Microsatellite variation and significant population genetic structure of endangered finless porpoises (Neophocaena phocaenoides) in Chinese coastal waters and the Yangtze River

Marine Biology

Volumn 157, Issue 7, 2010, Pages 1453-1462

  Chen, Lian ^a   Bruford, Michael W ^b   Xu, Shixia ^a   Zhou, Kaiya ^a   Yang, Guang ^a,b  

^a NANJING NORMAL UNIVERSITY   (China)

^b CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; COASTAL WATER; CONSERVATION GENETICS; ENDANGERED SPECIES; FRESHWATER ENVIRONMENT; GENE FLOW; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENETIC MARKER; GENETIC STRUCTURE; PORPOISE; SPECIES CONSERVATION;

CHINA; PACIFIC OCEAN; SOUTH CHINA SEA; YANGTZE RIVER; YELLOW SEA;

NEOPHOCAENA PHOCAENOIDES; PHOCOENIDAE;

EID: 85000336868     PISSN: 00253162     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00227-010-1420-x     Document Type: Article

References (62)

1. Avise JC (1998) Conservation genetics in the marine realm. J Hered 89: 377-382.
2. Bérubé M, Aguilar A, Dendanto D, Larsen F, Disciara GN, Sears R, Sigurjónsson J, Urban-R J, PalsbØll PJ (1998) Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus 1758): analysis of mitochondrial and nuclear loci. Mol Ecol 7: 585-599.
3. Caughley G (1994) Directions in conservation biology. J Anim Ecol 63: 215-244.
4. Chen L, Yang G (2008) Development of tetranucleotide microsatellite loci for the finless porpoise (Neophocaena phocaenoides). Conserv Genet 9: 1033-1035.
5. Chen L, Bruford M, Yang G (2007) Isolation and characterization of microsatellite loci in the finless porpoise (Neophocaena phocaenoides). Mol Ecol Notes 7: 1129-1131.
6. Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15: 290-291.
7. Crawford NG (2009) SMOGD: software for the measurement of genetic diversity. Mol Ecol Resour (Accepted for publication).
8. Escorza-Trevino S, Dizon AE (2000) Phylogeography, intraspecific structure and sex-biased dispersal of Dall's porpoise, Phocoenoides dalli, revealed by mitochondrial and microsatellite DNA analyses. Mol Ecol 9: 1049-1060.
9. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3. 0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1: 47-50.
10. Faubet P, Waples RS, Gaggiotti OE (2007) Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates. Mol Ecol 16: 1149-1166.
11. Fontaine MC, Baird SJE, Piry S et al (2007) Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters. BMC Biol 5: 30.
12. Frankham R, Ballou JD, Briscoe DA (2003) Introduction to conservation genetics. Cambridge University Press, Cambridge.
13. Gao AL (1991) Morphological differences and generic variation among the populations of Neophocaena phocaenoides. Ph. D. thesis, Nanjing Normal University, Nanjing, 116 pp.
14. Gao AL, Zhou KY (1993) Growth and reproduction of three populations of finless porpoise, Neophocaena phocaenoides, in Chinese waters. Aquat Mamm 19: 3-12.
15. Gao AL, Zhou KY (1995a) Geographical variation of external measurements and three subspecies of Neophocaena phocaenoides in Chinese waters. Acta Theriol Sinica 15: 81-92.
16. Gao AL, Zhou KY (1995b) Geographical variation of skull among the populations of Neophocaena phocaenoides in Chinese waters. Acta Theriol Sinica 15: 161-169.
17. Gao AL, Zhou KY (1995c) Geographical variation of postcranial skeleton among the populations of Neophocaena phocaenoides in Chinese waters. Acta Theriol Sinica 15: 246-253.
18. Gaspari S, Azzellino A, Airoldi S, Hoelzel AR (2007) Social kin associations and genetic structuring of striped dolphin populations (Stenella coeruleoalba) in the Mediterranean Sea. Mol Ecol 16: 2922-2933.
19. Gibbs HL, Dawson RJG, Hobson KA (2000) Limited differentiation in microsatellite DNA variation among northern populations of the yellow warbler: evidence for male-biased gene flow? Mol Ecol 9: 2137-2147.
20. Gilpin ME, Soulé ME (1986) Minimum viable populations: the processes of species extinction. In: Soulé ME (ed) Conservation biology. Sinauer Associates, Sunderland, pp 19-34.
21. Goodman SJ (1997) RSTCALC: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Mol Ecol 6: 881-885.
22. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2. 9. 3). Available from http://www2.unil.ch/popgen/softwares/fstat. htm.
23. Hartl D, Clark AG (1997) Principles of population genetics, 3rd edn. Sinauer Associates, Sunderland.
24. Hastings A (1993) Complex interactions between dispersal and dynamics-lessons from coupled logistic equations. Ecology 74: 1362-1372.
25. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6: 65-70.
26. Kasuya T (1999) Finless porpoise, Neophocaena phocaenoides (G. Cuvier 1829). In: Ridgway SH, Harrison R (eds) Handbook of marine mammals, vol 6: The second book of dolphins and the porpoises. Academic, San Diego, pp 411-442.
27. Krützen M, Sherwin WB, Berggren P, Gales N (2004) Population structure in an inshore cetacean revealed by microsatellite and mtDNA analysis: bottlenose dolphins (Tursiops sp.) in shark bay, western Australia. Mar Mamm Sci 20: 28-47.
28. Lynch M, Conery J, Burger R (1995) Mutation accumulation and the extinction of small populations. Am Nat 146: 489-518.
29. Maudet C, Miller C, Bassano B, Breitenrnoser-Würsten C, Gauthier D, Obexer-Ruff G, Michallet J, Luikart G (2002) Microsatellite DNA and recent statistical methods in wildlife conservation management: applications in alpine ibex (Capra ibex [ibex]). Mol Ecol 11: 421-436.
30. Moritz C (1994) Defining 'evolutionary significant units' for conservation. Trends Ecol Evol 9: 373-375.
31. Palstra FP, O'Connell MF, Ruzzante DE (2007) Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history. Mol Ecol 16: 4504-4522.
32. Parsons KM, Durban JW, Claridge DE (2006) Population genetic structure of coastal bottlenose dolphins (Tursiops Truncatus) in the northern Bahamas. Mar Mamm Sci 22: 276-298.
33. Pilleri G, Chen P (1980) Neophocaena phocaenoides and Neophocaena asiaeorientalis: taxonomical differences. Invest Cetacea 11: 25-32.
34. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
35. Racey PA, Barratt EM, Burland TM, Deaville R, Gotelli D, Jones G, Piertney SB (2007) Microsatellite DNA polymorphism confirms reproductive isolation and reveals differences in population genetic structure of cryptic pipistrelle bat species. Biol J Linn Soc 90: 539-550.
36. Randi E, Lucchini V (2002) Detecting rare introgression of domestic dog genes into wild wolf (Canis lupus) populations by Bayesian admixture analyses of microsatellite variation. Conserv Genet 3: 29-43.
37. Raymond M, Rousset F (1995) GENEPOP (version 1. 2): population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
38. Reeves RR, Wang JY, Leatherwood S (1997) The finless porpoise, Neophocaena phocaenoides (G. Cuvier 1829): a summary of current knowledge and recommendations for conservation action. Asian Mar Biol 14: 111-143.
39. Rice DW (1998) Marine mammals of the world: systematics and distribution. Society for Marine Mammalogy Special Publication 4: 1-231.
40. Rosel PE, Dizon AE, Haygood MG (1995) Variability of the mitochondrial control region in populations of the harbour porpoise, Phocoena phocoena, on interoceanic and regional scales. Can J Fish Aquat Sci 52: 1210-1219.
41. Rosel PE, France SC, Wang JY, Kocher TD (1999) Genetic structure of harbour porpoise Phocoena phocoena populations in the northwest Atlantic based on mitochondrial and nuclear markers. Mol Ecol 8: 41-54.
42. Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MAM, Hillel J, Maki-Tanila A, Tixier-Boichard M, Vignal A, Wimmers K, Weigend S (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699-713.
43. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298: 2981-2985.
44. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
45. Terry A, Bucciarelli G, Bernardi G (2000) Restricted gene flow and incipient speciation in disjunct Pacific Ocean and sea of Cortez populations of a reef fish species, Girella nigricans. Evolution 54: 652-659.
46. Turvey ST, Pitman RL, Taylor BL, Barlow J, Akamatsu T, Barrett LA, Zhao XJ, Reeves RR, Stewart BS, Wang KX, Wei Z, Zhang XF, Pusser LT, Richlen M, Brandon JR, Wang D (2007) First human-caused extinction of a cetacean species? Biol Lett 3: 537-540.
47. Valsecchi E, Amos W (1996) Microsatellite markers for the study of cetacean populations. Mol Ecol 5: 151-156.
48. van Rossum F, Vekemans X, Meerts P, Gratia E, Lefèbvre C (1997) Allozyme variation in relation to ecotypic differentiation and population size in marginal populations of Silene nutans. Heredity 78: 552-560.
49. Wang KX, Wang D, Zhang XF, Pfluger A, Barrett L (2006) Range-wide Yangtze freshwater dolphin expedition: The last chance to see Baiji? Environ Sci Pollut R 13: 418-424.
50. Wang JY, Frasier TR, Yang SC, White BN (2008) Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena). Heredity 101: 145-155.
51. Waples RS, Gaggiotti OE (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15: 1419-1439.
52. Wei Z, Wang D, Zhang XF, Zhao QZ, Wang KX, Kuang XA (2002) Population size, behavior, movement pattern and protection of Yangtze finless porpoise at Balijiang section of the Yangtze River. Resour Environ Yangtze Basin 11: 427-432.
53. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
54. Westemeier RL, Brawn JD, Simpson SA, Esker TL, Jansen RW, Walk JW, Kershner EL, Bouzat JL, Paige KN (1998) Tracking the long-term decline and recovery of an isolated population. Science 282: 1695-1698.
55. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163: 1177-1191.
56. Wilson PJ, Grewal S, Rodgers A, Rempel R, Saquet J, Hristienko H et al (2003) Genetic variation and population structure of moose (Alces alces) at neutral and functional loci. Can J Zool 81: 670-683.
57. Yang G, Ren WH, Zhou KY, Liu S, Ji GQ, Yan J, Wang LM (2002) Population genetic structure of finless porpoises, Neophocaena phocaenoides, in Chinese waters, inferred from mitochondrial control region sequences. Mar Mamm Sci 18: 336-347.
58. Yang G, Liu S, Ren WH, Zhou KY, Wei FW (2003) Mitochondrial control region variability of baiji and the Yangtze finless porpoises, two sympatric small cetaceans in the Yangtze River. Acta Theriol 48: 469-483.
59. Yang G, Guo L, Bruford M, Wei FW, Zhou KY (2008) Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters. Biol J Linn Soc 95: 193-204.
60. Yoshida H, Yoshioka M, Shirakihara M, Chow S (2001) Population structure of finless porpoises (Neophocaena phocaenoides) in coastal waters of Japan based on mitochondrial DNA sequences. J Mammal 82: 123-130.
61. Zhang XF, Wang KX (1999) Population variability analysis of the Yangtze finless porpoises. Acta Ecol Sinica 19: 529-533.
62. Zhang XF, Liu RJ, Zhao QZ, Zhang GC, Wei Z, Wang XQ, Yang J (1993) The population of finless porpoise in the middle and lower reaches of Yangtze River. Acta Theriol Sin 13: 260-270.