Comparison of structure and genetic diversity of Common Pochard (Aythya ferina) using cytochrome B mitochondrial gene in northern and southern regions of the country
Subject Areas :
Biodiversity
Shabnam chavoshi
1
(Ph, D., Faculty of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Trhran, Iran.)
Jalil Imani
2
(Assistant Prof., Faculty of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Trhran, Iran. *(Corresponding Authors))
hamidReza Rezaei
3
(Associate PR., Gorgan University of Agricultural Sciences and Natural Resources.)
Pargol Ghavam Mostafav
4
(Assistant Prof., Faculty of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Trhran, Iran.)
Received: 2022-06-12
Accepted : 2022-09-10
Published : 2023-03-21
Keywords:
Aythya ferina,
mitochondrial genome,
Genetic diversity,
Cytochrome b gene,
Abstract :
Background & Objective: The Common Pochard (Aythya ferina) is one of the most abundant and widely distributed species in the world, among ducks. The aim of this study was to investigate the structure and genetic diversity of Aythya ferina in Iran using cytochrome b gene.
Material and Methodology: For this study, samples were taken from 10 pieces of Aythya ferina that were taken from the north and south of the country. Haplotypic and nucleotide analyzes were performed using MEGA, Papart, DNAsp and Network software.
Findings: In general, 7 different haplotypes were identified by examining 8 fragments of 929 pairs of cytochrome b gene of Aythya ferina. Haplotype diversity was calculated 0.818, nucleotide diversity was calculated 0.00149. The value of Nm or the amount of gene flow between the sampling logic was 1.383, which indicates a high gene flow and in other words, a very small gene distance between the populations of this species and its European and Asian populations. Rogers-Harping index, Tajima index and Fu Fs were calculated 0.112, -0.028 and -1.288, respectively. The mismatch distribution diagram is also plotted as a single view, all of which show an indeterminate population history similar to the model of sudden expansion.
Discussion and Conclusion: According to the results obtained from the haplotype network and the cognitive tree, as well as a slight genetic difference between the studied populations, there is a possibility of migration of this bird from both Europe and East Asia to Iran. Considering the results of the present study, Iranian wetlands should be recognized as important and key areas and the necessary management and protection measures should be taken in these areas.
References:
Mansori, J., 2008. Ornithology, First Edition, Farzaneh Book Publishing, pp:114-118. (In persian)
Dayan, K., 1988. Birds of the Middle orient and the Near orient, First edition, University of Tehran Press, pp:63-65. (In persian)
Ahmadpour, M., Lan-Hai, L., Ahmadpour, M. et al. (2016). Mercury concentration in the feathers of birds from various trophic levels in Fereydunkenar International wetland (Iran). Environ Monit Assess 188, 666 (2016). https://doi.org/10.1007/s10661-016-5671-y
Nafiseh Momeni, Hamid Reza Rezaei, Mohsen Ahmadpour, Paul Hapeman, (2022). Mitochondrial DNA cytochrome b diversity and phylogeny of the Eurasian coot (Fulica atra; Linnaeus, 1758) (Gruiformes: Rallidae), Journal of Wildlife and Biodiversity: 6 (2): 22-34.
Yang Liu, Irene Keller, and Gerald Heckel, 2011. Range-wide genetic population structure of common pochard (Aythya ferina): a potentially important vector of highly pathogenic avian influenza viruses Ecol Evol. Dec; 1(4): 529–545
J.M. Amezaga, L. antamaría, A.J. Green, 2002. Biotic wetland connectivity—supporting a new approach for wetland policy Acta Oecologica 23; 213–222
Madsen, T.; Olsson, M.; Wittzell, H.; Stille, B.; Gullberg, A.; Shine, R.; Andersson, S.and Tegelstro, H., 2000. Population size and genetic diversity in sand lizards (Lacerta agilis) and adders (Vipera berus). Biological Conservation. 94: 257-262.
Mohammadabadi, M.R.; Nikbakhti, M.; Mirzaee, H.R.; Shandi, A.; Saghi, D.A.; Romanov, M.N. and Moiseyeva, I.G., 2010. Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers. Russian journal of genetics. Vol. 46, No. 4, pp: 505-509.
Askari, N.; Abadi, M.R.M. and Baghizadeh. A., 2011. ISSR markers for assessing DNA polymorphism and genetic characterization of cattle, goat and sheep populations. Iranian Journal of Biotechnology. Vol. 9, pp: 222-229.
Thorp, J. P., 1982. The molecular clock hypothesis: Biochemical evolution, genetic differentiation and systematic. Annual Review of Ecology and Systematics; vol. 13, pp. 139-168.
Moazeni, S.; Mohammadabadi, M.R.; Sadeghi, M.; Shahrbabak, H.; Koshkoieh, A. and Bordbar, F., 2016. Association between UCP Gene Polymorphisms and Growth, Breeding Value of Growth and Reproductive Traits in Mazandaran Indigenous Chicken. Open Journal of Animal Sciences. Vol. 6, No. 1, pp: 1-8.
Friland, J., 2005. Molocular ecology. Jahad university publishers, Mashhad. Iran. pp:44-67
Gunter, K., 2009. The dictionary of gene Technology Genomies. Transcription protemics, wiley-vch Verlag GmbH and Co. KgaA, Weinheim. 1862 P
Bataillon, T.M., David, J.L., Schoen, D.J., 1996. Neutral genetic markers and conservation: simulated germplasm collections. Genetics; vol. 144, pp: 409-417.
Jahn, A.E.; Levey, D.J.; Farias, I.P.; Mamani, A.M.; Vidoz, J.Q. and Freeman, B., 2010. Morphological and genetic variation between migratory and non-migratory Tropical Kingbirds during spring migration in central South America. The Wilson Journal of Ornithology. Vol. 122, No.5, pp: 236-243.
Zwartjes, P.W., 2001. Genetic structuring among migratory populations of the black-whiskered vireo, with a comparison to the red-eyed vireo. The Condor. Vol. 103, No. 3, pp:439-448.
Haig, S.M.; Rhymer, J.M. and Heckel, D.G., 1994.Population differentiation in randomly mplified polymorphic DNA of red‐cockaded woodpeckers Picoides borealis. Molecular Ecology. Vol. 3, No. 6, pp: 581-595.
Nabholz, B.; Mauffrey, J.F.; Bazin, E.; Galtier, N. and Glemin, S., 2008. Determination of mitochondrial genetic diversity in mammals. Genetics. Vol. 178, No. 1, pp: 351-361.
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. pp: 489-552.
Hurst, G.D.D. and Jiggins, F.M., 2005. Problems with mitochondrial DNA as a marker in pulation, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proceedings of the Royal Society of London B: Biological Sciences. Vol. 272, No. 1572, pp:1525-1534.
Johnson, K.P. and Sorenson, M.D., 1998. Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND5) in the dabbling ducks (Tribe: Anatini). Molecular phylogenetics and evolution. Vol. 10, No. 1, pp: 82-94.
Zardoya, R. and Meyer, A., 1996. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Molecular biology and evolution. Vol. 09, No. 8, pp: 399-315.
Johnson, K.P. and Sorenson, M.D., 1989. Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND5) in the dabbling ducks (Tribe: Anatini). Molecular phylogenetics and evolution. Vol. 10, No. 1, pp: 82-94.
Bakhtiari, S.2000. Geological Atlas of Iranian Provinces, Tehran: Institute of Geography and Cartography.
Kiabi, B.; GHaemi, B., and Abdoli, Am., 1989. Wetland and river ecosystems of Golestan province. Administration Environmental protection of Golestan province. 182 pages.
Nei, M. and Kumar S., 2000. Molecular evolution and phylogenetics. Oxford University Press, New York.
Tamura, K. and Nei, M., 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular biology and evolution. Vol. 10, No. 3, pp: 512-526.
Kumar, S., Stecher, G. and Tamura, K., 2016 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, 33, 1870-1874.
Tajima, F., 1989. Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. Vol., 123 pp: 585-595.
Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. Vol. 147, pp: 915-925
Avise, J.C.; Nelson, W.S. and Sibley, C.G., 1994. DNA sequence support for a close phylogenetic relationship between some storks and New World vultures. Proceedings of the National Academy of Sciences of the United States of America. Vol. 91, No. 11, pp:5173-5177.
Liu, Y.; Keller, I. and Heckel, G., 2012. Breeding site fidelity and winter admixture in a long-distance migrant, the tufted duck (Aythya fuligula). Heredity. Vol 109, No. 2, pp: 108-116.
Keller, I.; Korner-Nievergelt, F. and Jenni. L., 2009. Within-winter movements: acommon phenomenon in the Common Pochard Aythya ferina. Journal of Ornithology. Vol. 150, No. 2, pp:483-494
He, H.; Yuan, X.; Wei, C. and Yuan, F., 2006. Genetic variation of the Mmitochondrial ND1 region among geographical populations of Sitodiplosis mosellana (Gehin) (Diptera: Cecidomyiidae) in China. Journal of Kansas Entomology Society. Vol. 79, pp: 211-222.
Rogers, A.R., and Harpending, H., 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution. Vol. 9, No. 3, pp: 552-569.
Ramos-Onsins, S.E. and Rozas, J., 2002. Statistical properties of new neutrality tests against population growth. Molecular biology and evolution. Vol. 19, No. 12, pp: 2092-2100.
Gonzalez, J.; Düttmann, H. and Wink, M., 2009. Phylogenetic relationships based on two mitochondrial genes and hybridization patterns in Anatidae. Journal of Zoology. Vol.279., No. 3, pp: 310-317.
_||_
Mansori, J., 2008. Ornithology, First Edition, Farzaneh Book Publishing, pp:114-118. (In persian)
Dayan, K., 1988. Birds of the Middle orient and the Near orient, First edition, University of Tehran Press, pp:63-65. (In persian)
Ahmadpour, M., Lan-Hai, L., Ahmadpour, M. et al. (2016). Mercury concentration in the feathers of birds from various trophic levels in Fereydunkenar International wetland (Iran). Environ Monit Assess 188, 666 (2016). https://doi.org/10.1007/s10661-016-5671-y
Nafiseh Momeni, Hamid Reza Rezaei, Mohsen Ahmadpour, Paul Hapeman, (2022). Mitochondrial DNA cytochrome b diversity and phylogeny of the Eurasian coot (Fulica atra; Linnaeus, 1758) (Gruiformes: Rallidae), Journal of Wildlife and Biodiversity: 6 (2): 22-34.
Yang Liu, Irene Keller, and Gerald Heckel, 2011. Range-wide genetic population structure of common pochard (Aythya ferina): a potentially important vector of highly pathogenic avian influenza viruses Ecol Evol. Dec; 1(4): 529–545
J.M. Amezaga, L. antamaría, A.J. Green, 2002. Biotic wetland connectivity—supporting a new approach for wetland policy Acta Oecologica 23; 213–222
Madsen, T.; Olsson, M.; Wittzell, H.; Stille, B.; Gullberg, A.; Shine, R.; Andersson, S.and Tegelstro, H., 2000. Population size and genetic diversity in sand lizards (Lacerta agilis) and adders (Vipera berus). Biological Conservation. 94: 257-262.
Mohammadabadi, M.R.; Nikbakhti, M.; Mirzaee, H.R.; Shandi, A.; Saghi, D.A.; Romanov, M.N. and Moiseyeva, I.G., 2010. Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers. Russian journal of genetics. Vol. 46, No. 4, pp: 505-509.
Askari, N.; Abadi, M.R.M. and Baghizadeh. A., 2011. ISSR markers for assessing DNA polymorphism and genetic characterization of cattle, goat and sheep populations. Iranian Journal of Biotechnology. Vol. 9, pp: 222-229.
Thorp, J. P., 1982. The molecular clock hypothesis: Biochemical evolution, genetic differentiation and systematic. Annual Review of Ecology and Systematics; vol. 13, pp. 139-168.
Moazeni, S.; Mohammadabadi, M.R.; Sadeghi, M.; Shahrbabak, H.; Koshkoieh, A. and Bordbar, F., 2016. Association between UCP Gene Polymorphisms and Growth, Breeding Value of Growth and Reproductive Traits in Mazandaran Indigenous Chicken. Open Journal of Animal Sciences. Vol. 6, No. 1, pp: 1-8.
Friland, J., 2005. Molocular ecology. Jahad university publishers, Mashhad. Iran. pp:44-67
Gunter, K., 2009. The dictionary of gene Technology Genomies. Transcription protemics, wiley-vch Verlag GmbH and Co. KgaA, Weinheim. 1862 P
Bataillon, T.M., David, J.L., Schoen, D.J., 1996. Neutral genetic markers and conservation: simulated germplasm collections. Genetics; vol. 144, pp: 409-417.
Jahn, A.E.; Levey, D.J.; Farias, I.P.; Mamani, A.M.; Vidoz, J.Q. and Freeman, B., 2010. Morphological and genetic variation between migratory and non-migratory Tropical Kingbirds during spring migration in central South America. The Wilson Journal of Ornithology. Vol. 122, No.5, pp: 236-243.
Zwartjes, P.W., 2001. Genetic structuring among migratory populations of the black-whiskered vireo, with a comparison to the red-eyed vireo. The Condor. Vol. 103, No. 3, pp:439-448.
Haig, S.M.; Rhymer, J.M. and Heckel, D.G., 1994.Population differentiation in randomly mplified polymorphic DNA of red‐cockaded woodpeckers Picoides borealis. Molecular Ecology. Vol. 3, No. 6, pp: 581-595.
Nabholz, B.; Mauffrey, J.F.; Bazin, E.; Galtier, N. and Glemin, S., 2008. Determination of mitochondrial genetic diversity in mammals. Genetics. Vol. 178, No. 1, pp: 351-361.
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. pp: 489-552.
Hurst, G.D.D. and Jiggins, F.M., 2005. Problems with mitochondrial DNA as a marker in pulation, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proceedings of the Royal Society of London B: Biological Sciences. Vol. 272, No. 1572, pp:1525-1534.
Johnson, K.P. and Sorenson, M.D., 1998. Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND5) in the dabbling ducks (Tribe: Anatini). Molecular phylogenetics and evolution. Vol. 10, No. 1, pp: 82-94.
Zardoya, R. and Meyer, A., 1996. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Molecular biology and evolution. Vol. 09, No. 8, pp: 399-315.
Johnson, K.P. and Sorenson, M.D., 1989. Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND5) in the dabbling ducks (Tribe: Anatini). Molecular phylogenetics and evolution. Vol. 10, No. 1, pp: 82-94.
Bakhtiari, S.2000. Geological Atlas of Iranian Provinces, Tehran: Institute of Geography and Cartography.
Kiabi, B.; GHaemi, B., and Abdoli, Am., 1989. Wetland and river ecosystems of Golestan province. Administration Environmental protection of Golestan province. 182 pages.
Nei, M. and Kumar S., 2000. Molecular evolution and phylogenetics. Oxford University Press, New York.
Tamura, K. and Nei, M., 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular biology and evolution. Vol. 10, No. 3, pp: 512-526.
Kumar, S., Stecher, G. and Tamura, K., 2016 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, 33, 1870-1874.
Tajima, F., 1989. Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. Vol., 123 pp: 585-595.
Fu, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. Vol. 147, pp: 915-925
Avise, J.C.; Nelson, W.S. and Sibley, C.G., 1994. DNA sequence support for a close phylogenetic relationship between some storks and New World vultures. Proceedings of the National Academy of Sciences of the United States of America. Vol. 91, No. 11, pp:5173-5177.
Liu, Y.; Keller, I. and Heckel, G., 2012. Breeding site fidelity and winter admixture in a long-distance migrant, the tufted duck (Aythya fuligula). Heredity. Vol 109, No. 2, pp: 108-116.
Keller, I.; Korner-Nievergelt, F. and Jenni. L., 2009. Within-winter movements: acommon phenomenon in the Common Pochard Aythya ferina. Journal of Ornithology. Vol. 150, No. 2, pp:483-494
He, H.; Yuan, X.; Wei, C. and Yuan, F., 2006. Genetic variation of the Mmitochondrial ND1 region among geographical populations of Sitodiplosis mosellana (Gehin) (Diptera: Cecidomyiidae) in China. Journal of Kansas Entomology Society. Vol. 79, pp: 211-222.
Rogers, A.R., and Harpending, H., 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution. Vol. 9, No. 3, pp: 552-569.
Ramos-Onsins, S.E. and Rozas, J., 2002. Statistical properties of new neutrality tests against population growth. Molecular biology and evolution. Vol. 19, No. 12, pp: 2092-2100.
Gonzalez, J.; Düttmann, H. and Wink, M., 2009. Phylogenetic relationships based on two mitochondrial genes and hybridization patterns in Anatidae. Journal of Zoology. Vol.279., No. 3, pp: 310-317.
