Nucleotide sequences of mitochondrial cytochrome b gene for phylogeny of some species of Rodentia

Lamiaa Elsayed Mokhtar Deef

doi:10.14393/BJ-v39n0a2023-66743

Authors

Lamiaa Elsayed Mokhtar Deef Damietta University https://orcid.org/0000-0002-4462-3432

DOI:

https://doi.org/10.14393/BJ-v39n0a2023-66743

Keywords:

Gene, Gerbils, Monophyly, Myomorpha, Taxon.

Abstract

Order Rodentia contains approximately half of all living mammalian species. Most of the living species diversity within rodents is within five monophyletic radiations: Hystricognathi, Sciuridae, Geomyoidea, Dipodidae, and Muroidea. The samples collected across different areas of Egypt were analyzed by means of mitochondrial cytochrome b gene sequence analysis to ascertain the true taxonomic status between the studied species. For phylogenetic analysis, the cytochrome b sequences from this study were combined with previously published data. This study reveals that all species were divided into two main clades, the first for the Gerbillinae taxon and the second for the other studied genera in the molecular phylogenetic trees and demonstrates that Gerbillus species form a sister group with Dipodillus species. The phylogenetic relationships specified for the murine genera. Clustering was obtained between Mus and Rattus as well as in all Gerbillinae species. This study provides the first insight into the genetic diversity of some rodents in Egypt.

Downloads

Download data is not yet available.

References

ABAZAID, AA. Efficiency of some common used rodenticide and some new alternatives against rodents in Qena Governorate. M.Sc. Thesis, Faculty of Agriculture, Assiut University, 1990, 93.

ANDERSON, S. and JONES, J.K. Orders and Families of Recent Mammals of the World, Wiley, New York, 1984.

BALAKIREV, A. and ROZHNOV, V.V. Contribution to the species composition and taxonomic status of some Rattus inhabiting Southern Vietnam and Sundaland. Russian journal of theriology. 2012, 11, 33-45. https://doi.org/10.15298/RUSJTHERIOL.11.1.03

BRYANT, J.D. and MCKENNA, M.C. Cranial anatomy and phylogenetic position of Tsaganomys altaicus (Mammalia: Roden tia) from the Hsanda Gol Formation (Oligocene), Mongolia. American Museum novitates. 1995, 3156, 1-42.

CATZEFLIS, F.M., et al. DNA-DNA hybridization evidence of the rapid rate of muroid rodent DNA evolution. Molecular Biology and Evolution. 1987, 4(3), 242-253. https://doi.org/10.1093/oxfordjournals.molbev.a040444

CHALINE, J. and MEIN, P. Les Rongeurs et l’Evolution, Doin, Paris, 1979.

CHARWORTH-MUSTERS, J.L. and ELLERMAN, J.R. A revision of the genus Meriones. Proceedings of the Zoological Society of London. 1947, 117, 478-504.

CHEVRET, P. and DOBIGNY, G. Systematics and evolution of the subfamily Gerbillinae (Mammalia, Rodentia, Muridae). Molecular Phylogenetics and Evolution. 2005, 35(3), 674-688. https://doi.org/10.1016/j.ympev.2005.01.001

CHEVRET, P., et al. Molecular evidence that the spiny mouse (Acomys) is more closely related to gerbils (Gerbillinae) than to true mice (Murinae). Proceedings of the National Academy of Sciences of the United States of America. 1993, 90(8), 3433-3436. https://doi.org/10.1073/pnas.90.8.3433

CHOUMOWITCH, W. Observations sur les mœurs et l’éthologie de quelques petits mammifères du Sud tunisiens. Bulletin de la Société de Sciences Naturelles de Tunisie. 1954, 7, 81-88.

COOPER, A. DNA from Museum Specimens. In: Herrmann B, Hummel S (Eds) Ancient DNA - Recovery and analysis of genetic material from paleontological, archaeological, mu¬seum, medical, and forensic specimens. Springer, New York, 1994, 49-165.

DAYRAT, B. Towards integrative taxonomy. Biological Journal of the Linnean Society. 2005, 85, 407-415. https://doi.org/10.1111/j.1095-8312.2005.00503.x

DEMENOCAL, P. African climate change and faunal evolution during the Pliocene-Pleistocene. Earth and Planetary Science Letters. 2004, 220, 3-24. https://doi.org/10.1016/S0012-821X(04)00003-2

D'ERCHIA, A.M., et al. The guinea-pig is not a rodent. Nature. 1996, 381(6583), 597-600. https://doi.org/10.1038/381597a0

DUBOIS, J.Y., CATZEFLIS, F.M. and BEINTEMA, J.J. The phylogenetic position of "Acomyinae" (Rodentia, Mammalia) as sister group of a Murinae + Gerbillinae clade: evidence from the nuclear ribonuclease gene. Molecular Phylogenetics and Evolution. 1999, 13(1), 181-192. https://doi.org/10.1006/mpev.1999.0674

EL-DEEP, H.T.H., LOKMA, H.E. and EL-FISHAWY, A. Field studies on population dynamics and reproductive biology of the Nile rat Arvicanthis niloticus. Zagazig Journal of Agriculture Research. 1992, 19(3), 1431-1435.

ELLERMAN, J.R. The Families and Genera of Living rodents. vol. 1. London. Rodents other than Muridae. Trustees of the British Museum (Natural History), London, 1940, 690.

ELLERMAN, J.R. The families and genera of living rodents. vol. 2. London. Family Muridae. British Museum (Natural History), 1941, 690.

ELLERMAN, J.R. Notes on some Asiatic rodents in the British Museum. Proceedings of the Zoological Society of London. 1947, 117(2), 259-271.

ELLERMAN, J.R. Key to the rodents of Southwest Asia in the British Museum collection. Proceedings of the Zoological Society of London. 1948, 118(3), 765-816.

EMBARAK, M.Z. Ecological and control studies on rodent and their ectorperasits in cultivated and newly reclaimed areas. M. Sc. Thesis, Faculty of Agriculture. Assiut University, 1997.

GRAUR, D. Reply from d. Graur. Trends in Ecology and Evolution. 1993, 8(9), 341-342. https://doi.org/10.1016/0169-5347(93)90247-M

GRAUR, D., HIDE, W.A. and LI, W.H. Is the guinea-pig a rodent?. Nature. 1991, 351(6328), 649-652. https://doi.org/10.1038/351649a0

GRAY, J.E. An outline of an attempt at the disposition of Mammalia into tribes and families, with a list of the genera apparently appertaining to each tribe. Annals of Philosophy. 1825, 10, 337-344.

GUINDON, S., et al. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology. 2010, 59(3), 307-321. https://doi.org/10.1093/sysbio/syq010

HARRISON, D.L. and BATES, P.J.J. The Mammals of Arabia. Harrison Zoological Museum, Sevenoaks, UK, 1991.

HARTENBERGER, J.-L. The order Rodentia: Major questions on their evolutionary origin, relationships, and suprafamilial systematics. In “Evolutionary Relationships among Rodents: A Multidisciplinary Analysis” (W. P. Luckett and J.-L. Hartenberger, Eds.), Plenum, New York. 1985, 1-33.

HEPTNER, W.G. Notizen uber die Gerbillidae (Mammala, Rodenta). V. Uber die einteilung der Gerbillidae. Zoologischer Anzeiger. 1933, 102(3/4), 107-112.

HOOGSTRAL, H. A Brief Review of the Contemporary Land Mammals of Egypt (including Sinai). 2. Lagomorpha and Rodentia. Journal of the Egyptian Public Health Association. 1963, 38, 1-35.

HUCHON, D., CATZEFLIS, F.M. and DOUZERY, E.J. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents. Molecular Biology and Evolution. 1999, 16(5), 577-589. https://doi.org/10.1093/oxfordjournals.molbev.a026140

HUCHON, D., CATZEFLIS, F.M. and DOUZERY, E.J. Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi. Proceedings Biological Sciences. 2000, 267(1441), 393-402. https://doi.org/10.1098/rspb.2000.1014

HUSSIEN, S.S.M. Ecological studies and control of certain rodents in Beni suef Governorate. M. Sc. Thesis, Faculty of Agriculture, Cairo University, 1991.

IRWIN, D.M., KOCHER, T.D. and WILSON, A.C. Evolution of the cytochrome b gene of mammals. Journal of Molecular Evolution. 1991, 32(2), 128-144. https://doi.org/10.1007/BF02515385

JACOBS, L.L. Fossil rodents (Rhizomyidae and Muridae): from Neogene Siwalik deposits, Pakistan. Museum of Northern Arizona Press Bulletin. 1978, 52, 1-103.

KHALIFA, M.A., YOUNES, M. and GHAZY, A. Cytochrome b shows signs of adaptive protein evolution in Gerbillus species from Egypt. The Journal of Basic and Applied Zoology. 2018, 79, 1-8. https://doi.org/10.1186/S41936-018-0014-X

KNOWLTON, N. Cryptic and sibling species among the decapod Crustacea. Journal of Crustacean Biology. 1986, 6(3), 356-363. https://doi.org/10.1163/193724086X00208

KUMAR, S., STECHER, G. and TAMURA, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 2016, 33(7), 1870-1874. https://doi.org/10.1093/molbev/msw 054

LARA, M.C., PATTON, J.L. and DA SILVA, M.N. The simultaneous diversification of South American echimyid rodents (Hystricognathi) based on complete cytochrome b sequences. Molecular Phylogenetics and Evolution. 1996, 5(2), 403-413. https://doi.org/10.1006/mpev.1996.0035

LAVOCAT, R. and PARENT, J.-P. Phylogenetic analysis of middle ear features in fossil and living rodents. In “Evolutionary Relationships among Rodents: A Multidisciplinary Analysis” (W. P. Luckett and J.-L. Hartenberger, Eds.), Plenum, New York. 1985, 333-354.

LAY, D.M. The anatomy, physiology, functional significance and evolution of specialized hearing organs of Gerbillinae rodents. Journal of Morphology. 1972, 138, 41-120.

LAY, D.L. Taxonomy of the genus Gerbillus (Mammalia: Muridae: Gerbillinae) with comments on applications of generic and subgeneric names and an annotated list of species. Zeitschrift fuer Saeugetierkunde. 1983, 48(6), 329-354.

LESSA, E.P. and COOK, J.A. The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation. Molecular Phylogenetics and Evolution. 1998, 9(1), 88-99. https://doi.org/10.1006/mpev.1997.0445

LUCKETT, W.P. and HARTENBERGER, J.-L., 1985. Evolutionary relationships among rodents: Comments and conclusions. In “Evolutionary Relationships among Rodents: A Multidisciplinary Analysis” (W. P. Luckett and J.-L. Hartenberger, Eds.), Plenum, New York. pp. 685-712.

MADDALENA, T., et al. Note sur la présence de Gerbillus henleyi (de Winton, 1903) au Burkina Faso. Mammalia. 1988, 52(2), 282-284.

MENG, C. The auditory region of Reithroparamys delicatissimus (Mammalia, Rodentia) and its systematic implications. American Museum novitates. 1990, 2972, 1-35.

MONADJEM, A., et al. Rodents of Sub-Saharan Africa. A biogeographic and taxonomic synthesis. Walter de Gruyter GmbH, Berlin/Munich/Boston, 2015.

MUSSER, G.C. and CARLETON, M.D. Family Muroidea. A taxonomic and geographic reference, in: D.E. Wilson, D.M. Reeder (Eds.), Mammal species of the world, Second ed., Smithsonian Institution Press, Washington and London. 1993, 501-755.

MUSSER, G.C. and CARLETON, M.D. Superfamily Muroidea, in: D.E. Wilson, D.M. Reeder (Eds.), Third ed., Mammal species of the world: a taxonomic and geographic reference, Vol. 2, Johns Hopkins University Press, Baltimore. 2005, 894-1531.

NEDBAL, M.A., HONEYCUTT, R.L. and SCHILITTER, D.A. Higher-level systematics of rodents (Mammalia, Rodentia): Evidence from the mitochondrial 12S rRNA gene. Journal of Mammalian Evolution. 1996, 3, 201-237. https://doi.org/10.1007/BF01458181

NIKOLETOPOULOS, N.P., CHONDROPOULOS, B. and FRAGUEDAKIS-TSOLIS, S. Albumin evolution and phylogenetic relationships among Greek rodents of the families Arvicolidae and Muridae. Journal of Zoology. 1992, 228(3), 445-453. https://doi.org/10.1111/J.1469-7998.1992.TB04447.X

NOVACEK, M.J. Mammalian phylogeny: Morphology and molecules. Trends in Ecology and Evolution. 1993, 8(9), 339-340. https://doi.org/10.1016/0169-5347(93)90245-K

NOWAK, R.M. Walker’s Mammals of the World, 6th edn. The Johns Hopkins University Press, Baltimore, MD, 1999.

OSBORN, D.J. and HELMY, I. The contemporary land mammals of Egypt (including Sinai). Fieldiana Zoology. 1980, 5, 1-579.

PÄÄBO, S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proceedings of the National Academy of Sciences of the United States of America. 1989, 86(6), 1939-1943. https://doi.org/10.1073/pnas.86.6.1939

PAVLINOV, I.J., 2001. Current concepts of Gerbillidae phylogeny and classification, African small mammals, in: Proceedings of the 8th International Symposium on African Small Mammals, Paris. pp. 141-149.

PETTER, F. Evolution du dessin de la surface d’usure des molaires des Gerbillides. Mammalia. 1959, 23(3), 304-315. https://doi.org/10.1515/mamm.1959.23.3.304

PETTER, F. Répartition géographique et écologique des rongeurs désertiques; du Sahara occidental à l' Iran oriental. Mammalia. 1961, 25, 1-222.

QUMSIYEH, M.B. and SCHLITTER, D.A. Cytogenetic data on the rodent family Gerbillidae, Occas. Papers Mus Texas Tech University. 1991, 144, 1-20.

REYES, A., et al. Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris. Molecular Biology and Evolution. 2000, 17(6), 979-983. https://doi.org/10.1093/oxfordjournals.molbev.a026379

SALIT, A.M., et al. Composition of the rodent species in newly reclaimed semi-desert area comparing with cultivated land. Assiut Journal of Agriculture Sciences. 1982, 13(2), 53-62.

SARICH, V.M. Rodent macromolecular systematics. In “Evolutionary Relationships among Rodents” (W.P. Luckett and J.-L. Hartenberger, Eds.), Plenum, New York. 1985, 423-452.

TONG, H. Origine et evolution des Gerbillidae (Mammalia, Rodentia) en Afrique du Nord. Mémoires de la Société géologique de France. 1989, 155, 1-120.

TULLBERG, T. Ueber das system der Nagetiere: Eine phylogenetische studie. Nova acta Regiae Societatis Scientiarum Upsaliensis. 1899, 18, 1-514.

WASSIF, K. Studies on Gerbils of the subgenus Dipodillus recorded from Egypt. A’ins Shams Science Bulletin. 1956, 1, 173-194.

WIENS, J.J. Species delimitation: New approaches for discovering diversity. Systematic Biology. 2007, 56(6), 875-878. https://doi.org/10.1080/10635150701748506

WILSON, D.E. and REEDER, D.M. Mammal Species of the World: A Taxonomic and Geographic Reference, Smithsonian Institute, Washington, DC, 1993.