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Goldman MR, Shinderman M, Jeffress MR, Rodhouse TJ, Shoemaker KT. Integrating multiple sign types to improve occupancy estimation for inconspicuous species. Ecol Evol 2023; 13:e10019. [PMID: 37197209 PMCID: PMC10183821 DOI: 10.1002/ece3.10019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 05/19/2023] Open
Abstract
Standard occupancy models enable unbiased estimation of occupancy by accounting for observation errors such as missed detections (false negatives) and, less commonly, incorrect detections (false positives). Occupancy models are fitted to data from repeated site visits in which surveyors record evidence of species presence. Use of indirect sign (e.g., scat, tracks) as evidence of presence can vastly improve survey efficiency for inconspicuous species but can also introduce additional sources of error. We developed a "multi-sign" occupancy approach to model the detection process separately for unique sign types and used this method to improve estimates of occupancy dynamics for an inconspicuous species, the American pika (Ochotona princeps). We investigated how estimates of pika occupancy and environmental drivers differed under four increasingly realistic representations of the observation process: (1) perfect detection (commonly assumed for modeling pika occupancy), (2) standard occupancy model (single observation process without possibility of false detection), (3) multi-sign with no false detections (non-false positive model), and (4) multi-sign with false detections (full model). For the multi-sign occupancy models, we modeled the detection of each sign type (fresh scat, fresh haypiles, pika calls, and pika sightings) separately as a function of climatic and environmental covariates. Estimates of occupancy processes and inferences about environmental drivers were sensitive to different detection models. Simplified representations of the detection processes generally resulted in higher occupancy estimates and higher turnover rates than the full multi-sign model. Environmental drivers also varied in their influence on occupancy models, where (e.g.) forb cover was estimated to more strongly influence occupancy in the full multi-sign model than the simpler models. As has been reported previously in other contexts, unmodeled heterogeneity in the observation process can lead to biases in occupancy processes and uncertainty in the relationships between occupancy and environmental covariates. Overall, our multi-sign approach to dynamic occupancy modeling, which accounts for spatio-temporal variation in reliability among sign types, has strong potential to generate more realistic estimates of occupancy dynamics for inconspicuous species.
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Affiliation(s)
- Mia R. Goldman
- Department of Natural Resources and Environmental SciencesUniversity of Nevada – RenoRenoNevadaUSA
- School of BiologyUniversity of St AndrewsSt AndrewsUK
- Department of Biology and Center for Research into Environmental and Ecological ModelingUniversity of St AndrewsSt AndrewsUK
| | - Matthew Shinderman
- Department of Natural Resources and SustainabilityOregon State University‐CascadesBendOregonUSA
| | | | - Thomas J. Rodhouse
- Department of Natural Resources and SustainabilityOregon State University‐CascadesBendOregonUSA
- National Park ServiceBendOregonUSA
| | - Kevin T. Shoemaker
- Department of Natural Resources and Environmental SciencesUniversity of Nevada – RenoRenoNevadaUSA
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2
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Daniel A, Savary P, Foltête JC, Khimoun A, Faivre B, Ollivier A, Éraud C, Moal H, Vuidel G, Garnier S. Validating graph-based connectivity models with independent presence-absence and genetic data sets. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14047. [PMID: 36661070 DOI: 10.1111/cobi.14047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 05/11/2023]
Abstract
Habitat connectivity is a key objective of current conservation policies and is commonly modeled by landscape graphs (i.e., sets of habitat patches [nodes] connected by potential dispersal paths [links]). These graphs are often built based on expert opinion or species distribution models (SDMs) and therefore lack empirical validation from data more closely reflecting functional connectivity. Accordingly, we tested whether landscape graphs reflect how habitat connectivity influences gene flow, which is one of the main ecoevolutionary processes. To that purpose, we modeled the habitat network of a forest bird (plumbeous warbler [Setophaga plumbea]) on Guadeloupe with graphs based on expert opinion, Jacobs' specialization indices, and an SDM. We used genetic data (712 birds from 27 populations) to compute local genetic indices and pairwise genetic distances. Finally, we assessed the relationships between genetic distances or indices and cost distances or connectivity metrics with maximum-likelihood population-effects distance models and Spearman correlations between metrics. Overall, the landscape graphs reliably reflected the influence of connectivity on population genetic structure; validation R2 was up to 0.30 and correlation coefficients were up to 0.71. Yet, the relationship among graph ecological relevance, data requirements, and construction and analysis methods was not straightforward because the graph based on the most complex construction method (species distribution modeling) sometimes had less ecological relevance than the others. Cross-validation methods and sensitivity analyzes allowed us to make the advantages and limitations of each construction method spatially explicit. We confirmed the relevance of landscape graphs for conservation modeling but recommend a case-specific consideration of the cost-effectiveness of their construction methods. We hope the replication of independent validation approaches across species and landscapes will strengthen the ecological relevance of connectivity models.
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Affiliation(s)
- Alexandrine Daniel
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Paul Savary
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
- ThéMA, UMR 6049 CNRS, Université de Franche-Comté, Besançon, France
- ARP-Astrance, Paris, France
| | | | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Cyril Éraud
- Office Français de la Biodiversité, Chizé, France
| | | | - Gilles Vuidel
- ThéMA, UMR 6049 CNRS, Université de Franche-Comté, Besançon, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
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3
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Thompson LM, Thurman LL, Cook CN, Beever EA, Sgrò CM, Battles A, Botero CA, Gross JE, Hall KR, Hendry AP, Hoffmann AA, Hoving C, LeDee OE, Mengelt C, Nicotra AB, Niver RA, Pérez‐Jvostov F, Quiñones RM, Schuurman GW, Schwartz MK, Szymanski J, Whiteley A. Connecting research and practice to enhance the evolutionary potential of species under climate change. CONSERVATION SCIENCE AND PRACTICE 2023. [DOI: 10.1111/csp2.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Laura M. Thompson
- U.S. Geological Survey (USGS), National Climate Adaptation Science Center and the University of Tennessee Knoxville Tennessee USA
| | | | - Carly N. Cook
- School of Biological Sciences Monash University Melbourne Australia
| | - Erik A. Beever
- USGS, Northern Rocky Mountain Science Center and Montana State University Bozeman Montana USA
| | - Carla M. Sgrò
- School of Biological Sciences Monash University Melbourne Australia
| | | | | | - John E. Gross
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | | | | | | | | | - Olivia E. LeDee
- USGS, Midwest Climate Adaptation Science Center Saint Paul Minnesota USA
| | | | | | - Robyn A. Niver
- U.S. Fish and Wildlife Service (USFWS), Branch of Listing and Policy Support Bailey's Crossroads Virginia USA
| | | | - Rebecca M. Quiñones
- Massachusetts Division of Fisheries and Wildlife Westborough Massachusetts USA
| | - Gregor W. Schuurman
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | - Michael K. Schwartz
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation Missoula Montana USA
| | - Jennifer Szymanski
- USFWS, Branch of SSA Science Support, Division of Endangered Species Onalaska Wisconsin USA
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4
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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas. Heredity (Edinb) 2021; 127:443-454. [PMID: 34537819 PMCID: PMC8551249 DOI: 10.1038/s41437-021-00472-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 02/07/2023] Open
Abstract
Understanding the role of adaptation in species' responses to climate change is important for evaluating the evolutionary potential of populations and informing conservation efforts. Population genomics provides a useful approach for identifying putative signatures of selection and the underlying environmental factors or biological processes that may be involved. Here, we employed a population genomic approach within a space-for-time study design to investigate the genetic basis of local adaptation and reconstruct patterns of movement across rapidly changing environments in a thermally sensitive mammal, the American pika (Ochotona princeps). Using genotypic data at 49,074 single-nucleotide polymorphisms (SNPs), we analyzed patterns of genome-wide diversity, structure, and migration along three independent elevational transects located at the northern extent (Tweedsmuir South Provincial Park, British Columbia, Canada) and core (North Cascades National Park, Washington, USA) of the Cascades lineage. We identified 899 robust outlier SNPs within- and among-transects. Of those annotated to genes with known function, many were linked with cellular processes related to climate stress including ATP-binding, ATP citrate synthase activity, ATPase activity, hormone activity, metal ion-binding, and protein-binding. Moreover, we detected evidence for contrasting patterns of directional migration along transects across geographic regions that suggest an increased propensity for American pikas to disperse among lower elevation populations at higher latitudes where environments are generally cooler. Ultimately, our data indicate that fine-scale demographic patterns and adaptive processes may vary among populations of American pikas, providing an important context for evaluating biotic responses to climate change in this species and other alpine-adapted mammals.
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Billman PD, Beever EA, McWethy DB, Thurman LL, Wilson KC. Factors influencing distributional shifts and abundance at the range core of a climate-sensitive mammal. GLOBAL CHANGE BIOLOGY 2021; 27:4498-4515. [PMID: 34236759 DOI: 10.1111/gcb.15793] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
Species are frequently responding to contemporary climate change by shifting to higher elevations and poleward to track suitable climate space. However, depending on local conditions and species' sensitivity, the nature of these shifts can be highly variable and difficult to predict. Here, we examine how the American pika (Ochotona princeps), a philopatric, montane lagomorph, responds to climatic gradients at three spatial scales. Using mixed-effects modeling in an information-theoretic approach, we evaluated a priori model suites regarding predictors of site occupancy, relative abundance, and elevational-range retraction across 760 talus patches, nested within 64 watersheds across the Northern Rocky Mountains of North America, during 2017-2020. The top environmental predictors differed across these response metrics. Warmer temperatures in summer and winter were associated with lower occupancy, lower relative abundances, and greater elevational retraction across watersheds. Occupancy was also strongly influenced by habitat patch size, but only when combined with climate metrics such as actual evapotranspiration. Using a second analytical approach, acute heat stress and summer precipitation best explained retraction residuals (i.e., the relative extent of retraction given the original elevational range of occupancy). Despite the study domain occurring near the species' geographic-range center, where populations might have higher abundances and be at lower risk of climate-related stress, 33.9% of patches showed evidence of recent extirpations. Pika-extirpated sites averaged 1.44℃ warmer in summer than did occupied sites. Additionally, the minimum elevation of pika occupancy has retracted upslope in 69% of watersheds (mean: 281 m). Our results emphasize the nuance associated with evaluating species' range dynamics in response to climate gradients, variability, and temperature exceedances, especially in regions where species occupy gradients of conditions that may constitute multiple range edges. Furthermore, this study highlights the importance of evaluating diverse drivers across response metrics to improve the predictive accuracy of widely used, correlative models.
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Affiliation(s)
- Peter D Billman
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Erik A Beever
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT, USA
- Department of Ecology, Montana State University, Bozeman, MT, USA
| | - David B McWethy
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Lindsey L Thurman
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT, USA
- U.S. Geological Survey, Northwest Climate Adaptation Science Center, Corvallis, OR, USA
| | - Kenneth C Wilson
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
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6
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Burgess SM, Garrick RC. The effect of sampling density and study area size on landscape genetics inferences for the Mississippi slimy salamander ( Plethodon mississippi). Ecol Evol 2021; 11:6289-6304. [PMID: 34141218 PMCID: PMC8207395 DOI: 10.1002/ece3.7481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual's dispersal distance, for low-mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal-limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite-based genetic distances among individuals were divided into three datasets representing sparse sampling across a large study area, dense sampling across a small study area, or sparse sampling across the same small study area. These datasets were a proxy for gene flow (i.e., the response variable) in maximum-likelihood population effects models that assessed the nature and strength of their relationship with each of five land-use classes (i.e., potential predictor variables). Comparisons of outcomes were based on the rank order of effect, sign of effect (i.e., gene flow resistance vs. facilitation), spatial scale of effect, and functional relationship with gene flow. The best-fit model for each dataset had the same sign of effect for hardwood forests, manmade structures, and pine forests, indicating the impacts of these land-use classes on dispersal and gene flow in P. mississippi are robust to sampling scheme. Contrasting sampling densities led to a different inferred functional relationship between agricultural areas and gene flow. Study area size appeared to influence the scale of effect of manmade structures and the sign of effect of pine forests. Our findings provided evidence for an influence of sampling density, study area size, and sampling effort upon inferences. Accordingly, we recommend iterative subsampling of empirical datasets and continued investigation into the sensitivities of landscape genetic analyses using simulations.
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7
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Sullivan LL, Michalska-Smith MJ, Sperry KP, Moeller DA, Shaw AK. Consequences of ignoring dispersal variation in network models for landscape connectivity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:944-954. [PMID: 32975336 DOI: 10.1111/cobi.13640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/03/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Habitat loss and fragmentation can negatively influence population persistence and biodiversity, but the effects can be mitigated if species successfully disperse between isolated habitat patches. Network models are the primary tool for quantifying landscape connectivity, yet in practice, an overly simplistic view of species dispersal is applied. These models often ignore individual variation in dispersal ability under the assumption that all individuals move the same fixed distance with equal probability. We developed a modeling approach to address this problem. We incorporated dispersal kernels into network models to determine how individual variation in dispersal alters understanding of landscape-level connectivity and implemented our approach on a fragmented grassland landscape in Minnesota. Ignoring dispersal variation consistently overestimated a population's robustness to local extinctions and underestimated its robustness to local habitat loss. Furthermore, a simplified view of dispersal underestimated the amount of habitat substructure for small populations but overestimated habitat substructure for large populations. Our results demonstrate that considering biologically realistic dispersal alters understanding of landscape connectivity in ecological theory and conservation practice.
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Affiliation(s)
- Lauren L Sullivan
- Division of Biological Sciences, University of Missouri, Columbia, MO, U.S.A
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, U.S.A
| | - Matthew J Michalska-Smith
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, U.S.A
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, U.S.A
| | - Katie P Sperry
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, U.S.A
- Marine and Environmental Sciences, Northeastern University, Boston, MA, U.S.A
| | - David A Moeller
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, U.S.A
| | - Allison K Shaw
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, U.S.A
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8
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Whipple AL, Ray C, Wasser M, Kitchens JN, Hove AA, Varner J, Wilkening JL. Temporal vs. spatial variation in stress-associated metabolites within a population of climate-sensitive small mammals. CONSERVATION PHYSIOLOGY 2021; 9:coab024. [PMID: 34026212 PMCID: PMC8127223 DOI: 10.1093/conphys/coab024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/04/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Temporal variation in stress might signify changes in an animal's internal or external environment, while spatial variation in stress might signify variation in the quality of the habitats that individual animals experience. Habitat-induced variations in stress might be easiest to detect in highly territorial animals, and especially in species that do not take advantage of common strategies for modulating habitat-induced stress, such as migration (escape in space) or hibernation (escape in time). Spatial and temporal variation in response to potential stressors has received little study in wild animals, especially at scales appropriate for relating stress to specific habitat characteristics. Here, we use the American pika (Ochotona princeps), a territorial small mammal, to investigate stress response within and among territories. For individually territorial animals such as pikas, differences in habitat quality should lead to differences in stress exhibited by territory owners. We indexed stress using stress-associated hormone metabolites in feces collected non-invasively from pika territories every 2 weeks from June to September 2018. We hypothesized that differences in territory quality would lead to spatial differences in mean stress and that seasonal variation in physiology or the physical environment would lead to synchronous variation across territories through time. We used linear mixed-effects models to explore spatiotemporal variation in stress using fixed effects of day-of-year and broad habitat characteristics (elevation, aspect, site), as well as local variation in habitat characteristics hypothesized to affect territory quality for this saxicolous species (talus depth, clast size, available forage types). We found that temporal variation within territories was greater than spatial variation among territories, suggesting that shared seasonal stressors are more influential than differences in individual habitat quality. This approach could be used in other wildlife studies to refine our understanding of habitat quality and its effect on individual stress levels as a driver of population decline.
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Affiliation(s)
- Ashley L Whipple
- Department of Ecology and Evolutionary Biology, University of
Colorado, Boulder, CO 80309, USA
- Institute of Arctic and Alpine Research, University of
Colorado, Boulder, CO 80303, USA
| | - Chris Ray
- Department of Ecology and Evolutionary Biology, University of
Colorado, Boulder, CO 80309, USA
- Institute of Arctic and Alpine Research, University of
Colorado, Boulder, CO 80303, USA
| | - Max Wasser
- Department of Ecology and Evolutionary Biology, University of
Colorado, Boulder, CO 80309, USA
| | - James N Kitchens
- Department of Biology, Warren Wilson College,
Asheville, NC 28778, USA
| | - Alisa A Hove
- Department of Biology, Warren Wilson College,
Asheville, NC 28778, USA
| | - Johanna Varner
- Department of Biological Sciences, Colorado Mesa
University, Grand Junction, CO 81501, USA
| | - Jennifer L Wilkening
- US Fish and Wildlife Service, Southern Nevada Fish and Wildlife
Office, Las Vegas, NV 89130, USA
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9
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Abstract
The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.
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10
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Klingler KB, Jahner JP, Parchman TL, Ray C, Peacock MM. Genomic variation in the American pika: signatures of geographic isolation and implications for conservation. BMC Ecol Evol 2021; 21:2. [PMID: 33514306 PMCID: PMC7853312 DOI: 10.1186/s12862-020-01739-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/17/2020] [Indexed: 01/12/2023] Open
Abstract
Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.
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Affiliation(s)
| | - Joshua P Jahner
- Department of Biology, University of Nevada, Reno, 89557, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, 89557, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
| | - Chris Ray
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309-0334, USA
| | - Mary M Peacock
- Department of Biology, University of Nevada, Reno, 89557, USA. .,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.
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11
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Abstract
Abstract
The American pika (Ochotona princeps) is commonly perceived as a species that is at high risk of extinction due to climate change. The purpose of this review is two-fold: to evaluate the claim that climate change is threatening pikas with extinction, and to summarize the conservation status of the American pika. Most American pikas inhabit major cordilleras, such as the Rocky Mountain, Sierra Nevada, and Cascade ranges. Occupancy of potential pika habitat in these ranges is uniformly high and no discernible climate signal has been found that discriminates between the many occupied and relatively few unoccupied sites that have been recently surveyed. Pikas therefore are thriving across most of their range. The story differs in more marginal parts of the species range, primarily across the Great Basin, where a higher percentage of available habitat is unoccupied. A comprehensive review of Great Basin pikas revealed that occupied sites, sites of recent extirpation, and old sites, were regularly found within the same geographic and climatic space as extant sites, and suggested that pikas in the Great Basin tolerated a broader set of habitat and climatic conditions than previously understood. Studies of a small subset of extirpated sites in the Great Basin and in California found that climate variables (most notably measures of hot temperature) were associated more often with extirpated sites than occupied sites. Importantly, upward contraction of the lower elevation boundary also was found at some sites. However, models that incorporated variables other than climate (such as availability of upslope talus habitat) often were better predictors of site persistence. Many extirpations occurred on small habitat patches, which were subject to stochastic extinction, as informed by a long-term pika metapopulation study in Bodie, California. In addition, several sites may have been compromised by cattle grazing or other anthropogenic factors. In contrast, several low, hot sites (Bodie, Mono Craters, Craters of the Moon National Monument and Preserve, Lava Beds National Monument, Columbia River Gorge) retain active pika populations, demonstrating the adaptive capacity and resilience of pikas in response to adverse environmental conditions. Pikas cope with warm temperatures by retreating into cool interstices of their talus habitat and augment their restricted daytime foraging with nocturnal activity. Pikas exhibit significant flexibility in their foraging tactics and are highly selective in their choice of available vegetation. The trait that places pikas at greatest risk from climate change is their poor dispersal capability. Dispersal is more restricted in hotter environments, and isolated low-elevation sites that become extirpated are unlikely to be recolonized in a warming climate. The narrative that American pikas are going extinct appears to be an overreach. Pikas are doing well across most of their range, but there are limited, low-elevation losses that are likely to be permanent in what is currently marginal pika habitat. The resilience of pikas in the face of climate change, and their ability or inability to persist in marginal, hot environments, will continue to contribute to our understanding of the impact of climate change on individual species.
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Affiliation(s)
- Andrew T Smith
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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12
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Jahnke M, Moksnes PO, Olsen JL, Serra Serra N, Nilsson Jacobi M, Kuusemäe K, Corell H, Jonsson PR. Integrating genetics, biophysical, and demographic insights identifies critical sites for seagrass conservation. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02121. [PMID: 32159897 DOI: 10.1002/eap.2121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
The eelgrass Zostera marina is an important foundation species of coastal areas in the Northern Hemisphere, but is continuing to decline, despite management actions. The development of new management tools is therefore urgent in order to prioritize limited resources for protecting meadows most vulnerable to local extinctions and identifying most valuable present and historic meadows to protect and restore, respectively. We assessed 377 eelgrass meadows along the complex coastlines of two fjord regions on the Swedish west coast-one is currently healthy and the other is substantially degraded. Shoot dispersal for all meadows was assessed with Lagrangian biophysical modeling (scale: 100-1,000 m) and used for barrier analysis and clustering; a subset (n = 22) was also assessed with population genetic methods (20 microsatellites) including diversity, structure, and network connectivity. Both approaches were in very good agreement, resulting in seven subpopulation groupings or management units (MUs). The MUs correspond to a spatial scale appropriate for coastal management of "waterbodies" used in the European Water Framework Directive. Adding demographic modeling based on the genetic and biophysical data as a third approach, we are able to assess past, present, and future metapopulation dynamics to identify especially vulnerable and valuable meadows. In a further application, we show how the biophysical approach, using eigenvalue perturbation theory (EPT) and distribution records from the 1980s, can be used to identify lost meadows where restoration would best benefit the present metapopulation. The combination of methods, presented here as a toolbox, allows the assessment of different temporal and spatial scales at the same time, as well as ranking of specific meadows according to key genetic, demographic and ecological metrics. It could be applied to any species or region, and we exemplify its versatility as a management guide for eelgrass along the Swedish west coast.
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Affiliation(s)
- Marlene Jahnke
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, SE-45296, Strömstad, Sweden
| | - Per-Olav Moksnes
- Department of Marine Science, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences, Section: Ecology and Evolutionary Genomics in Nature (GREEN), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Núria Serra Serra
- Groningen Institute for Evolutionary Life Sciences, Section: Ecology and Evolutionary Genomics in Nature (GREEN), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Martin Nilsson Jacobi
- Complex Systems Group, Department of Energy and Environment, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | | | - Hanna Corell
- DHI Sverige, Svartmangatan 18, SE-111 29, Stockholm, Sweden
| | - Per R Jonsson
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, SE-45296, Strömstad, Sweden
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13
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Chubaty AM, Galpern P, Doctolero SC. The
r
toolbox
grainscape
for modelling and visualizing landscape connectivity using spatially explicit networks. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13350] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alex M. Chubaty
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Paul Galpern
- Department of Biological Sciences University of Calgary Calgary AB Canada
| | - Sam C. Doctolero
- Department of Electrical and Computer Engineering University of Calgary Calgary AB Canada
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14
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Multiscale landscape genetics of American marten at their southern range periphery. Heredity (Edinb) 2020; 124:550-561. [PMID: 31992842 PMCID: PMC7080830 DOI: 10.1038/s41437-020-0295-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 11/08/2022] Open
Abstract
American marten (Martes americana) are a conservation priority in many forested regions of North America. Populations are fragmented at the southern edge of their distribution due to suboptimal habitat conditions. Facilitating gene flow may improve population resilience through genetic and demographic rescue. We used a multiscale approach to estimate the relationship between genetic connectivity and landscape characteristics among individuals at three scales in the northeastern United States: regional, subregional, and local. We integrated multiple modeling techniques and identified top models based on consensus. Top models were used to parameterize resistance surfaces at each scale, and circuit theory was used to identify potential movement corridors. Regional gene flow was affected by forest cover, elevation, developed land cover, and slope. At subregional and local scales, the effects were site specific and included subsets of temperature, elevation, developed land cover, and slope. Developed land cover significantly affected gene flow at each scale. At finer scales, lack of variance in forest cover may have limited the ability to detect a relationship with gene flow. The effect of slope on gene flow was positive or negative, depending on the site examined. Occupancy probability was a relatively poor predictor, and we caution its use as a proxy for landscape resistance. Our results underscore the importance of replication and multiscale approaches in landscape genetics. Climate warming and landscape conversion may reduce the genetic connectivity of marten populations in the northeastern United States, and represent the primary challenges to marten conservation at the southern periphery of their range.
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15
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Differing, multiscale landscape effects on genetic diversity and differentiation in eastern chipmunks. Heredity (Edinb) 2020; 124:457-468. [PMID: 31919481 DOI: 10.1038/s41437-020-0293-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 11/08/2022] Open
Abstract
Understanding how habitat loss and fragmentation impact genetic variation is a major goal in landscape genetics, but to date, most studies have focused solely on the correlation between intervening matrix and genetic differentiation at a single spatial scale. Several caveats exist in these study designs, among them is the inability to include measures of genetic diversity in addition to differentiation. Both genetic metrics help predict population persistence, but are expected to function at differing spatial scales, which requires a multiscale investigation. In this study, we sampled two distinct spatial scales in 31 independent landscapes along a gradient of landscape context (i.e., forest amount, configuration, and types of intervening matrix) to investigate how landscape heterogeneity influences genetic diversity and differentiation in the forest-associated eastern chipmunk (Tamias striatus). Overall, quality of intervening matrix was correlated with genetic differentiation at multiple spatial scales, whereas only configuration was associated with regional scale genetic diversity. Habitat amount, in contrast, did not influence genetic differentiation or diversity at either spatial scale. Based on our findings, landscape effects on genetic variation appears to differ based on spatial scale, the type of genetic response variable, and random variation among landscapes, making extrapolation of results from single scale, unreplicated studies difficult. We encourage landscape geneticists to utilize multiscale, replicated landscapes with both genetic diversity, and differentiation to gain a more comprehensive understanding of how habitat loss and fragmentation influence genetic variation.
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16
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Emel SL, Olson DH, Knowles LL, Storfer A. Comparative landscape genetics of two endemic torrent salamander species, Rhyacotriton kezeri and R. variegatus: implications for forest management and species conservation. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01172-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Bhattacharyya S, Ishtiaq F. Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya. Ecol Evol 2019; 9:180-191. [PMID: 30680105 PMCID: PMC6342111 DOI: 10.1002/ece3.4707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 10/11/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022] Open
Abstract
Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (F IS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (F ST range = 0.04-0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus-dwelling species.
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Affiliation(s)
| | - Farah Ishtiaq
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
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18
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White ER, Smith AT. The role of spatial structure in the collapse of regional metapopulations. Ecology 2018; 99:2815-2822. [PMID: 30347111 DOI: 10.1002/ecy.2546] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/02/2018] [Indexed: 11/10/2022]
Abstract
Many wildlife populations are either naturally, or as a result of human land use, patchily distributed in space. The degree of fragmentation-specifically the remaining patch sizes and habitat configuration-is an important part of population dynamics. Demographic stochasticity is also likely to play an important role in patchy habitats that host small local populations. We develop a simulation model to evaluate the significance of demographic stochasticity and the role fragmentation plays in the determination of population dynamics and the risk of extinction of populations on habitat patches. Our model is formulated as a Markov-chain stochastic process on a finite, spatially explicit array of patches in which probability of successful dispersal is a function of interpatch distance. Unlike past work, we explicitly model local population dynamics and examine how these scale up to the entire population. As a test case, we apply the model to the American pika (Ochotona princeps) population living on the ore dumps in the ghost mining town of Bodie, California. This population has been studied nearly continuously for over four decades and has been of conservation concern as the southern half of the population declined precipitously beginning in 1989. Our model suggests that both the specific configuration of habitat and landscape heterogeneity are necessary and sufficient predictors of the eventual extinction of the southern constellation of patches. This example has important implications, as it suggests that fragmentation alone can lead to regional extinctions within metapopulations.
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Affiliation(s)
- Easton R White
- Center for Population Biology, University of California-Davis, Davis, California, 95616, USA
| | - Andrew T Smith
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287-4501, USA
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19
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Guerrero J, Byrne AW, Lavery J, Presho E, Kelly G, Courcier EA, O'Keeffe J, Fogarty U, O'Meara DB, Ensing D, McCormick C, Biek R, Skuce RA, Allen AR. The population and landscape genetics of the European badger ( Meles meles) in Ireland. Ecol Evol 2018; 8:10233-10246. [PMID: 30397461 PMCID: PMC6206220 DOI: 10.1002/ece3.4498] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/20/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023] Open
Abstract
The population genetic structure of free-ranging species is expected to reflect landscape-level effects. Quantifying the role of these factors and their relative contribution often has important implications for wildlife management. The population genetics of the European badger (Meles meles) have received considerable attention, not least because the species acts as a potential wildlife reservoir for bovine tuberculosis (bTB) in Britain and Ireland. Herein, we detail the most comprehensive population and landscape genetic study of the badger in Ireland to date-comprised of 454 Irish badger samples, genotyped at 14 microsatellite loci. Bayesian and multivariate clustering methods demonstrated continuous clinal variation across the island, with potentially distinct differentiation observed in Northern Ireland. Landscape genetic analyses identified geographic distance and elevation as the primary drivers of genetic differentiation, in keeping with badgers exhibiting high levels of philopatry. Other factors hypothesized to affect gene flow, including earth worm habitat suitability, land cover type, and the River Shannon, had little to no detectable effect. By providing a more accurate picture of badger population structure and the factors effecting it, these data can guide current efforts to manage the species in Ireland and to better understand its role in bTB.
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Affiliation(s)
- Jimena Guerrero
- Centre D'Ecologie Fonctionelle et EvolutiveCEFE‐CNRSMontpellierFrance
| | - Andrew W. Byrne
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - John Lavery
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Eleanor Presho
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Gavin Kelly
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Emily A. Courcier
- Department of Agriculture, Environment and Rural Affairs Northern Ireland (DAERA‐NI)Veterinary Epidemiology UnitBelfastUK
| | - James O'Keeffe
- Department of Agriculture Food and the Marine (DAFM)DublinIreland
| | | | - Denise B. O'Meara
- Department of Chemical and Life SciencesWaterford Institute of TechnologyWaterfordIreland
| | - Dennis Ensing
- Agriculture, Sustainable Agri‐Food Sciences DivisionAgri‐Food and Biosciences InstituteBelfastUK
| | - Carl McCormick
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Roman Biek
- Institute of Biodiversity Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Robin A. Skuce
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Adrian R. Allen
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
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20
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Identification of a contact zone and hybridization for two subspecies of the American pika (Ochotona princeps) within a single protected area. PLoS One 2018; 13:e0199032. [PMID: 29995897 PMCID: PMC6040701 DOI: 10.1371/journal.pone.0199032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/30/2018] [Indexed: 12/15/2022] Open
Abstract
Genetic variation is the basis upon which natural selection acts to yield evolutionary change. In a rapidly changing environment, increasing genetic variation should increase evolutionary potential, particularly for small, isolated populations. However, the introduction of new alleles, either through natural or human-mediated processes, may have unpredictable consequences such as outbreeding depression. In this study, we identified a contact zone and limited gene flow between historically separated genetic lineages of American pikas (Ochotona princeps), representing the northern and southern Rocky Mountain subspecies, within Rocky Mountain National Park. The limited spatial extent of gene flow observed may be the result of geographic barriers to dispersal, selection against hybrid individuals, or both. Our fine-scale population genetic analysis suggests gene flow is limited but not completely obstructed by extreme topography such as glacial valleys, as well as streams including the Colorado River. The discovery of two subspecies within this single protected area has implications for monitoring and management, particularly in the light of recent analyses suggesting that the pikas in this park are vulnerable to fragmentation and local extinction under future projected climates. Future research should focus on the fitness consequences of introgression among distinct genetic lineages in this location and elsewhere, as well as within the context of genetic rescue as a conservation and management strategy for a climate sensitive species.
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21
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Rodhouse TJ, Jeffress MR, Sherrill KR, Mohren SR, Nordensten NJ, Magnuson ML, Schwalm D, Castillo JA, Shinderman M, Epps CW. Geographical variation in the influence of habitat and climate on site occupancy turnover in American pika (
Ochotona princeps
). DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12791] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Thomas J. Rodhouse
- National Park Service Upper Columbia Basin Network Oregon State University‐Cascades Bend Oregon
| | | | | | | | | | | | - Donelle Schwalm
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon
| | - Jessica A. Castillo
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon
| | - Matthew Shinderman
- Human and Ecosystem Resilience and Sustainability Lab Oregon State University‐Cascades Bend Oregon
| | - Clinton W. Epps
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon
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22
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Waterhouse MD, Erb LP, Beever EA, Russello MA. Adaptive population divergence and directional gene flow across steep elevational gradients in a climate-sensitive mammal. Mol Ecol 2018; 27:2512-2528. [DOI: 10.1111/mec.14701] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/29/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Matthew D. Waterhouse
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
| | - Liesl P. Erb
- Departments of Biology and Environmental Studies; Warren Wilson College; Asheville North Carolina
| | - Erik A. Beever
- U.S. Geological Survey; Northern Rocky Mountain Science Center; Bozeman Montana
- Department of Ecology; Montana State University; Bozeman Montana
| | - Michael A. Russello
- Department of Biology; University of British Columbia; Kelowna British Columbia Canada
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23
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Balbi M, Ernoult A, Poli P, Madec L, Guiller A, Martin MC, Nabucet J, Beaujouan V, Petit EJ. Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum). Mol Ecol 2018; 27:1357-1370. [PMID: 29412498 DOI: 10.1111/mec.14521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/11/2022]
Abstract
Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multiscale analysis to determine how landscape composition, configuration and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side by side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analysed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavourable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results and shows how multiscale analyses provide insight into scale-dependent processes.
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Affiliation(s)
- Manon Balbi
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Aude Ernoult
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Pedro Poli
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Luc Madec
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Annie Guiller
- Edysan FRE 3498, CNRS, Université de Picardie Jules Vernes, Amiens, France
| | - Marie-Claire Martin
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Jean Nabucet
- UMR LETG, CNRS, Université de Rennes 2, Rennes Cedex, France
| | | | - Eric J Petit
- ESE, Ecology and Ecosystem Health, INRA, Rennes, France
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24
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Apparent climate-mediated loss and fragmentation of core habitat of the American pika in the Northern Sierra Nevada, California, USA. PLoS One 2017; 12:e0181834. [PMID: 28854268 PMCID: PMC5576638 DOI: 10.1371/journal.pone.0181834] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/08/2017] [Indexed: 12/03/2022] Open
Abstract
Contemporary climate change has been widely documented as the apparent cause of range contraction at the edge of many species distributions but documentation of climate change as a cause of extirpation and fragmentation of the interior of a species’ core habitat has been lacking. Here, we report the extirpation of the American pika (Ochotona princeps), a temperature-sensitive small mammal, from a 165-km2 area located within its core habitat in California’s Sierra Nevada mountains. While sites surrounding the area still maintain pikas, radiocarbon analyses of pika fecal pellets recovered within this area indicate that former patch occupancy ranges from before 1955, the beginning of the atmospheric spike in radiocarbon associated with above ground atomic bomb testing, to c. 1991. Despite an abundance of suitable rocky habitat climate warming appears to have precipitated their demise. Weather station data reveal a 1.9°C rise in local temperature and a significant decline in snowpack over the period of record, 1910–2015, pushing pika habitat into increasingly tenuous climate conditions during the period of extirpation. This is among the first accounts of an apparently climate-mediated, modern extirpation of a species from an interior portion of its geographic distribution, resulting in habitat fragmentation, and is the largest area yet reported for a modern-era pika extirpation. Our finding provides empirical support to model projections, indicating that even core areas of species habitat are vulnerable to climate change within a timeframe of decades.
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25
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Jeffress MR, Gunst KJV, Millar CI. A Surprising Discovery of American Pika Sites in the Northwestern Great Basin. WEST N AM NATURALIST 2017. [DOI: 10.3398/064.077.0213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - K. Jane Van Gunst
- Nevada Department of Wildlife, 815 E. Fourth St., Winnemucca, NV 89445
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26
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Rodhouse TJ, Hovland M, Jeffress MR. Variation in subsurface thermal characteristics of microrefuges used by range core and peripheral populations of the American pika ( Ochotona princeps). Ecol Evol 2017; 7:1514-1526. [PMID: 28261461 PMCID: PMC5330895 DOI: 10.1002/ece3.2763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 11/28/2022] Open
Abstract
Microrefuges provide microclimates decoupled from inhospitable regional climate regimes that enable range‐peripheral populations to persist and are important to cold‐adapted species in an era of accelerated climate change. However, identifying and describing the thermal characteristics of microrefuge habitats is challenging, particularly for mobile organisms in cryptic, patchy habitats. We examined variation in subsurface thermal conditions of microrefuge habitats among different rock substrate types used by the American pika (Ochotona princeps), a climate‐sensitive, rock‐dwelling Lagomorph. We compared subsurface temperatures in talus and lava substrates in pika survey sites in two US national park units; one park study area on the range periphery and the other in the range core. We deployed paired sensors to examine within‐site temperature variation. We hypothesized that subsurface temperatures within occupied sites and structurally complex substrates would be cooler in summer and warmer in winter than unoccupied and less complex sites. Although within‐site variability was high, with correlations between paired sensors as low as 47%, we found compelling evidence that pikas occupy microrefuge habitats where subsurface conditions provide more thermal stability than in unoccupied microhabitats. The percentage of days in which microhabitat temperatures were between −2.5 and 25.5°C was significantly higher in occupied sites. Interestingly, thermal conditions were substantially more stable (p < .05) in the lava substrate type identified to be preferentially used by pikas (pahoehoe vs. a'a) in a previous study. Our study and others suggest that thermal stability appears to be the defining characteristic of subsurface microrefuges used by American pikas and is a likely explanation for enigmatic population persistence at the range periphery. Our study exemplifies an integrated approach for studying complex microhabitat conditions, paired with site use surveys and contextualized with information about gene flow provided by complementary studies.
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Affiliation(s)
| | - Matthew Hovland
- Department of Fish and Wildlife University of Idaho Moscow ID USA; Present address: Department of Animal and Rangeland Sciences Oregon State University 112 Withycombe Hall Corvallis OR 97331 USA
| | - Mackenzie R Jeffress
- Department of Fish and Wildlife University of Idaho Moscow ID USA; Nevada Department of Wildlife Elko NV USA
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27
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Moyer-Horner L, Beever EA, Johnson DH, Biel M, Belt J. Predictors of Current and Longer-Term Patterns of Abundance of American Pikas (Ochotona princeps) across a Leading-Edge Protected Area. PLoS One 2016; 11:e0167051. [PMID: 27902732 PMCID: PMC5130250 DOI: 10.1371/journal.pone.0167051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/08/2016] [Indexed: 11/19/2022] Open
Abstract
American pikas (Ochotona princeps) have been heralded as indicators of montane-mammal response to contemporary climate change. Pikas no longer occupy the driest and lowest-elevation sites in numerous parts of their geographic range. Conversely, pikas have exhibited higher rates of occupancy and persistence in Rocky Mountain and Sierra Nevada montane 'mainlands'. Research and monitoring efforts on pikas across the western USA have collectively shown the nuance and complexity with which climate will often act on species in diverse topographic and climatic contexts. However, to date no studies have investigated habitat, distribution, and abundance of pikas across hundreds of sites within a remote wilderness area. Additionally, relatively little is known about whether climate acts most strongly on pikas through direct or indirect (e.g., vegetation-mediated) mechanisms. During 2007-2009, we collectively hiked >16,000 km throughout the 410,077-ha Glacier National Park, Montana, USA, in an effort to identify topographic, microrefugial, and vegetative characteristics predictive of pika abundance. We identified 411 apparently pika-suitable habitat patches with binoculars (in situ), and surveyed 314 of them for pika signs. Ranking of alternative logistic-regression models based on AICc scores revealed that short-term pika abundances were positively associated with intermediate elevations, greater cover of mosses, and taller forbs, and decreased each year, for a total decline of 68% during the three-year study; whereas longer-term abundances were associated only with static variables (longitude, elevation, gradient) and were lower on north-facing slopes. Earlier Julian date and time of day of the survey (i.e., midday vs. not) were associated with lower observed pika abundance. We recommend that wildlife monitoring account for this seasonal and diel variation when surveying pikas. Broad-scale information on status and abundance determinants of montane mammals, especially for remote protected areas, is crucial for land and wildlife-resource managers trying to anticipate mammalian responses to climate change.
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Affiliation(s)
- Lucas Moyer-Horner
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Erik A. Beever
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
- Department of Ecology, Montana State University, Bozeman, Montana, United States of America
| | - Douglas H. Johnson
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, Saint Paul, Minnesota, United States of America
- Fisheries, Wildlife, and Conservation Biology Department, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Mark Biel
- Glacier National Park, National Park Service, West Glacier, Montana, United States of America
| | - Jami Belt
- Klondike Gold Rush National Historical Park, National Park Service, Skagway, Alaska, United States of America
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Leonard PB, Duffy EB, Baldwin RF, McRae BH, Shah VB, Mohapatra TK. gflow
: software for modelling circuit theory‐based connectivity at any scale. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12689] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Paul B. Leonard
- Department of Forestry and Environmental Conservation Clemson University Clemson SC 29634 USA
| | - Edward B. Duffy
- Cyberinfrastructure Technology Integration Group Clemson University Clemson SC 29634 USA
| | - Robert F. Baldwin
- Department of Forestry and Environmental Conservation Clemson University Clemson SC 29634 USA
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