Genetic structure and population dynamics of the silver pheasant (Lophura nycthemera) in southern China

In southern China, the silver pheasant (Lophura nycthemera) is a widespread species due to complex topography and sufficient habitats and food resources. We investigated the microsatellite and mitochondrial DNA control region sequence of 115 individuals from 7 locations in China to study population dynamics of the silver pheasant during the Pleistocene. The neutrality test and mismatch distribution analyses showed that population expansion began in the interglacial period (76,053 years ago), and the latest common ancestor appeared approximately 970,300 years ago. Most populations exhibited a high level of genetic diversity as well as gene flow. Results of phylogenetic trees and network and STRUCTURE analyses provided insights into the weak population structure of this species. The weak phylogeographic and complex historical expansion population of the silver pheasant during the interglacial period could probably be related to its complex topography and the sufficient amount of suitable habitats and food resources in southern China.

___

  • Alain H, Randi E, Lucchini V (1998). Genetic diversity, phylogenetic relationships and conservation of Edwards’s Pheasant Lophura edwardsi. Bird Conservation International 8 (4): 395-410. doi: 10.1017/s095927090000215x
  • Alasaad S, Soriguer RC, Chelomina G, Sushitsky YP, Fickel J (2011). Siberian tiger’s recent population bottleneck in the Russian Far East revealed by microsatellite markers. Mammalian Biology 76 (6): 722-726.
  • Aleixo A (2004). Historical diversification of a Terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification. Evolution 58 (6): 1303-1317. doi: 10.2307/3449226
  • Anthony NM, Johnson-Bawe M, Jeffery K, Clifford SL, Abernethy KA et al. (2007). The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa. Proceedings of the National Academy of Sciences of the United States of America 104 (51): 20432-20436.
  • Bandelt HJ, Forster P, Röhl A (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16 (1): 37-48. doi: 10.1093/oxfordjournals.molbev. a026036
  • Beerli P, Palczewski M (2010). Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185 (1): 313-326.
  • Brown JA, Swank RT (1983). Subcellular redistribution of newly synthesized macrophage lysosomal enzymes. Correlation between delivery to the lysosomes and maturation. Journal of Biological Chemistry 258 (24): 15323-15328. doi: 10.1016/ S0015-7368(92)73045-X
  • Cao F, Qi C, Li G, Zhong C, Tang D et al. (2012). Climate change effects on southern subtropical and tropical tree species in Ganzhou City, China. British Journal of Environment and Climate Change 2 (2): 163-179. doi: 10.9734/BJECC/2012/1114
  • Clement M, Crandall KPD (2000). TCS: A computer program to estimate gene genealogies. Molecular Ecology 9 (10): 1657- 1659. doi: 10.1046/j.1365-294x.2000.01020.x
  • Clinton LK, Billings LM, Green KN, Caccamo A, Ngo J et al. (2007). Age-dependent sexual dimorphism in cognition and stress response in the 3xTg-AD mice. Neurobiology of Disease 28 (1): 76-82. doi: 10.1016/j.nbd.2007.06.013
  • Cornuet JM, Luikart G (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144 (4): 2001-2014.
  • Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999). New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153 (4): 1989- 2000. doi: 10.1017/S0016672399004188
  • Cracraft J (1973). Continental drift, paleoclimatology, and the evolution and biogeography of birds. Journal of Zoology 169 (4): 455-543. doi: 10.1111/j.1469-7998.1973.tb03122.x
  • Crooijmans RP, Groen AF, Van Kampen AJ, Van DBS, JJ VDP et al. (1996). Microsatellite polymorphism in commercial broiler and layer lines estimated using pooled blood samples. Poultry Science 75 (7): 904-909.
  • Crooijmans RP, van der Poel JJ, Groenen M, Bierbooms V, Komen H et al. (1997). Microsatellite markers in common carp (Cyprinus carpio L.). Animal Genetics 28 (2): 129-134.
  • Crowe TM, Bloomer BP, Mandiwana TG, Hedderson TAJ, Randi E et al. (2006). Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data. Cladistics 22 (6): 495-532. doi: 10.1111/j.1096- 0031.2006.00120.x
  • Dong L (2011). Intraspecific taxonomy study of silver pheasant Lophura nycthemera. Acta Zootaxonomica Sinica 36 (2): 431- 446. doi: 10.1111/j.1749-4877.2010.00232.x
  • Dong L, Heckel G, Liang W, Zhang Y (2013). Phylogeography of silver pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers. Molecular Ecology 22 (12): 3376-3390.
  • Drummond A, Oliver GP, Rambaut A (2003). Inference of viral evolutionary rates from molecular sequences. Advances in Parasitology 54 (54): 331-358. doi: 10.1016/S0065- 308X(03)54008-8
  • Earl DA, Vonholdt BM (2012). STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4 (2): 359-361. doi: 10.1007/s12686-011-9548-7
  • Excoffier L, Foll M, Petit RJ (2009). Genetic consequences of range expansions. Annual Review of Ecology Evolution and Systematics 40 (1): 481-501. doi: 10.1146/annurev. ecolsys.39.110707.173414
  • Excoffier L, Lischer H (2010). Arlequin suite ver3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10 (3): 564- 567. doi: 10.1111/j.1755-0998.2010.02847.x
  • Fenster CVX, Hardy OJ (2003). Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculata (Leguminosae). Evolution 57 (5): 995-1007. doi: 10.1111/j.0014-3820.2003.tb00311.x
  • Garza JC, Williamson EG (2001). Detection of reduction in population size using data from microsatellite loci. Molecular Ecology 10 (2): 305-318. doi: 10.1046/j.1365-294X.2001.01190.x
  • Gibbs MJ, Koga R, Moriyama H, Pfeiffer P, Fukuhara T (2000). Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus. Journal of General Virology 81 (Pt 1): 227-233. doi: 10.1099/0022-1317-81-1-227
  • Greer DT (2013). Grassland bird abundance and habitat quality, and Sedge Wren (Cistothorus platensis) ecology on Fort Drum, New York. MSc, State University of New York, Brockport, NY, USA.
  • Hale DA, Kirk AD (2004). Mammalian target of rapamycin inhibitors in transplantation: novel immunosuppressive strategies with sirolimus. Current Opinion in Organ Transplantation 9 (4): 400-405
  • Hamilton WD, May RM (1977). Dispersal in stable habitats. Nature 269 (5629): 578-581. doi: 10.1038/269578a0
  • Hermet JP, Besson-Faure I, Houlle-Declomesnil AE (2013). Method for Extracting Deoxyribonucleic Acids (DNA) from Microorganisms Possibly Present in a Blood Sample. US Patent US20100240023A1.
  • Hewitt CD (2000). A study of the mechanisms of climate change at the Last Glacial Maximum. PhD, University of Reading, Reading, UK.
  • Hewitt G (2000). The genetic legacy of the Quaternary ice ages. Nature 405 (6789): 907-913. doi: 10.1038/35016000
  • Huang Z, Liu N, Wei L, Zhang Y, Liao X et al. (2010). Phylogeography of Chinese bamboo partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in south China: Inference from mitochondrial DNA control-region sequences. Molecular Phylogenetics and Evolution 56 (1): 273-280. doi: 10.1016/j. ympev.2010.01.028
  • Jiang L, Wang G, Peng R, Peng Q, Zou F (2014). Phylogenetic and molecular dating analysis of Taiwan Blue Pheasant (Lophura swinhoii). Gene 539 (1): 21-29. doi: 10.1016/j.gene.2014.01.067
  • Jiang PP, Ding P, Fang SG (2006). Isolation and characterization of microsatellite markers in Elliot’s pheasant (Syrmaticus ellioti). Molecular Ecology Notes 6 (4): 1160-1161. doi: 10.1111/j.1471- 8286.2006.01472.x
  • Kalinowski ST (2005). hp-rare 1.0: A computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Resources 5 (1): 187-189.
  • Li R, Tian H, Li X (2010). Climate change induced range shifts of Galliformes in China. Integrative Zoology 5 (2): 154-163. doi: 10.1111/j.1749-4877.2010.00198.x
  • Li Z, Kruger U, Lei X, Almansoori A, Su H (2015). Adaptive KPCA modeling of nonlinear systems. IEEE Transactions on Signal Processing 63 (9): 2364-2376. doi: 10.1109/tsp.2015.2412913
  • Luikart G, Allendorf FW, Cornuet JM, Sherwin WB (1998). Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity 89 (3): 238- 247.
  • Luo X, Keqian XU (2004). A solid phase method for extracting DNA from whole blood. Chinese Journal of Clinical Laboratory Science 22: 123-125.
  • Mantel N (1967). The detection of disease clustering and a generalized regression approach. Cancer Research 59 (2-3): 209-220. doi: 10.1007/s00253-002-1013-9
  • Marín JC, Varas V, Vila AR, López R, Orozco-Ter WP et al. (2013). Refugia in Patagonian fjords and the eastern Andes during the Last Glacial Maximum revealed by huemul (Hippocamelus bisulcus) phylogeographical patterns and genetic diversity. Journal of Biogeography 40 (12): 2285-2298. doi: 10.1111/ jbi.12161
  • Miller MJ, Kennedy AD, Eckhart AD, Burrage LC, Wulff JE et al. (2015). Untargeted metabolomic analysis for the clinical screening of inborn errors of metabolism. Journal of Inherited Metabolic Disease 38 (6): 1029-1039. doi: 10.1007/s10545-015- 9843-7
  • Miller MP, Haig SM, Mullins TD, Popper KJ, Green M (2012). Evidence for population bottlenecks and subtle genetic structure in the yellow rail. Condor 114 (1): 100-112. doi: 10.1525/cond.2012.110055
  • Muhs DR, Ager TA, Begét JE (2001). Vegetation and paleoclimate of the last interglacial period, central Alaska. Quaternary Science Reviews 20 (1): 41-61.
  • Nicolas V, Missoup AD, Denys C, Peterhans JK, Katuala P et al. (2011). The roles of rivers and Pleistocene refugia shaping genetic diversity in Praomys misonnei in tropical Africa. Journal of Biogeography 38 (1): 191-207. doi: 10.1111/j.1365- 2699.2010.02399.x
  • Paris D, Nicholls AO, Hall A, Harvey A, Massaro M (2016). Femalebiased dispersal in a spatially restricted endemic island bird. Behavioral Ecology and Sociobiology 70 (12): 2061-2069. doi: 10.1007/s00265-016-2210-3
  • Pernetta AP, Allen JA, Beebee TJ, Reading CJ (2011). Fine-scale population genetic structure and sex-biased dispersal in the smooth snake (Coronella austriaca) in southern England. Heredity 107 (3): 231-238.
  • Posada D (1998). MODELTEST: Testing the model of DNA substitution. Bioinformatics 14 (9): 817-818. doi: 10.1093/ bioinformatics/14.9.817
  • Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155 (2): 945-959.
  • Randi E, Lucchini V, Hennache A, Kimball RT, Braun EL et al. (2001). Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Molecular Phylogenetics and Evolution 19 (2): 187-201. doi: 10.1006/mpev.2001.0922
  • Rogers AR, Harpending H (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9 (3): 552-569. doi: 10.1093/ oxfordjournals.molbev.a040727
  • Rozas J, Sánchez-Delbarrio JC, Xavier M, Ricardo R (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (18): 2496-2497. doi: 10.1079/9780851994758.0139
  • Ruan L, Wei X, Han Y, Zhu C, Guan B et al. (2018). Gene flow from multiple sources maintains high genetic diversity and stable population history of common moorhen Gallinula chloropus in China. Ibis 160 (4): 855-869. doi: 10.1111/ibi.12579
  • Slatkin M (1995). Hitchhiking and associative overdominance at a microsatellite locus. Molecular Biology and Evolution 12 (3): 473-480. doi: 10.1006/jhev.1995.1036
  • Song G, Lei F (2014). Gene flow maintains genetic diversity and colonization potential in recently range-expanded populations of an Oriental bird, the Light-vented Bulbul (Pycnonotus sinensis, Aves: Pycnonotidae). Diversity and Distributions 19 (10): 1248-1262. doi: 10.1111/ddi.12067
  • Swofford DL (1998). PAUP (Phylogenetic Analysis Using Parsimony). Champaign, IL, USA: Illinois Natural History Survey.
  • Taylor D (1988). Ethnographic educational evaluation for children, families, and schools. Theory into Practice 27 (1): 67-76.
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25 (25): 4876-4882.
  • Trask AE, Bignal EM, McCracken DI, Piertney SB, Reid JM (2017). Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity. Journal of Animal Ecology 86 (5): 1082-1093. doi: 10.1111/1365- 2656.12703
  • Trifinopoulos J, Nguyen LT, Von HA, Minh BQ (2016). W-IQTREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44(W1): W232-235. doi: 10.1093/nar/gkw256
  • Tuinen MV, Dyke GJ (2004). Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Molecular Phylogenetics and Evolution 30 (1): 74-86.
  • Wang B, Li J, Wang G, Liang W, Zhang Y et al. (2013). Methodology for robust superhydrophobic fabrics and sponges from in situ growth of transition metal/metal oxide nanocrystals with thiol modification and their applications in oil/water separation. ACS Applied Materials & Interfaces 5 (5): 1827-1839. doi: 10.1007/s10592-008-9773-0
  • Wang N, Liu Y, Zhang ZW (2009). Characterization of nine microsatellite loci for a globally vulnerable species, Reeves’s Pheasant (Syrmaticus reevesii). Conservation Genetics 10 (5): 1511-1514.
  • Wang T, Zhang H, Lei Z, Hai H (2017). Responses of a phytoplankton community to seasonal and environmental changes in Lake Nansihu, China. Marine and Freshwater Research 68 (10): 1877-1886. doi: 10.1071/MF16331
  • Williamson-Natesan EG (2005). Comparison of methods for detecting bottlenecks from microsatellite loci. Conservation Genetics 6 (4): 551-562. doi: 10.1007/s10592-005-9009-5
  • Wu Y, Huang J, Zhang M, Zhang Y (2012). Genetic divergence and population demography of the Hainan endemic Blackthroated Laughingthrush (Aves: Timaliidae, Garrulax chinensis monachus) and adjacent mainland subspecies. Molecular Phylogenetics and Evolution 65 (2): 482-489. doi: 10.1016/j. ympev.2012.07.005
  • Xu ZF, Han YQ, Zhu CY, Chen P, Xu W et al. (2019). Bi-parentally inherited genetic evidence for male-biased dispersal in common moorhen (Gallinula chloropus). Biochemical Genetics 57: 46-55, doi: 10.1007/s10528-018-9873-6
  • Zhang ZW, Ding CQ, Ding P, Zheng GM (2003). The current status and a conservation strategy for species of Galliformes in China. Chinese Biodiversity 11 (5): 414-421.
  • Zhu CY, Chen P, Han YQ, Ruan LZ (2018). Low genetic diversity and low gene flow corresponded to a weak genetic structure of ruddy-breasted crake (Porzana fusca) in China. Biochemical Genetics 56 (6): 586-617. doi: 10.1007/s10528-018-9862-9
Turkish Journal of Zoology-Cover
  • ISSN: 1300-0179
  • Yayın Aralığı: Yılda 6 Sayı
  • Yayıncı: TÜBİTAK
Sayıdaki Diğer Makaleler

Chaoying ZHU, Wenjing LU, Guanglong SUN, Zhen ZHANG, Zhen ZHANG, Liangjie YU, Peng CHEN, Yuqing HAN, Zhifeng XU, Junpeng BAI, Dongqin ZHAO, Luzhang RUAN

Identification of causes of death of Baikal seal (Pusa sibirica Gmelin, 1788)

Nina RYADINSKAYA, Ivan MELTSOV, Svetlana SAYVANOVA, Olga ILYINA, Tatyana POMOINIT SKAYA, Inna АNIKIENKO, Alena МOLKOVA, Maria ТABAKOVA

Genetic structure and population dynamics of the silver pheasant (Lophura nycthemera) in southern China

Peng CHEN, Wenjing LU, Liangjie YU, Zhifeng XU, Luzhang RUAN, Junpeng BAI, Yuqing HAN, Chaoying ZHU, Guanglong SUN, Dongqin ZHAO, Zhen ZHANG, Jiang CHENG

First record of Ahaetulla mycterizans (Linnaeus, 1758) (Serpentes: Colubridae) from the Lesser Sunda region, Indonesia, based on molecular and morphological identification

Lilin Ika Nur INDAHSARI, Fatchiyah FATCHIYAH, Eric Nelson SMITH, Nia KURNIAWAN

A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing

Hedieh JAFARI, Fatemeh SALABI, Alireza FOROUZAN

The partitioning of temporal movement patterns of breeding red-crowned crane (Grus japonensis) induced by temperature

Shiliang PANG, Huixin LI, Wanyu WEN, Wenfeng WANG, Minghao GONG, Qiang DAI, Zhongyan GAO, Xu PAN, Fawen QIAN

Francesco FAZIO, Concetta SAOCA, Ümit ACAR, Rifat TEZEL, Murat ÇELİK, Sevdan YILMAZ, Osman Sabri KESBİÇ, Ferhat YALGIN, Murat YİĞİT

Bogdan JOVANOVIĆ, Ethan J. KESSLER, Marija ILIĆ, Nataša TOMAŠEVIĆ KOLAROV, Jelena ĆOROVIĆ, Christopher A. PHILLIPS, Jelka CRNOBRNJA-ISAILOVIĆ

A comparative evaluation of hematological and biochemical parameters between the Italian mullet Mugil cephalus (Linnaeus 1758) and the Turkish mullet Chelon auratus (Risso 1810)

Osman Sabri KESBİÇ, Murat ÇELİK, Rifat TEZEL, Francesco FAZIO, Ümit ACAR, Ferhat YALGIN, Sevdan YILMAZ, Concetta SAOCA, Murat YİĞİT

Vertebrate insulin alters the expression profile of steroid hormone ecdysone receptor complex components and autophagy-related genes in the pupal fat body of the silkworm, Bombyx mori

Nesrin Ebru GÖNCÜ, Sedat YELKOVAN