Molecular Markers in Conservation Biology Studies
Subject Areas : environmental engineering
Nafiseh Momeni
1
*
,
Mohsen Ahmadpour
2
1 - Department of Environmental Sciences, Faculty of Fisheries and Environment, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
2 - Research Center for the Caspian Region, University of Mazandaran, Babolsar, Iran
Keywords: Molecular marker, Conservation genetics, Environmental Conservation, wildlife, ,
Abstract :
Introduction: Molecular science has an important role in the conservation and stability of animal species. Biology conservasion is essential to identify populations decline to implement adequate restoration programs. Despite molecular developments, there are many studies in this field to better understanding molecular merkers. Objective: In this study, the genetic markers were examined that were used in more than 100 Persian and English articles. Materials and Methods: Sources were selected from studies in the field of conservation biology, biology, molecular ecology, molecular markers and other related topics to provide a clearer model of each marker usage in the field of conservation biology. Results: In general, each molecular marker is not limited to one case, but there is a clear relationship between the characteristics of each marker and the maximum usage in many cases. Discussion: However, selecting the adequate marker in a wildlife conservation study the following steps are suggested: 1) study the species 2) Check the problems scale 3) Characteristics of molecular markers. Also, considering the mutation rate and the variability degree among nuclear and mitochondrial markers has a role in selecting of adequate marker. But in order to obtain accurate genetic and ecological information in conservation biology, the principles of population genetics and molecular evolution require more comprehensive education; By comparing molecular results with other sciences and quality control of the sequenced gene, more reliable results were obtained in the field of genetics and conservation.
Aghazadeh, L., & NIKBIN, S., & Mirzaei Aghjegheshlagh, f., & Hedaiat Evrigh, N. (2020). Using D-Loop region to study the genetic structure and phylogenetic analysis of Iranian red deer. ANIMAL SCIENCE RESEARCHES (FACULTY OF AGRICULTURE, UNIVERSITY OF TABRIZ), 29(4), 17-33. https://www.sid.ir/en/journal/ViewPaper.aspx?id=790645
Ahmadpour, M., Moradi, H. V., Rezaei, H. R., Oshaghi, M. A., Hapeman, P., & Hosseinzadeh Colagar, A. (2020). Genetic diversity and structure of the Great Gerbil, Rhombomys opimus, in Iran (Mammalia: Rodentia). Zoology in the Middle East, 66(1), 1-12.
Aliabadian, M., Kaboli, M., Prodon, R., Nijman, V., & Vences, M. (2007). Phylogeny of Palaearctic wheatears (genus Oenanthe)—Congruence between morphometric and molecular data. Molecular phylogenetics and evolution, 42(3), 665-675.
Amills, M., Capote, J., Tomas, A., Kelly, L., & Obexer-Ruff, G. (2004). Strong phylogeographic relationships among three goat breeds from the Canary Islands. Journal of Dairy Research 71(3):257-262
An, J., Lee, M. Y., Min, M. S., Lee, M. H., & Lee, H. (2007). A molecular genetic approach for species identification of mammals and sex determination of birds in a forensic case of poaching from South Korea. Forensic Sci. Int. 167, 59–61.
Anne, C. (2006). Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects. Genetica, 127(1-3), 101-120.
Arif, I. A., & Khan, H. A. (2009). Molecular markers for biodiversity analysis of wildlife animals: a brief review. Animal Biodiversity and Conservation, 32.1: 9–17.
Arif, I. A., Khan, H. A., Bahkali, A. H., Al Homaidan, A. A., Al Farhan, A. H., Al Sadoon, M, & Shobrak, M. (2011). DNA marker technology for wildlife conservation. Saudi journal of biological sciences, 18(3), 219-225.
Avise, J. C. (2004). Molecular markers, natural history an evolution. 2nd ed. New York, Sinauer Associates, 684p.
Ayele, T. B., Gailing, O., & Finkeldey, R. (2011). Assessment and integration of genetic, morphological and demographic variation in Hagenia abyssinica (Bruce) J. F. Gmel to guide its conservation. J Nat Conserv 19:8–17
Bensch, S., Akesson, M. (2005). Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol. 14:2899–2914.
Boontong, C., Pandey, M., & Changtragoon, S. (2008). Isolation and characterization of microsatellite markers in Indian Neem (Azadirachta Indica Var. Indica A. Juss) and cross-amplification in Thai Neem (A. Indica Var. Siamensis Valenton). Conserv Genet. doi:10. 1007/s10592-008- 9610-5
Boore, J. L. (1999). Animal mitochondrial genomes. Nucleic Acids Research 27:1767-1780
Buono, V., Galliani, G., Mancini, E., Davoli, F., Mengoni, C., Mucci, N., & Vignoli, L. (2018). An improved microsatellite panel to assess genetic variability of the Italian smooth newt (Lissotriton vulgaris meridionalis). Journal of genetics, 97(2), 569-573.
Cakmak, E., Akin Pekşen, C., Kirazli, C., Yamac, E., Bensch, S., & Bilgin, C. C. (2019). Genetic diversity is retained in a bottlenecked Cinereous Vulture population in Turkey. Ibis, 161(4), 793-805.
Campbell, D, Duchesne, P., & Bernatchez, L. )2003). AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites. Mol Ecol. 12:1979–1991.
Changtragoon, S., & Szmidt, A. E. (1997). The evaluation of genetic diversity and resources of tropical forest trees in Thailand by using molecular markers. In: The 6th annual international workshop of BIO-REFOR, the university of Queensland, Brisbane, Australia, 2–9 December 1997, pp 169–171
Changtragoon, S., Jalonen, R., & Lowe, A. J. (2017). Use of molecular markers in the conservation management of tropical trees. In Biodiversity and conservation of woody plants (pp. 155-195). Springer, Cham.
Chelomina, G. N., Spiridonova, L. N., Kozyrenko, M. M., et al, (1999). Use of RAPD-PCR-analysis of cellular DNA for the evaluation of genetic polymorphism and subspecies diagnostics of the Far Eastern leopard Panthera pardus orientalis. Genetika 35, 681– 687.
Chen, J., Zeng, YF., Liao, WJ. et al. (2017). A novel set of single-copy nuclear gene markers in white oak and implications for species delimitation. Tree Genetics & Genomes 13, 50 https://doi. org/10. 1007/s11295-017-1130-3
DeWoody, J. A., & Avise, J. C. (2000). Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J. Fish Biol, 56, 461–473.
Faizi, H., & Heidari, N., & Rastegar Pouyani, N., & Rastegar Pouyani, E. (2016). Molecular phylogeny of the genus eumeces wiegmann, 1834 (reptilia: scincidae) in iran, inferred from 16s mitochondrial dna. Nova biologica reperta, 3(2), 123-130. Https://www.sid.ir/en/journal/viewpaper.aspx?id=531035
Fox, G. E., & Woese, C. R. (1975). The architecture of 5S rRNA and its relation to function. J Mol Evol 6: 61-76.
Frankham, R., Ballou, J. D., & Briscoe, D. A. (2004). A primer of conservation genetic. Cambridge University Press, New York. 93.
Freeland, J., Kirk, H., & Petersen, S. (2011). Molecular Ecology (2nd ed. ). Chichester (UK): John Wiley & Sons.
Galtier, N., & Gouy, M. (1995). Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci U S A 92: 11317-11321.
Gerber, S., Mariette, S., Streiff, R., Bode´ne´s, C., & Kremer, A. (2000). Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis. Mol Ecol. 9:1037–1048.
Goerge, E. F., Pechman. C. R., Woese, C. R. (1977). Comparative cataloging of 16S ribosomal ribonucleic acid: Molecular approach to prokaryotic systematics. Int J Syst Bacteriol 27: 44-57.
Golestani, N., Gilkolaei, S. R., Safari, R., & Reyhani, S. (2010). Population genetic structure of the Silver Pomfret, Pampus argenteus (Euphrasén, 1788), in the Persian Gulf and the Sea of Oman as revealed by microsatellite variation: (Osteichthyes: Stromateidae). Zoology in the Middle East, 49(1), 63-72.
Gray, M., & Burger, G., & Lang, B. (1999). Mitochondrial Evolution. Science (New York, N. Y). 283. 1476-81. 10. 1126/science. 283. 5407. 1476.
Gupta, S. K., Verma, S. K., & Singh, L. (2005). Molecular insight into a wildlife crime: the case of a peafowl slaughter. Forensic Sci. Int. 154, 214–217.
Gurdeep, R. et al, (2004). Species determination and authentication of meat samples by mitochondrial 12S RRNA gene sequence analysis and conformation-sensitive gel electrophoresis. Curr. Sci. 87, 1278– 1281.
Gutell, R. R., Gray M. W., & Schnare, M. N. (1993). A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. Nucleic Acids Res 21: 3055- 3074
Haanes, H, Roed, K. H., Perez-Espona, S., & Rosef, O. (2011). Low genetic variation support bottlenecks in Scandinavian red deer. European journal of wildlife research, 57(6), 1137-1150.
Hadrys, H., Balick, M. and Schierwater, B. (1992). Application of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol. Ecol. 1: 55-63.
Hardouin, E. A., Butler, H., Cvitanović, M., Ulrich, R. G., Schulze, V., Schilling, A. K., & Hodder, K. H. (2021). Wildlife conservation in a fragmented landscape: the Eurasian red squirrel on the Isle of Wight. Conservation Genetics, 1-13.
Hasan, M., Islam, M. M., Khan, M. M. R., Alam, M. S., Kurabayashi, A., Igawa, T., & Sumida, M. (2012). Cryptic anuran biodiversity in Bangladesh revealed by mitochondrial 16S rRNA gene sequences. Zoological science, 29(3), 162-172.
Hassan, L. M., Arends, D., Rahmatalla, S. A., Reissmann, M., Reyer, H., Wimmers, K,. . . & Brockmann, G. A. (2018). Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species. European Journal of Wildlife Research, 64(5), 1-10.
Hedrick, P. W. (1999). Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution, 53, 313–318.
Hu, J., Fang, S. G., & Wan, Q. H. (2006). Genetic diversity of Chinese water deer (Hydropotes inermis inermis): implications for conservation. Biochem. Genet. 44, 161–172.
Imani Harsini, J., & Rezaei, H., & Naderi, S., & Varasteh Moradi, H. (2017). Genetic structure of red fox (vulpes vulpes) based on d-loop region sequence of mitochondrial genome in central region of Iran. Journal Of Natural Environment (Iranian Journal Of Natural Resources), 69(4), 917-933. https://www.sid.ir/en/journal/ViewPaper.aspx?id=547795
Janczewski, D. N., Modi, W. S., Stephens, J. C., O’Brain, S. J. (1995). Molecular evaluation of mitochondrial 12S RNA and cytochrome b sequences in the Pantherine lineage of Felidae. Mol. Biol. Evol. 12, 690–707
Jolodar, A. (2019). Molecular Characterization and Phylogeny Analysis Based on Sequences of Cytochrome Oxidase gene From Hemiscorpius lepturus of Iran. . BMC Res Notes 14:40. https://doi. org/10. 1186/s13104-021-05449-3
Kabiri Balajadeh, H.R., Rezaei, H.R., Naderi, S. (2013). Genetic diversity of Roe deer (Capreolus capreolus) in Golestan and Mazandaran Provinces based on mtDNA D-loop gene sequencing [In Persian]. Animal Environment, 9, 49–56.
Kashani, E., Rezaei, H., Khorasani, N., & Naderi, M. (2019). Phylogeny, genetic diversity and population structure of Brandts hedgehog Paraechinus hypomelas, inferred from the mitochondrial evidences. Journal of Wildlife and Biodiversity, 3(2), 18-28.
Khalilzadeh, P., Rezaei, H. R., Fadakar, D., Serati, M., Aliabadian, M., Haile, J., & Goshtasb, H. (2016). Contact zone of Asian and European wild boar at North West of Iran. PloS one, 11(7), e0159499.
Khan, H. A., Arif, I. A., Bahkali, A. H., Al Farhan, A. H,, Al Homaidan, A. A. (2008). b. Bayesian, maximum parsimony and UPGMA models for inferring the phylogenies of antelopes using mitochondrial markers. Evol. Bioinform. 4, 263–270.
Kjer, K. M. (1995). Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol Phylogenet Evol 4: 314-330.
Lander, E. S. (1996). The new genomics: global views of biology. Science,274:536–539.
Lapinski, A.G., Pavlenko, M.V., Solovenchuk, L.L. et al. (2016). Some limitations in the use of the mitochondrial DNA cytb gene as a molecular marker for phylogenetic and population-genetic studies by the example of the Apodemus genus. Russ J Genet Appl Res 6, 84–90. https://doi.org/10.1134/S2079059716010093
Lee, S. L., Ng, K. K. S., Saw, L. G. et al, (2006). Linking the gaps between conservation research and conservation management of rare dipterocarps: a case study of Shorea lumutensis. Biol Conserv 131(1):72–92
Lei, R., Hu, Z., Jiang, Z., & Yang, W. (2003). Phylogeography and genetic diversity of the critically endangered Przewalski's gazelle. In Animal Conservation Forum (Vol. 6, No. 4, pp. 361-367). Cambridge University Press.
Lougheed, S. C., Gibbs, H. L., Prior, K. A., & Weatherhead, P. J. (2000). A comparison of RAPD versus microsatellite DNA markers in population studies of the massasauga rattlesnake. J. Hered. 91, 458–463.
Lowe, A. J., Harris, S.A., & Ashton, P. (2004). b. Ecological genetics: design. Anal Appl, Blackwells, Oxford, p 326Laikre L (2010) Genetic diversity is overlooked in international conservation policy implementation. Conserv Genet 11:349–354
Lowe, A. J., Moule, C., Trick, M., & Edwards, K. J. (2004). a. Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theor Appl Genet 108:1103–1112
Lucchini, V. (2003). AFLP: a useful tool for biodiversity conservation and management. C. R. Biol. 326, S43–S48
Luikart, G. H., Aitken, S. N., & Allendorf, F. W. (2012). Conservation and the Genetics of Populations. Germany: Wiley.
Manel, S,, Joost, S., Epperson, B. K., Holderegger, R., Storfer, A., Rosenberg, M. S.,. . . & FORTIN, M. J. (2010). Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19(17), 3760-3772.
Manzari, S., Polaszek, A., Belshaw, R., & Quicke, D. L. (2002). Morphometric and molecular analysis of the Encarsia inaron species-group (Hymenoptera: Aphelinidae), parasitoids of whiteflies (Hemiptera: Aleyrodidae). Bull Entomol Res 92: 165-176.
Min, M. S., Okumura, H., Jo, D. J., et al, (2004). Molecular phylogenetic status of the Korean goral and Japanese serow based on partial sequences of the mitochondrial cytochrome b gene. Mol. Cells 17, 365–372.
Mirzakhah, M., Naderi, S., Rezaei, H. R., Fadakar, D., & Naseri, M. (2015). Phylogeny of gazelles in some islands of Iran based on mtDNA sequences: Species identification and implications for conservation. Caspian Journal of Environmental Sciences, 13, 21–30.
Moritz, C., Dowling, T. E., & Brown, W. M. (1987). Evolution of Animal mitochondrial DNA-revelence for population biology and systematic. Ann Rev Ecol Syst 18: 269-292.
Neff, B. D., & Gross, M. R. (2001). Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution, 55, 1717–1733.
Ng, W. L., & Szmidt, A. E. (2013) A simple and inexpensive molecular assay for species identification of Indo-West Pacific Rhizophora mangroves for conservation and management. Conserv Genet Resour. doi:10. 1007/s12686-013-9973-x
Ng, W. L., Chan, H. T., & Szmidt, A. E. (2013). Molecular identification of natural mangrove hybrids of Rhizophora in Peninsular Malaysia. Tree Genet Genomes. doi:10. 1007/s11295-013-0619-7
Ottewell, K. M., Bickerton, D. C., Byrne, M., & Lowe, A. J. (2015). Bridging the gap: A genetic assessment framework for population-level threatened plant conservation prioritization and decision-making. Divers Distrib 22:174–188
Pandey, P. K., Dhotre, D. P., Dharne, M. S., et al. (2007). Evaluation of mitochondrial 12S rRNA gene in the identification of Panthera pardus fusca (Meyer, 1794) from field-collected scat samples in the Western Ghats, Maharashtra, India. Curr. Sci. 92, 1129–1133.
Panicker, V. P., Haridas, P. C., Narayanan, A., Mohammed, S., & Babu, B. C. (2019). Mitochondrial 12S rRNA gene sequence analysis, a tool for species identification. Journal of Wildlife and Biodiversity, 3(3), 29-35.
Patwardhan, A., Ray, S., & Roy, A. (2014). Molecular markers in phylogenetic studies-a review. Journal of Phylogenetics & Evolutionary Biology, 2014.
Prakash, S., Patole, M. S., Ghumatkar, S. V., Nadode, S. D., Shinde, B. M., & Shouche, Y. S. (2000). Mitochondrial 12S rRNA sequence analysis in wildlife forensics. Curr. Sci. 78, 1239–1241.
Rastogi, G., Dharne, M. S., Walujkar, S., Kumar. A., Patole, M. S., & Shouche, Y. S. (2007). Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers. Meat science. 76: PP. 666-674.
Reineke, A., Schmidt, O., Zebitz, C. P (2003). Differential gene expression in two strains of the endoparasitic wasp Venturia canescens identified by cDNA-amplified fragment length polymorphism analysis. Mol Ecol. 2003 Dec;12(12):3485-92. doi: 10. 1046/j. 1365-294x. 2003. 01990. x.
Rodrigues, F. P., Garcia, J. F., Ramos, P. R. R., Bortolozzi, J., & Duarte, J. M. B. (2007). Genetic diversity of two Brazilian populations of the Pampas deer (Ozotoceros bezoarticus, Linnaeus 1758). Brazilian Journal of Biology, 67(4), 805-811.
Russo, C. A., Takezaki, N., Nei, M. (1996). Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol 13: 525-536.
Schmidt, S., Driver, F., Barro, P. D. (2006). The phylogenetic characteristics of three different 28S rRNA gene regions in Encarsia (Insecta, Hymenoptera, Aphelinidae). Org Divers Evol 6: 127-139.
Selkoe, K. A., & Toonen, R. J. (2006). Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology letters, 9(5), 615-629.
Squirrell, J., Hollingsworth, P. M., Woodhead, M., Russell, J., Lowe, A. J., Gibby, M., & Powell, W. (2003). How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339– 1348
Szmidt, A. E. (1995). Molecular population genetics and evolution: two missing elements in studies of biodiversity. In: Boyle TJ, Boontawee B (eds) Measuring and monitoring biodiversity in tropical and temperate forest. CIFOR, Bogor, Indonesia, pp 177–193
Tognoli, C., Saroglia, M., Terova, G., Gornati, R., & Bernardini, G. (2011). Identification of fish species by 5S rRNA gene amplification. Food chemistry, 129(4), 1860-1864.
Vignal, A., Milan, D., SanCristobal, M., & Eggen, A. (2002). A review on SNP and other types of molecular their use in animal genetics. Genet. Sel. Evol. 34: 275-305.
Vinceti, B., Loo, J., Gaisberger, H., van Zonneveld, M. J. et al, (2013). conservation priorities for Prunus africana defined with the aid of spatial analysis of genetic data and climatic variables. PLoS ONE 8(3):e59987. doi:10. 1371/journal. pone. 0059987
Wang, Z. , Baker, A. J. , Hill, G. E. , & Edwards, S. V. (2003). Reconciling actual and inferred population histories in the house finch (Carpodacus mexicanus) by AFLP analysis. Evolution, 57(12), 2852-2864.
Willing, E. M., Dreyer, C., & Van Oosterhout, C. (2012). Estimates of genetic differentiation measured by F ST do not necessarily require large sample sizes when using many SNP markers. PloS one, 7(8), e42649.
Wink, M., El-Sayed, A. A., Sauer-Gurth, H., & Gonzalez, J. (2010). Molecular Phylogeny of owls (Strigiformes) inferred from DNA sequences of the mitochondrial cytochrome b and the nuclear RAG-1 gene. Ardes. 97: PP. 581-591.
Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51: 221-271.
Yaish-Bachari, S., Zolgharnein, H., Mohammadi, M., Salari-AliAbadi, M., Ghasemi, S. (2012). Study of Genetic Diversity of mudskipper (Periophthalmus waltoni) using RAPD markers in the Persian Gulf. Journal of Marine Science and Technology, 11(3), 62-70.
Yang, W, Kang, X, Yang, Q, Lin, Y. and Fang, M. (2013). Review on the development of genotyping methods for assessing farm animal diversity. J Anim Sci Bio. 4(2):1– 6.
Yli-Mattila, T., Paavanen-Huhtala, S., Fenton, B., & Tuovinen, T. (2000). Species and strain identification of the predatory mite Euseius finlandicus by RAPD-PCR and ITS sequences. Exp Appl Acarol 24: 863-880.
Zardoya, R., & Meyer, A. (1996). Phylogenetic performance of mitochondrial proteincoding genes in resolving relationships among vertebrates. Mol Biol Evol 13: 933-942.
Zenger, K. R, Stow, A. J, Peddemors, V, Briscoe, D. A, Harcourt, R. G. (2006). Widespread utility of highly informative AFLP molecular markers across divergent shark species. J. Hered. 97, 607–611.
Zhang, F., & Jiang, Z. (2006). Mitochondrial phylogeography and genetic diversity of Tibetan gazelle (Procapra picticaudata): implications for conservation. Mol. Phylogenet. Evol. 41, 313–321
Zietkiewicz, E., Rafalski, A., & Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20(2), 176-183.