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Zimmerman SJ, Aldridge CL, O'Donnell MS, Edmunds DR, Coates PS, Prochazka BG, Fike JA, Cross TB, Fedy BC, Oyler-McCance SJ. A genetic warning system for a hierarchically structured wildlife monitoring framework. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2787. [PMID: 36482030 DOI: 10.1002/eap.2787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Michael S O'Donnell
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - David R Edmunds
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Peter S Coates
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Brian G Prochazka
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Todd B Cross
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Bradley C Fedy
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
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Cross TB, Tack JD, Naugle DE, Schwartz MK, Doherty KE, Oyler-McCance SJ, Pritchert RD, Fedy BC. The ties that bind the sagebrush biome: integrating genetic connectivity into range-wide conservation of greater sage-grouse. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220437. [PMID: 36844808 PMCID: PMC9943888 DOI: 10.1098/rsos.220437] [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: 05/03/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Conserving genetic connectivity is fundamental to species persistence, yet rarely is made actionable into spatial planning for imperilled species. Climate change and habitat degradation have added urgency to embrace connectivity into networks of protected areas. Our two-step process integrates a network model with a functional connectivity model, to identify population centres important to maintaining genetic connectivity then to delineate those pathways most likely to facilitate connectivity thereamong for the greater sage-grouse (Centrocercus urophasianus), a species of conservation concern ranging across eleven western US states and into two Canadian provinces. This replicable process yielded spatial action maps, able to be prioritized by importance to maintaining range-wide genetic connectivity. We used these maps to investigate the efficacy of 3.2 million ha designated as priority areas for conservation (PACs) to encompass functional connectivity. We discovered that PACs encompassed 41.1% of cumulative functional connectivity-twice the amount of connectivity as random-and disproportionately encompassed the highest-connectivity landscapes. Comparing spatial action maps to impedances to connectivity such as cultivation and woodland expansion allows both planning for future management and tracking outcomes from past efforts.
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Affiliation(s)
- Todd B. Cross
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Jason D. Tack
- Habitat and Population Evaluation Team, US Fish and Wildlife Service, 32 Campus Drive, Missoula, MT, USA
| | - David E. Naugle
- W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Michael K. Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | | | | | - Ronald D. Pritchert
- Habitat and Population Evaluation Team, US Fish and Wildlife Service, 3425 Miriam Avenue, Bismarck, ND, USA
| | - Bradley C. Fedy
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
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New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: A Greater Sage-grouse case study. PLoS One 2022; 17:e0274189. [PMID: 36099302 PMCID: PMC9469985 DOI: 10.1371/journal.pone.0274189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse (Centrocercus urophasianus), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species.
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O'Donnell MS, Edmunds DR, Aldridge CL, Heinrichs JA, Coates PS, Prochazka BG, Hanser SE. Designing multi‐scale hierarchical monitoring frameworks for wildlife to support management: a sage‐grouse case study. Ecosphere 2019. [DOI: 10.1002/ecs2.2872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Michael S. O'Donnell
- U.S. Geological Survey Fort Collins Science Center Fort Collins Colorado 80526 USA
| | - David R. Edmunds
- Natural Resource Ecology Laboratory Colorado State University, in cooperation with the Fort Collins Science Center, U.S. Geological Survey Fort Collins Colorado 80526 USA
| | - Cameron L. Aldridge
- Natural Resource Ecology Laboratory Department of Ecosystem Science and Sustainability Colorado State University, in cooperation with the Fort Collins Science Center, U.S. Geological Survey Fort Collins Colorado 80526 USA
| | - Julie A. Heinrichs
- Natural Resource Ecology Laboratory Colorado State University, in cooperation with the Fort Collins Science Center, U.S. Geological Survey Fort Collins Colorado 80526 USA
| | - Peter S. Coates
- U.S. Geological Survey Western Ecological Research Center Dixon California 95620 USA
| | - Brian G. Prochazka
- U.S. Geological Survey Western Ecological Research Center Dixon California 95620 USA
| | - Steve E. Hanser
- U.S. Geological Survey Ecosystems Mission Area Reston VA 20192 USA
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Row JR, Doherty KE, Cross TB, Schwartz MK, Oyler‐McCance SJ, Naugle DE, Knick ST, Fedy BC. Quantifying functional connectivity: The role of breeding habitat, abundance, and landscape features on range-wide gene flow in sage-grouse. Evol Appl 2018; 11:1305-1321. [PMID: 30151042 PMCID: PMC6099827 DOI: 10.1111/eva.12627] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/21/2018] [Indexed: 01/06/2023] Open
Abstract
Functional connectivity, quantified using landscape genetics, can inform conservation through the identification of factors linking genetic structure to landscape mechanisms. We used breeding habitat metrics, landscape attributes, and indices of grouse abundance, to compare fit between structural connectivity and genetic differentiation within five long-established Sage-Grouse Management Zones (MZ) I-V using microsatellite genotypes from 6,844 greater sage-grouse (Centrocercus urophasianus) collected across their 10.7 million-km2 range. We estimated structural connectivity using a circuit theory-based approach where we built resistance surfaces using thresholds dividing the landscape into "habitat" and "nonhabitat" and nodes were clusters of sage-grouse leks (where feather samples were collected using noninvasive techniques). As hypothesized, MZ-specific habitat metrics were the best predictors of differentiation. To our surprise, inclusion of grouse abundance-corrected indices did not greatly improve model fit in most MZs. Functional connectivity of breeding habitat was reduced when probability of lek occurrence dropped below 0.25 (MZs I, IV) and 0.5 (II), thresholds lower than those previously identified as required for the formation of breeding leks, which suggests that individuals are willing to travel through undesirable habitat. The individual MZ landscape results suggested terrain roughness and steepness shaped functional connectivity across all MZs. Across respective MZs, sagebrush availability (<10%-30%; II, IV, V), tree canopy cover (>10%; I, II, IV), and cultivation (>25%; I, II, IV, V) each reduced movement beyond their respective thresholds. Model validations confirmed variation in predictive ability across MZs with top resistance surfaces better predicting gene flow than geographic distance alone, especially in cases of low and high differentiation among lek groups. The resultant resistance maps we produced spatially depict the strength and redundancy of range-wide gene flow and can help direct conservation actions to maintain and restore functional connectivity for sage-grouse.
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Affiliation(s)
- Jeffrey R. Row
- School of Environment, Resources and SustainabilityUniversity of WaterlooWaterlooONCanada
| | | | - Todd B. Cross
- Rocky Mountain Research StationUSDA Forest ServiceNational Genomics Center for Wildlife and Fish ConservationMissoulaMTUSA
- College of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
| | - Michael K. Schwartz
- Rocky Mountain Research StationUSDA Forest ServiceNational Genomics Center for Wildlife and Fish ConservationMissoulaMTUSA
| | | | - Dave E. Naugle
- College of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
| | - Steven T. Knick
- Forest and Rangeland Ecosystem Science CenterU.S. Geological SurveyBoiseIDUSA
- Present address:
2140 White Pine Pl.BoiseID83706USA
| | - Bradley C. Fedy
- School of Environment, Resources and SustainabilityUniversity of WaterlooWaterlooONCanada
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