Abstract
It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices.
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References
Aldridge RD, Duvall D (2002) Evolution of the mating season in the pitvipers of North America. Herpetological Monographs 16:1–25
Allendorf FW, Ryman N (2002) The role of genetics in population viability analysis. In: Beissinger SR, McCollough DR (eds) Population viability analysis. University of Chicago Press, Chicago, pp 50–85
Andrews KM, Gibbons JW (2005) How do highways influence snake movement? Behavioral responses to roads and vehicles. Copeia 2005:772–782
Aresco MJ (2005) Mitigation measures to reduce highway mortality of turtles and other herpetofauna at a north Florida lake. J Wildl Manage 69:549–560
Ávila Cervantes J (2011) Análisis de la estructura y diversidad genética de cuatro poblaciones de Crotalus molossus nigrescens. Master’s Thesis, Facultad de Ciencias, UNAM, México. bibliotecacentral.unam.mx. Accessed 11 Feb 2014
Beaman KR, Hayes WK (2008) Rattlesnakes: Research trends and annotated checklist. In: Hayes WK, Beaman KR, Caldwell MD, Bush SP (eds) The biology of rattlesnakes. Loma Linda University Press, Loma Linda, pp 5–16
Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics 153:2013–2029
Beck DD (1995) Ecology and energetics of three sympatric rattlesnake species in the Sonoran Desert. J Herpetol 29:211–223
Beerli P (2008) Migrate version 3.0: a maximum likelihood and Bayesian estimator of gene flow using the coalescent. http://popgen.sc.fsu.edu/Migrate/Migrate-n. Accessed 13 Nov 2014
Beerli P (2009) How to use migrate or why are markov chain monte carlo programs dificult to use? In: Bertorelle G, Bruford MW, Haue HC, Rizzoli A, Vernesi C (eds) Population genetics for animal conservation, vol 17., Conservation BiologyCambridge University Press, Cambridge, pp 42–79
Beerli P (2012) Migrate documentation. http://popgen.sc.fsu.edu/migratedoc.pdf. Accessed 17 Aug 2015
Belkenhol N, Waits LP (2009) Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife. Mol Ecol 18:4151–4164
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B 57:289–300
Blouin-Demers G, Weatherhead PJ (2001a) Habitat use by black rat snakes (Elaphe obsolete obsoleta) in fragmented forests. Ecology 82:2882–2896
Blouin-Demers G, Weatherhead PJ (2001b) An experimental test of the link between foraging, habitat selection and thermoregulation in black rat snake, Elaphe obsolete obsoleta. J Anim Ecol 70:1006–1013
Booth W, Schuett GW (2011) Molecular genetic evidence for alternative reproductive strategies in North American pitvipers (Serpentes: Viperidae): long-term sperm storage and facultative parthenogenesis. Biol J Linn Soc Lond 104:934
Bryson RW Jr, Riddle BR (2012) Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard. Biol J Linn Soc 105:382–394
Bryson RW, Murphy RW, Lathrop A, Lazcano-Villareal D (2011) Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes. J Biogeogr 38:697–710
Bryson RW, Linkem CW, Dorcas ME, Lathrop A, Jones JM, Alvarado-Díaz J, Grünwald CI, Murphy RW (2014) Multilocus species delimitation in the Crotalus triseriatus species group (Serpentes: Viperidae: Crotalinae) with the description of two new species. Zootaxa 3:475–496
Bushar LM, Reinert HK, Gelbert L (1998) Genetic variation and gene flow within and between local populations of the timber rattlesnake, Crotalus horridus. Copeia 2:411–422
Campbell JA, Lamar WW (2004) The venomous reptiles of the western hemisphere, vol II. Comstock/Cornell University Press, Ithaca
Canseco-Márquez L, Mendoza-Quijano F (2007) Crotalus triseriatus In: IUCN 2013 IUCN Red List of Threatened Species, Version, 20132. www.iucnredlistorg. Downloaded on 05 May 2014
Castellano MJ, Valone TJ (2006) Effects of livestock removal and perennial grass recovery on the lizards of a desertified arid grassland. J Arid Environ 66:87–95
Challenger, A (1998) Utilización y conservación de los ecosistemas terrestres de México. Pasado, presente y futuro. CONABIO, Instituto de Biología, Agrupación Sierra Madre, México
Clark RW, Brown WS, Stechert R, Zamudio KR (2008) Integrating individual behaviour and landscape genetics: the population structure of timber rattlesnake hibernacula. Mol Ecol 17:719–730
Clark RW, Brown WS, Stechert R, Zamudio KR (2010) Roads, interrupted dispersal, and genetic diversity in Timber Rattlesnakes. Conserv Biol 24:1059–1069
Clark RW, Schuett GW, Repp RA, Amarello M, Smith CF et al (2014) Mating systems, reproductive success, and sexual selection in secretive species: a case study of the western diamond-backed rattlesnake, Crotalus atrox. PLoS ONE 9(3):e90616. doi:10.1371/journal.pone.0090616
CONAPO (2010) Delimitación de las zonas metropolitanas de México. http://www.conapo.gob.mx/en/CONAPO/Zonas_metropolitanas_2010
Cournet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent populations bottleneck from allele frequency data. Genetics 144:2001–2014
Dixon MD (2011) Population genetic structure and natal philopatry in the widespread North American bat Myotis lucifugus. J Mammal 92:1343–1351
Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR (2014) NeEstimator 2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 14:209–214
Doonan TJ, Slade NA (1995) Effects of supplemental food on population dynamics of cotton rats, Sigmodon hispidus. Ecology 76:814–826
Earl DA, vonHoldt BM (2011) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361
Eldridge MD, Kinnear JE, Zenger KR, McKenzie LM, Spencer PB (2004) Genetic diversity in remnant mainland and ‘‘pristine’’ island populations of three endemic Australian macropodids (Marsupialia): Macropus eugenii, Lagorchestes hirsutus and Petrogale lateralis. Conserv Genet 5:325–338
England PR, Cornuet JM, Berthier P, Tallmon DA, Luikart G (2005) Estimating effective population size from linkage disequilibrium: severe bias in small samples. Conserv Genet 7:3003–3008
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Figueroa-Rangel BL, Willis KJ, Olvera-Vargas M (2010) Cloud forest dynamics in the Mexican Neotropics during the last 1300 years. Glob Change Biol 16:1689–1704
Flores-Villela V, Canseco-Márquez L (2004) Nuevas especies y cambios taxonómicos para la herpetofauna de México. Acta Zool Mex Nueva 20:115–144
Frankham R (1998) Inbreeding and extinction: island populations. Conserv Biol 12:665–675
Galicia L, García-Romero A (2007) Land use and land cover change in highland temperate forests in the Izta-Popo National Park, central Mexico. Mt Res Dev 27:48–57
Gasca-Pineda J, Cassaigne I, Alonso RA, Eguiarte LE (2013) Effective population size, genetic variation, and their relevance for conservation: the bighorn sheep in Tiburon island and comparisons with managed artiodactyls. PLoS ONE 8(10):e78120. doi:10.1371/journal.pone.0078120
Gibbs HL, Prior KA, Weatherhead PJ, Johnson G (1997) Genetic structure of populations of the threatened eastern massasauga rattlesnake, Sistrurus c. catenatus: evidence from microsatellite DNA markers. Mol Ecol 6:1123–1132
Goldberg CS, Edwards T, Kaplan ME, Goode M (2003) PCR primers for microsatellite loci in the tiger rattlesnake (Crotalus tigris, Viperidae). Mol Ecol Notes 3:539–541
Greene HW, May PG, Hardy DL, Sciturro JM, Farrell TM (2002) Parental behavior in vipers. In: Schuett GW, Höggren M, Douglas ME, Greene HW (eds) Biology of the Vipers. Eagle Mountain Publishing, Eagle Mountain, Utah
Hammer Ø (2015) PAST: Paleontological Statistics software package for education and data analysis. Palaeontol Electron 4(1). http://folk.uio.no/ohammer/past/
Holycross AT, Douglas ME (2007) Geographic isolation, genetic divergence, and ecological non-exchangeability define ESUs in a threatened sky-island rattlesnake. Biol Conserv 134:142–154
Holycross AT, Douglas ME, Higbee JR, Bogden RH (2002) Isolation and characterization of microsatellite loci from a threatened rattlesnake (New Mexico Ridge-nosed Rattlesnake, Crotalus willardi obscurus). Mol Ecol Notes 2:537–539
Hoss SK, Guyer C, Smith LL, Schuett GW (2010) Multiscale influences of landscape composition and configuration on the spatial ecology of eastern diamond-backed rattlesnakes (Crotalus adamanteus). J Herpetol 44:110–123
Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322–1332
Huey RB (1982) Temperature, physiology, and the ecology of reptiles. In: Gans C, Pough FH (eds) Biology of the reptilia. Physiology C. Physiological ecology, vol 12. Academic Press, New York, pp 25–91
Jansen KP, Mushinsky HR, Karl SA (2008) Population genetics of the mangrove salt marsh snake, Nerodia clarkii compressicauda, in a linear fragmented habitat. Conserv Genet 9:401–410
Jiménez-Velázquez G (2013) Estructura y composición de la herpetofauna asociada a humedales en un paisaje urbano-agrícola del Eje Neovolcánico. Master’s Thesis, Facultad de Ciencias, Universidad Autónoma de Querétaro, México. http://ri.uaq.mx/bitstream/123456789/743/1/RI000333.pdf. Accessed 11 Feb 2014
Kalinowski S, Wagner AP, Taper ML (2006) ML-RELATE: a computer program for maximum likelihood estimation of relatedness and relationship. Mol Ecol Notes 6:576–579
Keyghobadi N (2007) The genetic implications of habitat fragmentation for animals. Can J Zool 85:1049–1064
Kohn MH, York EC, Kanradt DA, Haught G, Sauvajot RM, Wayne RK (1999) Estimating population size by genotyping feces. Proc R Soc Lond B Biol Sci 266:657–663
León-Paniagua L, Navarro-Sigüenza AG, Hernández-Baños BE, Morales JC (2007) Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands. Mol Phylogenet Evol 42:653–664
Lougheed SC, Gibbs HL, Prior KA, Weatherhead PJ (1999) Hierarchical patterns of genetic population structure in black rat snakes (Elaphe obsoleta obsoleta) as revealed by microsatellite DNA analysis. Evolution 5319:95–2001
Luna I, Morrone JJ, Espinosa D (2007) Biodiversidad de la Faja Volcánica Transmexicana. UNAM, D. F. México
Martin FD, Wike LD, Paddock LS (2000) Role of edge effect on small mammal populations in a forest fragment. Department of Energy Technical Report, Savannah River Ecology Lab, Aiken, SC
Matschiner M, Salzburger W (2009) TANDEM: integrating automated allele binning into genetics and genomics workflows. Bioinformatics 25:1982–1983
McCormack JE, Peterson AT, Bonaccorso E, Smith TB (2008) Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Mol Ecol 17:2505–2521
Mittermeier RA, Goettsch de Mittermeier C (1992) La importancia de la diversidad biológica de México. In: Sarukhán J, Dirzo R (eds) México ante los retos de la biodiversidad. CONABIO, México, pp 63–73
Monroy-Vilchis O, Cabrera L, Suárez P, Zarco-González M, Rodríguez-Soto C, Urios V (2008) Uso tradicional de vertebrados silvestres en la Sierra Nanchititla, México. Interciencia 33:08–313
Navarro-Sigüenza AG, Peterson AT, Nyari A, García-Deras G, García-Moreno J (2008) Phylogeography of the Buarremon brush-finch complex (Aves Emberizidae) in Mesoamerica. Mol Phylogenet Evol 47:21–35
Nei M (1972) Genetic distance between populations. Am Nat 106:283–292
Neuwald JL (2010) Population isolation exacerbates conservation genetic concerns in the endangered Amargosa vole, Microtus californicus scirpensis. Biol Conserv 143:2028–2038
Nomura T (2008) Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evol Appl 1:462–474
Oyler-McCance SJ, John J, Parker JM, Anderson SH (2005) Characterization of microsatellite loci isolated in midget faded rattlesnake (Crotalus viridis concolor). Mol Ecol Notes 5:452–453
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel Population genetic software for teaching and research. Mol Ecol Notes 6:288–295
Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90:502–503
Ponce-Reyes R, Reynoso-Rosales VH, Watson JEM, VanDerWal J, Fuller RA, Pressey RL, Possingham HP (2012) Vulnerability of cloud forest reserves in Mexico to climate change. Nat Clim Change 2:448–452
Pozarowski K, Bryan DS, Bosse R, Watson E, Herrmann H-W (2012) Development of polymorphic microsatellite loci for the rattlesnake species Crotalus atrox, C. cerastes and C. scutulatus (Viperidae: Crotalinae) and cross species amplification of microsatellite markers in Crotalus and Sistrurus species. Conserv Genet Resour 4:955–961
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Prosser ML, Gibbs HL, Weatherhead PJ, Brown GP (2000) Genetic analysis of the mating system and opportunity for sexual selection in northern water snakes (Nerodia sipedon). Behav Ecol 13:800–807
Rasband WS (2012) ImageJ. U.S. National Institutes of Health, Bethesda, Maryland, USA. imagej.nih.gov/ij/
Raymond M, Rousset F (1995) GENEPOP v 12: population genetics software for exact test and ecumenicism. J Hered 86:248–249
Ribeiro R, Santos X, Sillero N, Carretero MA, Llorente GA (2009) Biodiversity and land uses at a regional scale: Is agriculture the biggest threat for reptile assemblages? Acta Oecol 35:327–334
Rosen PC, Lowe CH (1994) Highway mortality of snakes in the Sonoran Desert of southern Arizona. Biol Conserv 68:143–148
Ruiz-Sanchez E, Specht CD (2013) Influence of the geological history of the Trans-Mexican Volcanic Belt on the diversification of Nolina parviflora (Asparagaceae: Nolinoideae). J Biogeogr 40:1336–1347
Sarukhán J, Koleff P, Carabias J, Soberon J. Dirzo R et al (2009) Capital Natural de México. Síntesis Conocimiento actual, evaluación y perspectivas de la sustentabilidad. Comision Nacional para el Uso y Conocimiento de la Biodiversidad. México
Schuett GW (1992) Is long-term sperm storage an important component of the reproductive biology of temperate pitvipers? In: Campbell JA, Brodie ED Jr (eds) Biology of the pitvipers. Selva, Tyler, pp 169–184
Sever DM, Hamlett WC (2001) Female sperm storage in reptiles. J Exp Zool 182:724–738
Shaw PW, Pierce GJ, Boyle PR (1999) Subtle population structuring within a highly vagile marine invertebrate, the veined squid Loligo forbesi, demonstrated with microsatellite DNA markers. Mol Ecol 8:407–417
Shine R, Lemaster M, Wall M, Langkilde T, Mason R (2004) Why did the snake cross the road? Effects of roads on movement and location of mates by garter snakes (Thamnophis sirtalis parietalis). Ecol Soc 9:9
Souza AM, Pires RC, Borges VS, Eterovick PC (2015) Road mortality of the herpetofauna in a Cerrado ecosystem, central Brazil. Herpetol J 25(3):141–148
Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc Series B 64:479–498
Sunny A, Monroy-Vilchis O, Fajardo V, Aguilera-Reyes U (2014a) Genetic diversity and structure of an endemic and critically endangered stream river salamander (Caudata: Ambystoma leorae) in Mexico. Conserv Genet 15:49–59
Sunny A, Monroy-Vilchis O, Reyna-Valencia C, Zarco-González MM (2014b) Microhabitat types promote the genetic structure of a micro-endemic and critically endangered mole salamander (Ambystoma leorae) of Central Mexico. PLoS ONE 9:e103595. doi:10.1371/journalpone0103595
Uetz P, Hošek J (eds) The reptile database. http://www.reptile-database.org. Accessed 13 Aug 2015
Uller T, Olsson M (2008) Multiple paternity in reptiles: patterns and processes. Mol Ecol 17:2566–2580
Valière N (2002) GIMLET: a computer program for analyzing genetic individual identification data. Mol Ecol Notes 10:1046–1048
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 4:535–538
Vargas-Rodríguez YL, Platt WJ, Vázquez-García JA, Boqiun G (2010) Selecting relict montane cloud forests for conservation priorities: the case of western Mexico. Nat Areas J 30:156–174
Vázquez-Domínguez E, Vega R (2006) ¿Dónde estamos y hacia dónde vamos en el conocimiento genético de los mamíferos mexicanos? In: Vázquez-Domínguez E, Hafner DJ (eds) Genética y mamíferos mexicanos: presente y futuro. New México Museum of Natural History and Science, New Mexico, pp 67–73
Vázquez-Domínguez E, Surárez-Atilano M, Booth W, González-Baca C, Cuarón AD (2012) Genetic evidence of a recent successful colonization of introduced species on islands: Boa constrictor imperator on Cozumel Island. Biol Invasions 14:2101–2116
Vázquez-Domínguez E, Mendoza-Martínez A, Orozco-Lugo L, Cuarón AD (2013) High dispersal and generalist habits of the bat Artibeus jamaicensis on Cozumel Island, Mexico: an assessment using molecular genetics. Acta Chiropt 15:411–421
Villarreal X, Bricker J, Reinert HK, Gelbert L, Bushar LM (1996) Isolation and characterization of microsatellite loci for use in population genetic analysis in the timber rattlesnake, Crotalus horridus. J Hered 87:152–155
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370
White D, Minotti PG, Barczak MJ, Sifneos JC, Freemark KE, Santelmann MV, Steinitz CF, Kiester AR, Preston EM (1997) Assessing risks to biodiversity from future landscape change. Conserv Biol 11:349–360
Yanes M, Velasco JM, Suarez F (1995) Permeability of roads and railways to vertebrates: the importance of culverts. Biol Conserv 71:217–222
Acknowledgments
We thank the following people for their help with field work: Andrea González-Fernández, Juan Carlos Guido-Patiño, Víctor Muñoz-Mora, Giovany Arturo González-Desales and Carlos Reyna-Valencia. We thank Víctor Ávila Akerberg for valuable comments and English editing. We thank the editor and two anonymous reviewers for their comments. AS is grateful to the graduate program “Ciencias Agropecuarias y Recursos Naturales” of the Autonomous University of the State of Mexico and for scholarships received from CONACYT (356612) and COMECYT.
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The authors declare that they have no conflict of interest. The manipulation of rattlesnakes was conducted with the approval of the ethics committee of Universidad Autónoma del Estado de México.
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Sunny, A., Monroy-Vilchis, O., Zarco-González, M.M. et al. Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation. Genetica 143, 705–716 (2015). https://doi.org/10.1007/s10709-015-9868-8
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DOI: https://doi.org/10.1007/s10709-015-9868-8