Population structure of the endangered Hume's pheasant (Syrmaticus humiae) inferred from a partial sequence of the mitochondrial DNA control region

Biochemical Systematics and Ecology

Volumn 57, Issue , 2014, Pages 69-77

  Bei, Yongjian ^a,b   Chen, Weicai ^c   Sun, Binghua ^a   Li, Jinhua ^a,d   Lai, Jieling ^b   Meng, Shaoquan ^b  

^a ANHUI UNIVERSITY   (China)

^b YULIN NORMAL UNIVERSITY   (China)

^c Natural History Museum of Guangxi   (China)

^d ANHUI NORMAL UNIVERSITY   (China)

Author keywords

Genetic diversity; Management unit; Population structure; Syrmaticus humiae

Indexed keywords

BIRD; CONSERVATION GENETICS; ENDANGERED SPECIES; GENE FLOW; GENETIC STRUCTURE; GENETIC VARIATION; HABITAT FRAGMENTATION; MITOCHONDRIAL DNA; PHYLOGENETICS; POPULATION GENETICS; POPULATION STRUCTURE; SPECIES CONSERVATION; CONSERVATION MANAGEMENT; GENETIC DIFFERENTIATION; HABITAT RESTORATION; GAMEBIRD; HABITAT LOSS;

CHINA; GUANGXI ZHUANGZU; GUIZHOU;

SYRMATICUS HUMIAE;

EID: 84905454619     PISSN: 03051978     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bse.2014.07.006     Document Type: Article

References (64)

1. Alda F., Sastre P., La Cruz-Cardiel D., Doadrio I. Population genetics of the endangered Cantabrian capercaillie in northern Spain. Anim. Conser. 2011, 14:249-260.
2. Andren H. Effects of habitat fragmentation on birds and mammals in landscapes with different proportions of suitable habitat: a review. Oikos 1994, 355-366.
3. Arbogast B.S., Kenagy G. Comparative phylogeography as an integrative approach to historical biogeography. J.Biogeogr. 2001, 28:819-825.
4. Avise J.C. Phylogeography: the History and Formation of Species 2000, Harvard University Press, Cambridge.
5. Bandelt H.J., Forster P. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16:37-48.
6. Bei Y.J. The Population Dispersion and Habitats Selection of Black-necked Bar-tailed Pheasant (Syrmaticus humiae) after Restocked in Cenwanglaoshan Nature Reserve 2005, Guangxi normal university, Guangxi Province.
7. BirdLife International Syrmaticus Humiae 2014, accessed 07. 06. 14. http://www.birdlife.org.
8. Brooks T.M., Mittermeier R.A., Mittermeier C.G., Da Fonseca G.A.B., Rylands A.B., Konstant W.R., Flick P., Pilgrim J., Oldfield S., Magin G. Habitat loss and extinction in the hotspots of biodiversity. Conserv. Biol. 2002, 16:909-923.
9. Brown G.G., Gadaleta G., Pepe G., Saccone C., Sbisà E. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J.Mole Biol. 1986, 192:503-511.
10. Brown W.M., George M., Wilson A.C. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 1979, 76:1967-1971.
11. Cao L., Liang X.F., Du Y.Q., Zheng H.Z., Yang M., Huang W. Genetic population structure in Siniperca scherzeri (Perciformes: Siniperca) in China inferred from mitochondrial DNA sequences and microsatellite loci. Biochem. Syst. Ecol. 2013, 51:160-170.
12. Develey P.F., Stouffer P.C. Effects of roads on movements by understory birds in mixed-species flocks in Central Amazonian Brazil. Conser. Biol. 2001, 15:1416-1422.
13. Dong L., Heckel G., Liang W., Zhang Y. Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers. Mole Ecol. 2013, 22:3376-3390.
14. Dong L., Zhang J., Sun Y., Liu Y., Zhang Y., Zheng G. Phylogeographic patterns and conservation units of a vulnerable species, Cabot's tragopan (Tragopan caboti), endemic to southeast China. Conserv. Genet. 2010, 11:2231-2242.
15. Drummond A.J., Rambaut A., Shapiro B., Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 2005, 22:1185-1192.
16. Drummond A.J., Rambaut A. BEAST v. 1.4 2006, Available from:. http://beast.bio.ed.ac.uk/.
17. Excoffier L., Laval G., Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinforma. 2005, 1:47. online.
18. Federman S., Hyseni C., Clement W., Oatham M., Caccone A. Habitat fragmentation and the genetic structure of the Amazonian palm Mauritia flexuosa L.f. (Arecaceae) on the island of Trinidad. J.Conserv. Genet. 2014, 15(2):355-362.
19. Fickel J., Bubliy O.A., Stache A., Noventa T., Jirsa A., Heurich M. Crossing the border? Structure of the red deer (Cervus elaphus) population from the Bavarian-Bohemian forest ecosystem. Mamm. Biol. 2012, 77(3):211-220.
20. Frankham R. Conservation genetics. Annu. Rev. Genet. 1995, 29:305-327.
21. Frankham R. Relationship of genetic variation to population size in wildlife. Conserv. Biol. 1996, 10:1500-1508.
22. Frantz A.C., Bertouille S., Eloy M.C., Licoppe A., Chaumont F., Flamand M.C. Comparative landscape genetic analyses show a Belgian motorway to be a gene flow barrier for red deer (Cervus elaphus), but not wild boars (Sus scrofa). Mol. Ecol. 2012, 21(14):3445-3457.
23. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925.
24. Fuller R.A., Garson P.J. Pheasant: status survey and conservation action plan 2000-2004. IUCN Reading, Cambridge, UK 2000, 66.
25. Höglund J. Evolutionary Conservation Genetics 2009, Oxford University Press.
26. Han L.X. The distribution and habitat selection of the Hume's pheasant in Yunnan. Chin. Biodivers. 1997, 5:185-189.
27. Hedrick P.W., Kalinowski S.T. Inbreeding depression in conservation biology. Annu. Rev. Ecol. Syst. 2000, 31:139-162.
28. Holder K., Montgomerie R., Friesen V.L. Genetic diversity and management of Nearctic Rock Ptarmigan (Lagopus mutus). Can. J. Zool. 2004, 82:564-575.
29. Huang Z.H., Liu N.F., Liang W., Zhang Y., Liao X., Ruan L., Yang Z. Phylogeography of Chinese bamboo partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in south China: inference from mitochondrial DNA control-region sequences. Mol. Phylogenet. Evol. 2010, 56:273-280.
30. IUCN IUCN Red List of Threatened Species 2014, Version 2013.2, Downloaded on 07 June 2014. http://www.iucnredlist.org.
31. Jiang A.W., Cheng Z.Y., Liang X. Discovery of Hume's pheasant (Syrmaticus humiae) in Guizhou Province, southwestern China. Chin. Birds 2012, 3:143-146.
32. Jiang P.P., Ge Y.F., Lang Q.L., Ding P. Genetic structure among wild populations of Elliot's Pheasant Syrmaticus ellioti in China from mitochondrial DNA analyses. Bird. Conserv. Int. 2007, 17:177-185.
33. Kimball R.T., Braun E.L. Amultigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. J.Avian Biol. 2008, 39:438-445.
34. Kimura M. Asimple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J.Mol. Evol. 1980, 16:111-120.
35. Li H.H., Yu T.L., Shen L.T. The birds of Tragopan cuvior and Syrmaticus wagler and theirs geological distribution in Guangxi, China. J.Guangxi Normal Univ. Neutral Sci. 1998, 16:76-80.
36. Lindenmayer D.B., Fischer J. Tackling the habitat fragmentation panchreston. Trends Ecol. Evol. 2007, 22(3):127-132.
37. Liukkonen-Anttila T., Ratti O., Kvist L., Helle P., Orell M. Lack of genetic structuring and subspecies differentiation in the capercaillie (Tetrao urogallus) in Finland. Ann. Zool. Fenn. 2004, 41:619-633.
38. Moritz C., Dowling T., Brown W. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 1987, 18:269-292.
39. Moritz C. Definning evolutionarily significant units' for conservation. Trends Ecol. Evol. 1994, 9(10):373-375.
40. Peng H., Liu S., Zou F., Zeng B., Yue B. Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control region. Anim. Genet. 2009, 40(1):65-72.
41. Randi E., Lucchini V. Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. J.Mol. Evol. 1998, 47:449-462.
42. Randi E., Tabarroni C., Rimondi S., Lucchini V., Sfougaris A. Phylogeography of the rock partridge (Alectoris graeca). Mol. Ecol. 2003, 12:2201-2214.
43. Reed D.H. Extinction risk in fragmented habitats. Anim. conserv. 2004, 7:181-191.
44. Rogers A.R., Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 1992, 9:552-569.
45. Saccheri I., Kuussaari M., Kankare M., Vikman P., Fortelius W., Hanski I. Inbreeding and extinction in a butterfly metapopulation. Nature 1998, 392:491-494.
46. Saccone C., Attimonelli M., Sbisa E. Structural elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA. J.Mol. Evol. 1987, 26:205-211.
47. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
48. Sambrook J., Russell D.W., Russell D.W. Molecular Cloning: a Laboratory Manual (3-volume Set) 2001, Cold Spring Habor, New York.
49. Segelbacher G., Storch I., Tomiuk J. Genetic evidence of capercaillie Tetrao urogallus dispersal sources and sinks in the Alps. Wildl. Biol. 2003, 9:267-273.
50. Slatkin M., Hudson R.R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 1991, 129:555-562.
51. Song J., Hou F.X., Zhang X.Y., Yue B.S., Song Z.B. Mitochondrial genetic diversity and population structure of a vulnerable freshwater fish, rock carp (Procypris rabaudi) in upper Yangtze River drainage. Biochem. Syst. Ecol. 2014, 55:1-9.
52. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
53. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
54. Thinh V.T., Doherty J.P.F., Bui T.H., Huyvaert K.P. Road crossing by birds in a tropical forest in northern Vietnam. Condor 2012, 114:639-644.
55. Thompson J.D., Gibson T.J., Plewniak F.D.R., Jeanmougin F.O., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acid. Res. 1997, 25:4876-4882.
56. Villard M., Metzger J.P. Beyond the fragmentation debate: a conceptual model to predict when habitat configuration really matters. J.Appl. Ecol. 2014, 51(2):309-318.
57. Wade M.J. Population structure. Nature Encyclo-pedia of Life Sciences 2001, Nature Publishing Group, London.
58. Weir B.S., Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 1984, 1358-1370.
59. Westemeier R.L., Brawn J.D., Simpson S.A., Esker T.L., Jansen R.W., Walk J.W., Kershner E.L., Bouzat J.L., Paige K.N. Tracking the long-term decline and recovery of an isolated population. Science 1998, 282:1695-1698.
60. Wright S. The genetical structure of populations. Ann. Eugen. 1949, 15:323-354.
61. Wu Z.K., Lin Q.W., Yang J.L. Guizhou Avifauna 1986, Guizhou People Press, Guiyang.
62. Zhang F., Jiang Z., Xu A., Zeng Y., Li C. Recent geological events and intrinsic behavior influence the population genetic structure of the Chiru and Tibetan Gazelle on the Tibetan Plateau. PLoS ONE 2013, 8(4):e60712.
63. Zhang Z.W., Ding C.Q., Ding P., Zheng G.M. The current status and a conservation strategy for species of Galliformes in China. Chin. Biodivers. 2003, 11:414-421.
64. Zheng G.M., Wang Q.S. China Red Data Book of Endangered Animals: Aves 1998, Science Press, Beijing.