effects of increasing temperatures on ectotherm metabolism

Kristina Riemer, Kristina J. Anderson-Teixeira, Felisa A. Smith, David J. Harris, S.K. Morgan Ernest & S. K. Morgan Ernest
Aim: Warmer temperatures directly increase metabolic rates of ectotherms, but temperature also indirectly affects metabolic rates. Higher temperatures result in smaller body sizes and associated decreases in metabolic rates, and it remains unknown whether this indirect effect of temperature increase could mitigate the direct positive effect of temperature on metabolic rate. Here, we assess whether temperature‐induced shifts in body size are likely to offset the direct influence of temperature on metabolic rate. Location: Global. Time...

Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild

Emily Humble, Pavel Dobrynin, Helen Senn, Justin Chuven, Alan F. Scott, David W. Mohr, Olga Dudchenko, Arina D. Omer, Zane Colaric, Erez Lieberman Aiden, Shaikha Salem Al Dhaheri, David Wildt, Shireen Oliaji, Gaik Tamazian, Budhan Pukazhenthi, Rob Ogden & Klaus‐Peter Koepfli
Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar‐horned oryx (Oryx dammah) is a North African antelope that has...

Data from: Tracking dragons: stable isotopes reveal the annual cycle of a long-distance migratory insect

Michael T. Hallworth, Peter P. Marra, Kent P. McFarland, Sara Zahendra & Colin E. Studds
Insect migration is globally ubiquitous and can involve continental-scale movements and complex life-histories. Apart from select species of migratory moths and butterflies, little is known about the structure of the annual cycle for migratory insects. Using stable-hydrogen isotope analysis of 852 wing samples from eight countries spanning 140 years, combined with 21 years of citizen science data, we determined the full annual cycle of a large migratory dragonfly, the common green darner (Anax junius). We...

Common field data limitations can substantially bias sexual selection metrics

Emily Cramer, Sara Ann Kaiser, Mike S Webster & T Brandt Ryder
Sexual selection studies widely estimate several metrics, but values may be inaccurate because standard field methods for studying wild populations produce limited data (e.g., incomplete sampling, inability to observe copulations directly). We compared four selection metrics (Bateman gradient, opportunity for sexual selection, opportunity for selection, and s’max) estimated with simulated complete and simulated limited data for 15 socially monogamous songbird species with extra-pair paternity (4-54% extra-pair offspring). Inferring copulation success from offspring parentage creates non-independence...

“Chancing on a spectacle:” co-occurring animal migrations and interspecific interactions

Emily Cohen & Dara Satterfield
Migrations of diverse wildlife species often converge in space and time, with their journeys shaped by similar forces (i.e., geographic barriers and seasonal resources and conditions); we term this “co-migration.” Supporting this, recent studies have elucidated co-migrations and seasonal patterns that govern the location and timing of multiple species’ journeys. Beyond their significance as natural wonders, species with overlapping migrations may interact ecologically, with potential effects on population and community dynamics. Direct and indirect ecological...

Data from: Microfluidic PCR-based target enrichment: a case study in two rapid radiations of Commiphora (Burseraceae) from Madagascar

Morgan R. Gostel, Kiera A. Coy & Andrea Weeks
Developing effective and cost-efficient multilocus nuclear datasets for angiosperm species is a continuing challenge to the systematics community. Here we describe the development and validation of a novel set of 91 nuclear markers for PCR-based target enrichment. Using microfluidic PCR and Illumina MiSeq, we generated nuclear, subgenomic libraries for 96 species simultaneously and sequenced them for a total cost of ca. $6000 USD. Approximately half of these costs include reusable reagents (primers, barcodes, and custom...

Data from: Direct fitness benefits and kinship of social foraging groups in an Old World tropical babbler

Sara A. Kaiser, Thomas E. Martin, Juan C. Oteyza, Connor Armstad & Robert C. Fleischer
Molecular studies have revealed that social groups composed mainly of non-relatives may be widespread in group-living vertebrates, but the benefits favoring such sociality are not well understood. In the Old World, birds often form conspecific foraging groups that are maintained year-round and offspring usually disperse to other social groups. We tested the hypothesis that non-breeding group members are largely unrelated and gain direct fitness benefits through breeding opportunities (males) and brood parasitism (females) in the...

Data from: Offspring growth and mobility in response to variation in parental care: a comparison between populations

Helen R. Sofaer, T. Scott Sillett, Jongmin Yoon, Michael L. Power, Scott A. Morrison & Cameron K. Ghalambor
Life history theory emphasizes the importance of trade-offs in how time and energy are allocated to the competing demands of growth, fecundity, and survival. However, avian studies have historically emphasized the importance of resource acquisition over resource allocation to explain geographic variation in fecundity, parental care, and offspring development. We compared the brood sizes and nestling mass and feather growth trajectories between orange-crowned warblers (Oreothlypis celata) breeding in Alaska versus California, and used 24-hour video...

Data from: Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population

Helen R. Sofaer, T Sillett, Kathryn M. Langin, Scott A. Morrison, Cameron K. Ghalambor & T. Scott Sillett
Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number...

Data from: Arboreal camera trapping: taking a proven method to new heights

Tremaine Gregory, Farah Carrasco Rueda, Jessica Deichmann, Joseph Kolowski & Alfonso Alonso
1. Although camera trapping has been shown to be a highly effective non-invasive tool for wildlife monitoring, the technique has not yet been widely applied to studies of arboreal species. Despite the unique challenges that camera trapping in the canopy poses, its versatility and relatively non-invasive nature, combined with recent technological improvements on the cameras themselves, make camera trapping a highly useful tool for arboreal research. 2. We present data on the methodology and effectiveness...

Data from: Serum amyloid A protein concentration in blood is influenced by genetic differences in the cheetah (Acinonyx jubatus)

Ashley D. Franklin, Anne Schmidt-Küntzel, Karen A. Terio, Laurie L. Marker & Adrienne E. Crosier
Systemic amyloid A (AA) amyloidosis is a major cause of morbidity and mortality among captive cheetahs. The self-aggregating AA protein responsible for this disease is a byproduct of serum amyloid A (SAA) protein degradation. Transcriptional induction of the SAA1 gene is dependent on both C/EBPβ and NF-κB cis-acting elements within the promoter region. In cheetahs, 2 alleles exist for a single guanine nucleotide deletion in the putative NF-κB binding site. In this study, a novel...

Data from: The large-scale drivers of population declines in a long-distance migratory shorebird

Nicholas J. Murray, Peter P. Marra, Richard A. Fuller, Robert S. Clemens, Kiran Dhanjal-Adams, Ken B. Gosbell, Chris J. Hassell, Takuya Iwamura, David Melville, Clive D. T. Minton, Adrian C. Riegen, Danny I. Rogers, Eric J. Woehler & Colin E. Studds
Migratory species can travel tens of thousands of kilometers each year, spending different parts of their annual cycle in geographically distinct locations. Understanding the drivers of population change is vital for conserving migratory species, yet the challenge of collecting data over entire geographic ranges has hindered attempts to identify the processes leading to observed population changes. Here, we use remotely sensed environmental data and count data to investigate the factors driving variability in abundance in...

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