Skip to main content
SpringerLink
Log in

Molecular Genetic Tools for Evaluating the Consequences of Habitat Fragmentation

  • Chapter
Primates in Fragments

Part of the book series: Developments in Primatology: Progress and Prospects ((DIPR))

Abstract

Fragmentation and loss of habitat is a serious problem facing the conservation of biodiversity. Habitat fragmentation can lead to reduction in the connectivity between primate populations and ultimately isolation of populations. Decreased levels of gene flow among small populations can lead to decreased genetic variability and concomitantly a reduced ability to adapt to changing environments. Habitat fragmentation may also lead to increased inbreeding, reduced reproductive success, reduction in survival and an increased probability of extinction. Using molecular genetic tools, scientists can measure genetic diversity within and between populations and investigate genetic differentiation between populations of primates living in fragments. Theory predicts a positive correlation between genetic variation and population size and between genetic differentiation and geographic distance among populations. Using genetic data, statistical methods, and computer programs, it is possible to test these predictions and to evaluate the consequences of fragmentation on primates. This chapter reviews the genetic tools available to primatologists interested in evaluating the consequences of habitat fragmentation. Since reduced genetic variation can also potentially lead to increased susceptibility to disease, it is increasingly important to determine what regions of the genome are affected by reduced gene flow and to understand the mechanisms by which genetic diversity changes in association with habitat loss and fragmentation. These are new and important challenges for primate geneticists in the coming decade.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Amos W, Worthington Wilmer J, Fullard K, Burg TM, Croxall JP, Bloch D, Coulson T (2001) The influence of parental relatedness on reproductive success. Proc R Soc Lond B 268:2021–2027

    Article  CAS  Google Scholar 

  • Beerli P (2009) How to use MIGRATE or why are Markov Chain Monte Carlo programs difficult to use. In: Bertorelle G, Bruford MW, Harcliffe HC, Rizzoli A, Vernesi C (eds) Population genetics for animal conservation. Cambridge University Press, Cambridge, pp 42–79

    Chapter  Google Scholar 

  • Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci USA 98:4563–4568

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bergl RA, Vigilant L (2007) Genetic analysis reveals population structure and recent migration within the highly fragmented range of the Cross River gorilla (Gorilla gorilla diehli). Mol Ecol 16:501–516

    Article  PubMed  Google Scholar 

  • Crow JF (1986) Basic concepts in population, quantitative, and evolutionary genetics. Freeman, New York

    Google Scholar 

  • Eriksson J, Siedel H, Lukas D, Kayser M, Erler A, Hashimoto C, Hohmann G, Boesch C, Vigilant L (2006) Y-chromosome analysis confirms highly sex-biaseddispersal and suggests a low male effective populationsize in bonobos (Pan paniscus). Mol Ecol 15:939–949

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Heckel G (2006) Computer programs for population genetics data analysis: a survival guide. Nat Rev Genet 7:745–758

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Smouse P, Quaitro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed Central  PubMed  Google Scholar 

  • Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Goldstein DB, Linares AR, Cavalli-Sforza LL, Feldman MW (1995) Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci USA 92(15):6723–6727

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Goossens B, Chikhi L, Ancrenaz M, Lackman-Ancrenaz I, Andau P, Bruford MW (2006) Genetic signature of anthropogenic population collapse in Orang-utans. PLoS Biol 4(2):285–291

    Article  CAS  Google Scholar 

  • IUCN Red List (2010) http://www.iucnredlist.org/

  • Jefferey KJ, Abernethy KA, Tutin CE, Bruford MW (2007) Biological and environmental degradation of gorilla hair and microsatellite amplification success. Biol J Linn Soc 91:281–294

    Article  Google Scholar 

  • Knapp LA (2005) The ABCs of MHC. Evol Anthropol 14(1):28–37

    Article  Google Scholar 

  • Lawler RR, Richard AF, Riley MA (2003) Genetic population structure of the white sifaka (Propithecus verreauxi verreauxi) at Beza Mahafaly Special Reserve, southwest Madagascar (1992–2001). Mol Ecol 12(9):2307–2317

    Article  PubMed  Google Scholar 

  • Meirmans PG, Hedrick PW (2010) Assessing population structure: FST and related measures. Mol Ecol Resour 11(1):5–18

    Article  PubMed  Google Scholar 

  • Morin PA, Chambers KE, Boesch C, Vigilant L (2001) Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes). Mol Ecol 10:1835–1844

    Article  CAS  PubMed  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distances from a small number of individuals. Genetics 89:583–590

    CAS  PubMed Central  PubMed  Google Scholar 

  • Neigel JE (1996) Estimation of effective population size and migration parameters from genetic data. In: Smith TB, Wayne RK (eds) Molecular genetic approaches in conservation. Oxford University Press, Oxford, pp 329–346

    Google Scholar 

  • Neigel JE (2002) Is FST obsolete? Conserv Genet 3:167–173

    Article  CAS  Google Scholar 

  • Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens MD, Pritchard JK, Gilad Y (2012) Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res 22(4):602–610

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pope TR (1998) Genetic variation in remnant populations of the woolly spider monkey (Brachyteles arachnoides). Int J Primatol 19(1):95–109

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rannala B, Hartigan JA (1996) Estimating gene flow in island populations. Genet Res 67:147–158

    Article  CAS  PubMed  Google Scholar 

  • Raymond M, Rousset F (1995) Genepop v. 3.0. Population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Google Scholar 

  • Ruiz-Garcia M, Escobar-Armel P, Alvarez D, Mudry M, Ascunce M, Gutierrez-Espeleta G, Shostell JM (2007) Genetic variability in four Alouatta species measured by means of nine DNA microsatellite markers: Genetic structure and recent bottlenecks. Folia Primatol 78:73–87

    Google Scholar 

  • Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sommer S (2008) Forest fragmentation effects on functional genes: immune gene variability (MHC) of Microcebus murinus and Rattus rattus in the Mandena Forest. In: Ganzhorn JU (ed) Biodiversity, ecology and conservation of littoral ecosystems in Southeastern Madagascar. Smithsonian Institution, Washington, DC

    Google Scholar 

  • Srikwan S, Woodruff DS (2000) Genetic erosion in isolated small-mammal populations. In: Young AG, Clarke GM (eds) Genetics. Demography and viability of fragmented populationsdemography and viability of fragmented populations. Cambridge University Press, Cambridge, pp 149–172

    Chapter  Google Scholar 

  • Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol Ecol 13:789–809

    Article  PubMed  Google Scholar 

  • Vigilant L (2002) Technical challenges in the microsatellite genotyping of a wild chimpanzee population using feces. Evol Anthropol S1:162–165

    Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    Article  Google Scholar 

  • Whitlock MC (2011) G′ST and D do not replace FST. Mol Ecol 20(6):1083–1091

    Article  PubMed  Google Scholar 

  • Winney BJ, Hammond RL, Macasero W, Flores B, Boug A, Biquand V, Biquand S, Bruford MW (2004) Crossing the Red Sea: phylogeography of the hamadryas baboon, Papio hamadryas hamadryas. Mol Ecol 13(9):2819–2827

    Article  CAS  PubMed  Google Scholar 

  • Wright S (1969) Evolution and the genetics of populations, vol 2 The Theory of Gene Frequencies. University of Chicago Press, Chicago

    Google Scholar 

Download references

Acknowledgments

Thanks to Laura Marsh for inviting me to contribute this chapter and for her helpful editorial comments. Thanks also to Colin Chapman for editorial suggestions.

Author information

Authors and Affiliations

  1. Primate Immunogenetics and Molecular Ecology Research Group, Division of Biological Anthropology, University of Cambridge, Pembroke Street, Cambridge, CB2 3QY, UK

    Leslie A. Knapp

  2. Department of Anthropology, University of Utah, 270 S. 1400 E., Salt Lake City, Utah, 84112, USA

    Leslie A. Knapp

Authors
  1. Leslie A. Knapp
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Leslie A. Knapp .

Editor information

Editors and Affiliations

  1. Global Conservation Institute, Santa Fe, New Mexico, USA

    Laura K. Marsh

  2. Department of Anthropology, McGill School of Environment, McGill University, Montreal, Québec, Canada

    Colin A. Chapman

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Knapp, L.A. (2013). Molecular Genetic Tools for Evaluating the Consequences of Habitat Fragmentation. In: Marsh, L., Chapman, C. (eds) Primates in Fragments. Developments in Primatology: Progress and Prospects. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8839-2_25

Download citation

Publish with us

Policies and ethics

Search

Navigation