Abstract
Conservation genetic studies make use of molecular methods to obtain valuable information which help optimizing management strategies especially for threatened species. This chapter presents an overview of different molecular markers (microsatellites, AFLPs, RFLPs, RAPDs, mtDNA, allozymes) and their applications in conservation and genetic studies. Microsatellites have shown to be, though expensive, currently the most popular genetic marker as the high degree of polymorphism is ideal to study small geographical scales of species. RFLPs, RAPDs and allozymes still represent useful markers for studies of both, small and larger geographical scales. Low degree of polymorphism, no detection of alleles and low reproducibility characterize some drawbacks. To examine phylogeography MtDNA seems to be the best choice.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abbott JK, Bensch S, Gosden TP, Svensson EI (2008) Patterns of differentiation in a colour polymorphism and in neutral markers reveal rapid genetic changes in natural damselfly populations. Mol Ecol 17:1597–1604
Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631
Apostolidis AP, Loukovitis D, Tsigenopoulos CS (2008) Genetic characterization of brown trout (Salmo trutta) populations from the Southern Balkans using mtDNA sequencing and RFLP analysis. Hydrobiologia 600:169–176
Ashley MV (1999) Molecular conservation genetics: tools for assaying the structure of DNA prove valuable in protecting endangered species. Am Sci 87:28–35
Assmann T, Buse J, Drees C, Härdtle HJW, Matern A, von Oheimb G, Schuldt A, Wrase DW (2007) From Latreille to DNA systematics - towards a modern synthesis for carabidology. In: Penev L, Erwin T, Assmann T (eds) Back to the Roots and Back to the Future. Towards a New Synthesis amongst Taxonomic, Ecological and Biogeographical Approaches in Carabidology - Proceedings of the XIII European Carabidologists Meeting, Blagoevgrad, August 20-24. Pensoft Publishers, Sofia, Moscow, pp 41–76
Avise JC (1991) 10 unorthodox perspectives on evolution prompted by comparative population genetic findings on mitochondrial DNA. Annu Rev Genet 25:45–69
Avise JC (1994) Molecular markers, natural history and evolution. Chapman and Hall, New York
Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA
Bartlett AC (1981) Isozyme polymorphism in populations of the pink-bollworm (Lepidoptera, Gelechiidae). Ann Entomol Soc Am 74:9–13
Behura SK (2006) Molecular marker systems in insects: current trends and future avenues. Mol Ecol 15:3087–3113
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Brouat C, McKey D, Douzery EJP (2004) Differentiation in a geographical mosaic of plants coevolving with ants: phylogeny of the Leonardoxa africana complex (Fabaceae : Caesalpinioideae) using amplified fragment length polymorphism markers. Mol Ecol 13:1157–1171
Bruford MW, Wayne RK (1993) Microsatellites and their application to population genetic studies. Curr Opin Genet Dev 3:939–943
Busti A, Caceres ME, Calderini O, Arcioni S, Pupilli F (2004) RFLP markers for cultivar identification in tall fescue (Festuca arundinacea Schreb.). Genet Resour Crop Evol 51:443–448
Chakraborty R, Hedrick PW (1983) Paternity exclusion and the paternity index for 2 linked loci. Hum Hered 33:13–23
Despres L, Gielly L, Redoutet W, Taberlet P (2003) Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability. Mol Phylogenet Evol 27:185–196
DeYoung RW, Honeycutt RL (2005) The molecular toolbox: genetic techniques in wildlife ecology and management. J Wildl Manage 69:1362–1384
Doyle JJ, Morgante M, Tingey SV, Powell W (1998) Size homoplasy in chloroplast microsatellites of wild perennial relatives of soybean (Glycine Subgenus Glycine). Mol Biol Evol 15:215–218
Eisen J (1999) Mechanistic explanations for variation in microsatellite stability within and between species. In: Goldstein D, Schlötterer C (eds) Microsatellites: evolution and applications. Oxford University Press, Oxford, pp 34–48
Finger A, Schmitt T, Zachos FE, Meyer M, Assmann T, Habel JC (2009) The genetic status of the violet copper Lycaena helle - a relict of the cold past in times of global warming. Ecography 32:382–390
Goldstein DB, Pollock DD (1997) Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J Hered 88:335–342
Hardy OJ, Maggia L, Bandou E, Breyne P, Caron H, Chevallier MH, Doligez A, Dutech C, Kremer A, Latouche-Halle C, Troispoux V, Veron V, Degen B (2006) Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree species. Mol Ecol 15:559–571
Hu DC, Zhang QL, Luo ZR (2008) Phylogenetic analysis in some Diospyros spp. (Ebenaceae) and Japanese persimmon using chloroplast DNA PCR-RFLP markers. Sci Hort 117:32–38
Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Mol Ecol 12:2511–2523
Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, vande Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390
Keim P, Schupp JM, Travis SE, Clayton K, Zhu T, Shi LA, Ferreira A, Webb DM (1997) A high-density soybean genetic map based on AFLP markers. Crop Sci 37:537–543
Kim C, Na HR, Choi HK (2008) Conservation genetics of endangered Brasenia schreberi based on RAPD and AFLP markers. J Plant Biol 51:260–268
Leberg P (2005) Genetic approaches for estimating the effective size of populations. J Wildl Manage 69:1385–1399
Levinson G, Gutman GA (1987) High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucleic Acids Res 15:5323–5338
Lowe A, Harris S, Ashton P (2004) Ecological genetics. Blackwell, Oxford
Loxdale HD, Tarr IJ, Weber CP, Brookes CP, Digby PGN (1985) Electrophoretic study of enzymes from cereal aphid populations.3. Spacial and temporal genetic variation of populations of Sitobion Avenae (F.) (Hemiptera: Aphididae). Bull Entomol Res 75:121–141
Luikart G, England PR (1999) Statistical analysis of microsatellite DNA data. Trends Ecol Evol 14:253–256
Lushai G, Smith DAS, Goulson D, Allen JA, Maclean N (2003) Mitochondrial DNA clocks and the phylogeny of Danaus butterflies. Insect Sci Appl 23:309–315
Meagher TR, Thompson E (1986) The relationship between single parent and parent pair genetic likelihoods in genealogy reconstruction. Theor Popul Biol 29:87–106
Meglécz E, Solignac M (1998) Microsatellite loci for Parnassius mnemosyne (Lepidoptera). Hereditas 128:179–180
Meudt HM, Clarke HC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci 12:106–117
Mullis KF, Caloona F, Scharf S, Saikl R, Horn G, Erlich H (1996) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51(1):263–273
Olivieri GL, Sousa V, Chikhi L, Radespiel U (2008) From genetic diversity and structure to conservation: genetic signature of recent population declines in three mouse lemur species (Microcebus spp.). Biol Conserv 141:1257–1271
Olmstead JW, Sebolt AM, Cabrera A, Sooriyapathirana SS, Hammar S, Iriarte G, Wang D, Chen CY, van der Knaap E, Iezzoni AF (2008) Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and synteny analysis with the Prunus reference map. Tree Genet Genomes 4:897–910
Orsini L, Corander J, Alasentie A, Hanski I (2008) Genetic spatial structure in a butterfly metapopulation correlates better with past than present demographic structure. Mol Ecol 17:2629–2642
Palo J, Varvio SL, Hanski I, Vainola R (1995) Developing microsatellite markers for insect population structure: complex variation in a checkerspot butterfly. Hereditas 123:295–300
Proudfoot GA, Honeycutt RL, Slack RD (2006) Mitochondrial DNA variation and phylogeography of the ferruginous pygmy-owl (Glaucidium brasilianum). Conserv Genet 7:1–12
Radoev M, Becker HC, Ecke W (2008) Genetic analysis of heterosis for yield and yield components in rapeseed (Brassica napus L.) by quantitative trait locus mapping. Genetics 179:1547–1558
Riddle BR, Honeycutt RL (1990) Historical biogeography in North-american arid regions - an approach using mitochondrial-DNA phylogeny in grasshopper mice (genus Onychomys). Evolution 44:1–15
Rocha LA, Rocha CR, Robertson DR, Bowen BW (2008) Comparative phylogeography of Atlantic reef fishes indicates both origin and accumulation of diversity in the Caribbean. BMC Evol Biol 8:157
Saal B, Wricke G (2002) Clustering of amplified fragment length polymorphism markers in a linkage map of rye. Plant Breeding 121:117–123
Schenk MF, Thienpont CN, Koopman WJM, Gilissen L, Smulders MJM (2008) Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers. Tree Genet Genomes 4:911–924
Schmitt T (2007) Molecular biogeography of Europe: Pleistocene cycles and postglacial trends. Front Zool 4:11
Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 9:615–629
Semagn K, Bjornstad A, Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540–2568
Simmons MP, Zhang LB, Webb CT, Muller K (2007) A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAMS) for phylogenetic inference. Mol Phylogenet Evol 42:528–542
Steiner WWM, Joslyn DJ (1979) Electrophoretic techniques for the genetic study of mosquitos. Mosq News 39:35–54
Sun ZN, Liu P, Li J, Meng XH, Zhang XM (2008) Construction of a genetic linkage map in Fenneropenaeus chinensis (Osbeck) using RAPD and SSR markers. Hydrobiologia 596:133–141
Sunnucks P (2000) Efficient genetic markers for population biology. Trends Ecol Evol 15:199–203
Tang SQ, Dai WJ, Li MS, Zhang Y, Geng YP, Wang L, Zhong Y (2008) Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers. Genetica 133:21–30
Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) Rflp mapping in plant-breeding - new tools for an old science. Biotechnology 7:257–264
van der Bank H, van der Bank M, van Wyk BE (2001) A review of the use of allozyme electrophoresis in plant systematics. Biochem Syst Ecol 29:469–483
Volkova PA, Shipunov AB, Elven R, Brochmann C (2008) The seashore sedges of the Russian Kola Peninsula: how many species? Flora 203:523–533
Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) Aflp - a new technique for DNA-fingerprinting. Nucleic Acids Res 23:4407–4414
Wan QH, Wu H, Fujihara T, Fang SG (2004) Which genetic marker for which conservation genetics issue? Electrophoresis 25:2165–2176
Weising K, Nybom H, Wolff K, Kahl G (2005) DNA fingerprinting in plants - principles, methods, and applications, 2nd edn. CRC Press, Boca Raton, FL
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic-markers. Nucleic Acids Res 18:6531–6535
Yang S, Bishop JG, Webster MS (2008) Colonization genetics of an animal-dispersed plant (Vaccinium membranaceum) at Mount St Helens, Washington. Mol Ecol 17:731–740
Young WP, Schupp JM, Keim P (1999) DNA methylation and AFLP marker distribution in the soybean genome. Theor Appl Genet 99:785–792
Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12:563–584
Acknowledgements
We would like to thank the professorship of Ecosystem Management, ETH (Jaboury Ghazoul) for funding. Furthermore, we are grateful for comments and corrections from Christopher Kaiser, Chris Kettle, Axel Hochkirch, and Andrea Pluess.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Finger, A., Klank, C. (2010). Review Molecular Methods: Blessing or Curse?. In: Habel, J.C., Assmann, T. (eds) Relict Species. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92160-8_18
Download citation
DOI: https://doi.org/10.1007/978-3-540-92160-8_18
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-92159-2
Online ISBN: 978-3-540-92160-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)