Landscape-level analysis of mountain goat population connectivity in Washington and southern British Columbia
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  • 作者:Leslie C. Parks ; David O. Wallin ; Samuel A. Cushman ; Brad H. McRae
  • 关键词:Population connectivity ; geneland ; Circuit theory ; Causal modeling ; Oreamnos americanus
  • 刊名:Conservation Genetics
  • 出版年:2015
  • 出版时间:October 2015
  • 年:2015
  • 卷:16
  • 期:5
  • 页码:1195-1207
  • 全文大小:3,363 KB
  • 参考文献:Amos J, Bennet AF, Mac Nally R, Newell G, Radford JQ, Pavlova A, Thompson J, White M, Sunnucks P (2012) Predicting landscape genetic consequences of habitat loss, fragmentation and mobility for species of woodland birds. PLoS One 7:1鈥?2
    Balkenhol N, Waits LP, Dezzani RJ (2009) Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography 32:818鈥?30CrossRef
    Balkenhol N, Pardini R, Cornelius C, Fernandes F, Sommer S (2013) Landscape-level comparison of genetic diversity and differentiation in a small mammal inhabiting different fragmented landscapes of the Brazilian Atlantic Forest. Conserv Genet 14:355鈥?67CrossRef
    Beier P, Spencer W, Baldwin RF, McRae BH (2011) Toward best practices for developing regional connectivity maps. Conserv Biol 25:879鈥?92CrossRef PubMed
    Blair C, Weigel DE, Balazik M, Keeley ATH, Walker FM, Landguth E, Cushman S, Murhpy M, Waits L, Balkenhol N (2012) A simulation-based evaluation of methods for inferring linear barriers to gene flow. Mol Ecol Resour 12:822鈥?33CrossRef PubMed
    Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455鈥?57CrossRef PubMed
    Butchart SHM, Walpole M, Collen B, van Strien A, Scharlemann JPW, Almond REA, Baillie JEM, Bomhard B, Brown C, Bruno J, Carpenter KE, Carr GM, Chanson J, Chenery AM, Csirke J, Davidson NC, Dentener F, Foster M, Galli A, Galloway JN, Genovesi P, Gregory RD, Hockings M, Kapos V, Lamarque JF, Leverington F, Loh J, McGeoch MA, McRae L, Minasyan A, Morcillo MH, Oldfield TEE, Pauly D, Quader S, Revenga C, Sauer JR, Skolnik B, Spear D, Stanwell-Smith D, Stuart SN, Symes A, Tierney M, Tyrrell TD, Vie JC, Watson R (2010) Global biodiversity: indicators of recent declines. Science 328:1164鈥?168CrossRef PubMed
    Castillo JA, Epps CW, Davis AR, Cushman SA (2014) Landscape effects on gene flow for a climate-sensitive montane species, the American pika. Mol Ecol 23:843鈥?56CrossRef PubMed
    Crnokrak P, Roff DA (1999) Inbreeding depression in the wild. Heredity 83:260鈥?70CrossRef PubMed
    Crooks KR, Sanjayan MA (2006) Connectivity conservation. Cambridge University Press, CambridgeCrossRef
    Cushman SA, Landguth EL (2010) Spurious correlations and inference in landscape genetics. Mol Ecol 19:3592鈥?602CrossRef PubMed
    Cushman SA, McKelvey KS, Hayden J, Schwartz MK (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am Nat 168:486鈥?99CrossRef PubMed
    Cushman SA, Raphael MG, Ruggiero LF, Shirk AJ, Wasserman TN, O鈥橠oherty EC (2011) Limiting factors and landscape connectivity: the American marten in the Rocky Mountains. Landsc Ecol 26:1137鈥?149CrossRef
    Cushman SA, Landguth EL, Shirk AJ (2012) Separating the effects of habitat area, fragmentation and matrix resistance on genetic differentiation in complex landscapes. Landsc Ecol 27:369鈥?80CrossRef
    Cushman SA, Shirk AJ, Landguth EL (2013a) Landscape genetics and limiting factors. Conserv Genet 14:263鈥?74CrossRef
    Cushman SA, Wasserman TN, Landguth EL, Shirk AJ (2013b) Re-evaluating causal modeling ith Mantel tests in landscape genetics. Diversity 5:51鈥?2CrossRef
    Dunn SJ, Clancey E, Waits LP, Byers J (2011) Inbreeding depression in pronghorn (Antilocapra americana) fawns. Mol Ecol 20:4889鈥?898CrossRef PubMed
    Etherington TR (2011) Python based GIS tools for landscape genetics: visualizing genetic relatedness and measuring landscape connectivity. Methods Ecol Evol 2:52鈥?5CrossRef
    Festa-Bianchet M, C么t茅 S (2008) Mountain goats: ecology, behavior, and conservation of an alpine ungulate. Island Press, Washington DC
    Fischer J, Lindenmayer DB (2007) Landscape modification and habitat fragmentation: a synthesis. Glob Ecol Biogeogr 16:265鈥?80CrossRef
    Galbreath K, Hafner D, Zamudio K (2009) When cold is better: climate-driven elevation shifts yield complex patterns of diversification and demography in an alpine specialist (American pika, Ochotona princeps). Evolution 63:2848鈥?863CrossRef PubMed
    Goslee SC, Urban DL (2007) The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 22:1鈥?9
    Graves TA, Beier P, Royle JA (2013) Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal. Mol Ecol 22:3888鈥?903CrossRef PubMed
    Guillot G, Rousset F (2011) On the use of the simple and partial Mantel tests in presence of spatial autocorrelation. Mol Ecol. doi:10.鈥?111/鈥媘ec.鈥?2172.鈥媋rXiv:鈥?112.鈥?651v1
    Guillot G, Rousset F (2013) Dismantling the Mantel tests. Methods Ecol Evol 4:336鈥?44CrossRef
    Guillot G, Estoup A, Mortier F, Cosson JF (2005) A spatial statistical model for landscape genetics. Genetics 170:1261鈥?280CrossRef PubMed Central PubMed
    Hampe A, Petit RJ (2005) Conserving biodiversity under climate change: the rear edge matters. Ecol Lett 8:461鈥?67CrossRef PubMed
    Heller NE, Zavaleta ES (2009) Biodiversity management in the face of climate change: a review of 22聽years of recommendations. Biol Conserv 142:14鈥?2CrossRef
    Holderegger R, Wagner H (2008) Landscape genetics. Bioscience 58:199鈥?07CrossRef
    Houston DB, Schreiner EG, Moorhead BB (1994) Mountain goats in Olympic National Park: biology and management of an introduced species. USDI National Park Service Scientific Monograph, Denver
    Jaqui茅ry J, Broquet T, Hirzel AH, Yearsley J, Perrin N (2011) Inferring landscape effects on dispersal from genetic distances: how far can we go? Mol Ecol 20:692鈥?05CrossRef PubMed
    Keller L, Waller D (2002) Inbreeding effects in wild populations. Trends Ecol Evol 17:230鈥?41CrossRef
    Keyghobadi N (2007) The genetic implications of habitat fragmentation for animals. Can J Zool 85:1049鈥?064CrossRef
    Krosby M, Tewksbury J, Haddad NM, Hoekstra J (2010) Ecological connectivity for a changing climate. Conserv Biol 24:1686鈥?689CrossRef PubMed
    Lande R (1995) Mutation and conservation. Conserv Biol 9:782鈥?91CrossRef
    Lande R (1998) Risk of population extinction from fixation of deleterious and reverse mutations. Genetica 103:21鈥?7CrossRef
    Legendre P, Fortin M (2010) Comparison of the Mantel test and alternative approaches or detecting complex multivariate relationships in the spatial analysis of genetic data. Mol Ecol Resour 10:831鈥?44CrossRef PubMed
    Legendre P, Legendre L (1998) Numerical ecology, 2nd edn. Elsevier, Amsterdam
    Lynch M, Conery J, Burger R (1995) Mutation accumulation and the extinction of small populations. Am Nat 146:489鈥?18CrossRef
    Mainguy J, C么t茅 SD, Coltman DW (2009) Multilocus heterozygosity, parental relatedness and individual fitness components in a wild mountain goat Oreamnos americanus population. Mol Ecol 18:2297鈥?306CrossRef PubMed
    Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189鈥?97CrossRef
    Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209鈥?20PubMed
    McRae BH (2006) Isolation by resistance. Evolution 60:1551鈥?561CrossRef PubMed
    McRae BH, Beier P (2007) Circuit theory predicts gene flow in plant and animal populations. Proc Natl Acad Sci USA 104:19885鈥?9890CrossRef PubMed Central PubMed
    McRae BH, Shah VB (2009) Circuitscape user guide. The University of California, Santa Barbara. http://鈥媤ww.鈥媍ircuitscape.鈥媜rg . Accessed 12 Sep 2011
    Meirmans PG (2012) The trouble with isolation by distance. Molecular Ecol 21:2839鈥?846CrossRef
    Ortega J, Yannic G, Shafer ABA, Mainguy J, Festa-Bianchet M, Coltman DW, C么t茅 SD (2011) Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population. Mol Ecol 20:1601鈥?611CrossRef
    Parks LC (2013) Mountain goat genetic diversity and population connectivity in Washington and southern British Columbia. Thesis, Western Washington University
    Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2:2074鈥?093CrossRef
    Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288鈥?95CrossRef
    Poole KG, Reynolds DM (2010) Mt. Meager mountain goat aerial survey and DNA census, 2009. British Columbia Conservation Foundation. http://鈥媤ww.鈥媏nv.鈥媑ov.鈥媌c.鈥媍a/鈥媤ildlife/鈥媤si/鈥媟eports/鈥?668_鈥媁SI_鈥?668_鈥婻PT_鈥?009.鈥婸DF . Accessed 14 Apr 2012
    Pritchard JK, Stehpens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945鈥?59PubMed Central PubMed
    Raufaste N, Rousset F (2001) Are partial Mantel tests inadequate? Evolution 55:1703鈥?705CrossRef PubMed
    Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248鈥?49
    Rice C, Gay D (2010) Effects of mountain goat harvest on historic and contemporary populations. Northwestern Nat 91:40鈥?7CrossRef
    Root TL, Price JT, Hall KR, Schneider SH, Rosenzweig C, Pounds JA (2003) Fingerprints of global warming on wild animals and plants. Nature 421:57鈥?0CrossRef PubMed
    Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219鈥?228PubMed Central PubMed
    Rousset F (2000) Genetic differentiation between individuals. J Evol Biol 13:58鈥?2CrossRef
    Rousset F (2008) genepop 鈥?07: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103鈥?06CrossRef PubMed
    Rutledge LY, Holloway JJ, Patterson BR, White BN (2009) An improved field method to obtain DNA for individual identification from wolf scat. J Wildl Manag 8:1430鈥?435CrossRef
    Segelbacher G, Cushman SA, Epperson BK, Fortin M, Francois O, Hardy OJ, Holderegger R, Taberlet P, Waits LP, Manel S (2010) Applications of landscape genetics in conservation biology: concepts and challenges. Conserv Genet 11:375鈥?85CrossRef
    Seutin G, White BN, Boag PT (1991) Preservation of avian blood and tissue samples for DNA analysis. Can J Zool 69:82鈥?0CrossRef
    Sexton JP, Strauss SY, Rice KJ (2011) Gene flow increases fitness at the warm edge of a species鈥?range. Proc Natl Acad Sci USA 108:11704鈥?1709CrossRef PubMed Central PubMed
    Shafer ABA, C么t茅 SD, Coltman DW (2011) Hot spots of genetic diversity descended from multiple Pleistocene refugia in an alpine ungulate. Evolution 65:125鈥?38CrossRef PubMed
    Shafer ABA, Northrup JM, White KS, Boyce MS, C么t茅 SD, Coltman DW (2012) Habitat selection predicts genetic relatedness in an alpine ungulate. Ecology 93:1317鈥?329CrossRef PubMed
    Shirk AJ (2009) Mountain goat genetic structure, molecular diversity, and gene flow in the Cascade Range, Washington. Thesis, Western Washington University
    Shirk AJ, Cushman SA (2011) sGD: software for estimating spatially explicit indices of genetic diversity. Mol Ecol Resour 11:922鈥?34CrossRef PubMed
    Shirk AJ, Wallin DO, Cushman SA, Rice CG, Warheit KI (2010) Inferring landscape effects on gene flow: a new model selection framework. Mol Ecol 19:3603鈥?619CrossRef PubMed
    Shirk AJ, Cushman SA, Landguth EL (2012) Simulating pattern-process relationships to validate landscape genetic models. Int J Ecol 2012:1鈥?CrossRef
    Short Bull RA, Cushman SA, Mace R, Chilton T, Kendall KC, Landguth EL, Schwartz MK, McKelvey KS, Allendorf FW, Luikart G (2011) Why replication is important in landscape genetics: american black bear in the Rocky Mountains. Mol Ecol 20:1092鈥?107CrossRef
    Smith CA (1994) Bi-level analysis of habitat selection by mountain goats in coastal Alaska. Proceedings of the biennial symposium of the northern wild sheep and goat council, vol, pp 5366鈥?79
    Smouse PE, Long JC, Sokal RR (1986) Multiple-regression and correlation extensions of the Mantel test of matrix correspondence. Syst Zool 35:627鈥?32CrossRef
    Spear SF, Balkenhol N, Fortin MJ, McRae BH, Scribner K (2010) Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis. Mol Ecol 19:3576鈥?591CrossRef PubMed
    Taylor PD, Fahrig L, Henein K, Merriam G (1993) Connectivity is a vital element of landscape structure. Oikos 68:571鈥?73CrossRef
    Thomas CD, Cameron A, Green RE, Bakkenes M, Beaumont LJ, Collingham YC, Erasmus BFN, de Siqueira MF, Grainger A, Hannah L, Hughes L, Huntley B, van Jaarsveld AS, Midgley GF, Miles L, Ortega-Huerta MA, Peterson AT, Phillips OL, Williams SE (2004) Extinction risk from climate change. Nature 427:145鈥?48CrossRef PubMed
    US Geological Survey, GAP Analysis Program (GAP) (2012) Protected Areas Database of the United States (PADUS), version 1.3
    Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535鈥?38CrossRef
    Warren MJ, Wallin DO, Beausoleil RA, Warheit KI (2015) Genetic structure and landscape resistance to gene flow in cougars in Washington and southern British Columbia. Manuscript submitted for publication
    Washington Wildlife Habitat Connectivity Working Group (WHCWG) (2010) Washington connected landscapes project: statewide analysis. Washington Departments of Fish and Wildlife, and Transportation, Olympia. http://鈥媤aconnected.鈥媜rg/鈥媠tatewide-analysis/鈥?/span> . Accessed 15 Oct 2011
    Wells A, Wallin DO, Rice CG, Wan-Ying C (2011) GPS bias correction and habitat selection by mountain goats. Remote Sens 3:435鈥?59
    Wiegand T, Revilla E, Moloney KA (2005) Effects of habitat loss and fragmentation on population dynamics. Conserv Biol 19:108鈥?21CrossRef
    Willi Y, Van Buskirk J, Hoffmann AA (2006) Limits to the adaptive potential of small populations. Ann Rev Ecol Evol Syst 37:433鈥?58CrossRef
  • 作者单位:Leslie C. Parks (1)
    David O. Wallin (1)
    Samuel A. Cushman (2)
    Brad H. McRae (3)

    1. Department of Environmental Sciences, Huxley College of the Environment, Western Washington University, 516 High St., Bellingham, WA, 98225, USA
    2. Rocky Mountain Research Station, U.S. Forest Service, 2500 S. Pine Knoll Dr., Flagstaff, AZ, 86001, USA
    3. The Nature Conservancy, North America Region, 117 Mountain Ave., Suite 201, Fort Collins, CO, 80524, USA
  • 刊物类别:Biomedical and Life Sciences
  • 刊物主题:Biomedicine
    Human Genetics
    Animal Anatomy, Morphology and Histology
    Plant Sciences
    Evolutionary Biology
  • 出版者:Springer Netherlands
  • ISSN:1572-9737
文摘
Habitat fragmentation and habitat loss diminish population connectivity, reducing genetic diversity and increasing extinction risk over time. Improving connectivity is widely recommended to preserve the long-term viability of populations, but this requires accurate knowledge of how landscapes influence connectivity. Detectability of landscape effects on gene flow is highly dependent on landscape context, and drawing conclusions from single landscape studies may lead to ineffective management strategies. We present a novel approach to elucidate regional variation in the relative importance of landscape variable effects on gene flow. We demonstrate this approach by evaluating gene flow between isolated, genetically impoverished mountain goat (Oreamnos americanus) populations in Washington and much larger, genetically robust populations in southern British Columbia. We used geneland to identify steep genetic gradients and then employed individual-based landscape genetics in a causal modeling framework to independently evaluate landscape variables that may be generating each of these genetic gradients. Our results support previous findings that freeways, highways, water, agriculture and urban landcover limit gene flow in this species. Additionally, we found that a previously unsupported landscape variable, distance to escape terrain, also limits gene flow in some contexts. By integrating geneland and individual-based methods we effectively identified regional limiting factors that have landscape-level implications for population viability. Keywords Population connectivity geneland Circuit theory Causal modeling Oreamnos americanus
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