Mitochondrial D-loop diversity of grasscutter (Thryonomys swinderianus Rodentia: Hystricomorpha) in Ghana

Abstract

Attempts are being made to domesticate the grasscutter (Thryonomys swinderianus) for commercial production in Sub-Saharan Africa to cater for the protein needs of the people and to satisfy the craving for bushmeat, thereby reducing habitat destruction through hunting. The objective of this study was to determine the genetic diversity of grasscutter populations in Ghana. DNA was extracted from roots of hair samples collected from 84 grasscutters from three agro-ecological zones in Ghana, namely Guinea Savanna (n = 17), Forest (n = 22), and Coastal Savanna (n = 45). Mitochondrial D-loop was sequenced and the diversity was determined across the zones. Out of 26 haplotypes found, 15 were obtained from Guinea Savanna, 7 from Forest and 13 from Coastal Savanna. Haplotype diversities were 0.978, 0.853 and 0.875 respectively for Guinea Savanna, Forest and Coastal Savanna zones. Analysis of molecular variance (AMOVA) revealed significant differentiation between Forest and Savanna populations (FST = 0.14, p < 0.05). Network analysis indicated two clusters, one of which consisted of only Savanna haplotypes. Population neutrality tests showed that Forest and Coastal Savanna populations had been stable while the Guinea Savanna zone population had undergone an expansion (Fu’s FS = ‐7.132, p < 0.05). The results of this study demonstrated that the Ghanaian populations of grasscutters are highly diverse but are less distinctive.

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Adenyo, C. , Hayano, A. , Kayang, B. , Owusu, E. and Inoue-Murayama, M. (2013) Mitochondrial D-loop diversity of grasscutter (Thryonomys swinderianus Rodentia: Hystricomorpha) in Ghana. Open Journal of Animal Sciences, 3, 145-153. doi: 10.4236/ojas.2013.33022.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] Jori, F., Mensah, G.A. and Adjanohoun, E. (1995) Grasscutter production: An example of rational exploitation of wildlife. Biodiversity and Conservation, 4, 257-265. doi.org/10.1007/BF00055972
[2] Opara, M.N. (2010) The Grasscutter I: A livestock of tomorrow. Research Journal of Forestry, 4, 119-135. doi.org/10.3923/rjf.2010.119.135
[3] Annor, S.K., Adu, E.K., Donkor, J., Otsyina, H.R. and Ahiaba, J. (2009) Grasscutter production: A handbook. GTZ/MOAP, Accra.
[4] Ntiamoa-Baidu, Y. (1998) Wildlife development plan 1998-2003, Vol. 6: Sustainable use of Bushmeat. Wildlife Department, Ministry of Lands and Forestry, Accra.
[5] Owusu, E.H., Ntiamoa-Baidu, Y. and Ekpe, E.K. (2006) The dependence of local people on bushmeat in the Afadjato and Agumatsa Conservation Area, Ghana. Nature & Faune, 21, 33-44.
[6] Opara, M.N. (2010b) Grasscutter: The haematology and major parasites. Research Journal of Parasitology, 5, 214-223. doi.org/10.3923/jp.2010.214.223
[7] Adu, E.K., Alhassan, W.S. and Nelson, F.S. (1999) Smallholder farming of the greater cane rat, Thryonomys swinderianus, Temminck, in southern Ghana: A baseline survey of management practices. Tropical Animal Health and Production, 31, 223-232. doi.org/10.1023/A:1005267110830
[8] Asibey, E.O.A. (1981) Maternal and neo-natal weight in the grasscutter, Thryonomys swinderianus (Temminck) in Ghana. African Journal of Ecology, 19, 355-360. doi.org/10.1111/j.1365-2028.1981.tb01072.x
[9] Adu, E.K. and Yeboah, S. (2000) The efficacy of the vaginal plug formation after mating for pregnancy diagnosis, and embryonic resorption in utero in the greater cane rat (Thryonomys swinderianus, Temminck). Tropical Animal Health and Production, 32, 1-10. doi.org/10.1023/A:100524480092
[10] Addo, P., Dodoo, A., Adjei, S., Awumbila, B. and Awotwi, E. (2002) Determination of the ovulatory mechanism of the grasscutter. Animal Reproduction Science, 71, 125-137. doi.org/10.1016/S0378-4320(01)00184-1
[11] Adu, E.K. (2003) Patterns of parturition and mortality in weaned greater cane rats (Thryonomys swinderianus, Temminck). Tropical Animal Health and Production, 35, 425-431. doi.org/10.1023/A:1025815528916
[12] Owusu, B.A., Adu, E.K., Awotwi, E.K. and Awumbila, B. (2010) Embryonic resorption, litter size and sex ratio in the grasscutter, Thryonomys swinderianus. Animal Reproduction Science, 118, 366-371. doi.org/10.1016/j.anireprosci.2009.08.013
[13] Henry, A.J. (2011) Reproductive performance of grasscutter does at first parity and growth performance of their F1 generation. Asian Journal of Animal Science, 5, 289295. doi.org/10.3923/ajas.2011.289.295
[14] Annor, S.Y., Kagya-Agyemang, J.K., Abbam, J.E.Y., Oppong, S.K. and Agoe, I.M. (2008) Growth performance of grasscutter (Thryonomys swinderianus) eating leaf and stem fractions of Guinea grass (Panicum maximum). http://www.lrrd.org/lrrd20/8/anno20125.htm
[15] Karikari, P.K. and Nyameasem, J.K. (2009) Productive performance and carcass characteristics of captive grasscutters (Thryonomys swinderianus) fed concentrate diets containing varying levels of guinea grass. World Applied Science Journal, 6, 557-563.
[16] Oboegbulem, S.I. and Okoronkwo, I. (1990) Salmonallae in the African great cane rat (Thryonomys swinderianus ). Journal of Wildlife Diseases, 26, 199-121.
[17] Opara, M.N. and Fagbemi, B.O. (2008) Occurence and prevalence of gastro-intestinal helminthes in the wild grasscutter (Thryonomys swinderianus, Temminck). Life Sciences Journal, 5, 50-56.
[18] Kankam, T., Adu, E.K. and Awumbila, B. (2009) Gastrointestinal parasites of the grasscutter (Thryonomys swinderianus, Temminck 1827) on the Accra Plains of Ghana. African Journal of Ecology, 47, 416-421. doi.org/10.1111/j.1365-2028.2008.01020.x
[19] Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. and Saunders, N.C. (1987) Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489522.
[20] Chen, J.Z. and Herbert, P.D.N. (1999) Intraindividual sequence diversity and a hierarchical approach to the study of mutations. Mutation Research, 434, 205-217. doi.org/10.1016/S0921-8777(99)00029-4
[21] Larizza, A., Pesole, G., Reyes, A., Sbisa, E. and Saccone, C. (2002) Lineage specificity of the evolutionary dynamics of the mtDNA D-loop region in rodents. Journal of Molecular Evolution, 54, 145-155. doi.org/10.1007/s00239-001-0063-4
[22] Abyankar, A., Park, H.-B., Tonolo, G. and Luthman, H. (2009) Comparative sequence analysis of the non-proteincoding mitochondrial DNA of inbred rat strains. PLoS ONE, 4, e8148. doi.org/10.1371/journal.pone.0008148
[23] Hirota, T., Hirohata, T., Mashima, H., Satoh, T. and Obara, Y. (2004) Population structure of the large field mouse, Apodemus speciosus (Rodentia: Muridae), in suburban landscape, based on mitochondrial D-loop sequences. Molecular Ecology, 13, 3275-3282. doi.org/10.1111/j.1365-294X.2004.02324.x
[24] Meyer, J., Kohnen, A. and Brandl, R. (2009) Genetic differentiation in an arboreal rodent from African savannas. African Journal of Ecology, 48, 831-836.
[25] Mouchaty, S.K., Catzeflis, F., Jankel, A. and Arnason, U. (2001) Molecular evidence of African Phiomorpha-South American Caviomorpha clade and support for Hystricognathi based on the complete mitochondrial genome of the cane rat (Thryonomys swinderianus). Molecular Phylogenetics and Evolution, 18, 127-135. doi.org/10.1006/mpev.2000.0870
[26] Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739. doi.org/10.1093/molbev/msr121
[27] Excoffier, L. and Lischer, H.E.L. (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567. doi.org/10.1111/j.1755-0998.2010.02847.x
[28] Clement, M., Posada, D. and Crandall, K.A. (2000) TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1660.
[29] Bromham, L., Rambaut, A. and Harvey, P.H. (1996) Determinants of rate variation in mammalian DNA sequence evolution. Journal of Molecular Evolution, 43, 610-621. doi.org/10.1007/BF02202109
[30] Li, W.H., Ellsworth, D.L., Krushkal, J., Chang, B.H. and Hewett-Emmett, D. (1996) Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Molecular Phylogenetics and Evolution, 5, 182-187. doi.org/10.1006/mpev.1996.0012
[31] Reynolds, J., Weir, B.S. and Cockerham, C.C. (1983) Estimation for the coancestry coefficient: Basis for a short-term genetic distance. Genetics, 105, 767-779.
[32] Harpending, R.C. (1994) Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology, 66, 591-600.
[33] Schneider, S. and Excoffier, L. (1999) Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: Application to human mitochondrial DNA. Genetics, 152, 1079-1089.
[34] Excoffier, L. (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: Lessons from the infinite-island model. Molecular Ecology, 13, 853-864. doi.org/10.1046/j.1365-294X.2003.02004.x
[35] Peakall, R. and Smouse, P.E. (2006) GENALEX 6: Genetic analysis in excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288295. doi.org/10.1111/j.1471-8286.2005.01155.x
[36] Fu, Y.-X. (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and backgroud selection. Genetics, 147, 915-925.
[37] Sassi, P.L., Chiappero, M.B., Borghi, C. and Gardenal, C.N. (2011) High genetic differentiation among populations of the small cavy Microcavia australis occupying different habitats. Journal of Experimental Zoology, 315, 337-348. doi.org/10.1002/jez.680
[38] Riviere-Dobigny, T., Herbreteau, V., Khamsavath, K., Douangboupha, B., Morand, S., Michaux, J.R. and Hugot, J.P. (2011) Preliminary assessment of the genetic population structure of the enigmatic species Laonastes aenigmamus (Rodentia: Diatomyidae). Journal of Mammalogy, 92, 620-628. doi.org/10.1644/10-MAMM-A-028.1
[39] Lacy, R.C. (1987) Loss of genetic diversity from managed population: Interacting effects of drift, mutation, immigration, selection and population subdivision. Conservation Biology, 1, 143-158. doi.org/10.1111/j.1523-1739.1987.tb00023.x
[40] Ojeda, A.A. (2010) Phylogeography and genetic variation in the South American rodent Tympanoctomys barrerae (Rodentia: Octodontidae). Journal of Mammalogy, 91, 302-313. http://dx.doi.org/10.1644/09-MAMM-A-177.1
[41] Slatkin, M. (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution, 47, 264-279.
[42] Bennett-Lartey, S.O., Ayerno, G.S., Markwei, C.M., Asante I.K., Abbiw, D.K., Boateng, S.K., Anchirinah, V.M. and Ekpe, P. (2002) Contribution of home gardens to in situ conservation of plant genetic resources farming systems in Ghana. Proceedings of the Second International Home Gardens Workshop, International Plant Genetic Resources Institute, Rome, 83-96.
[43] Ramos-Onsins, S.E. and Rozas, J. (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092-2100. doi.org/10.1093/oxfordjournals.molbev.a004034
[44] Gaines, M.S., Diffendorfer, J.E., Tamarin, R.H. and Whittam, T.S. (1997) The effects of habitat fragmentation on the genetic structure of small mammal populations. Journal of Heredity, 88, 294-304. doi.org/10.1093/oxfordjournals.jhered.a023107
[45] IUCN (2011) IUCN red list of threatened species. Version 2011.1. http://www.iucnredlist.org/
[46] Flanders, J., Jones, G., Benda, P., Dietz, C., Zhang, S., Li, G., Sharifi, M. and Rossiter, S.J. (2009) Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum: Contrasting results from mitochondrial and microsatellite data. Molecular Ecology, 18, 306-318. doi.org/10.1111/j.1365-294X.2008.04021.x

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