Effective size closely approximates the census size in the heavily exploited western Atlantic population of the sandbar shark, Carcharhinus plumbeus

Conservation Genetics

Volumn 10, Issue 6, 2009, Pages 1697-1705

  Portnoy, David S ^a   McDowell, Jan R ^a   McCandless, Camilla T ^b   Musick, John A ^a   Graves, John E ^a  

^a VIRGINIA INSTITUTE OF MARINE SCIENCE   (United States)

^b ALASKA FISHERIES SCIENCE CENTER   (United States)

Author keywords

Effective number of breeders; Effective population size; Elasmobranchs; Linkage disequilibrium; Microsatellites; Temporal method

Indexed keywords

CONSERVATION GENETICS; GENETIC MARKER; GENOTYPE; NURSERY GROUND; POPULATION SIZE; SHARK; SURVIVORSHIP;

DELAWARE BAY; MID-ATLANTIC STATES; NORTH AMERICA; UNITED STATES; VIRGINIA;

ANIMALIA; CARCHARHINUS PLUMBEUS; CHONDRICHTHYES; ELASMOBRANCHII; MAMMALIA; PISCES;

EID: 71349087773     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-008-9771-2     Document Type: Article

References (79)

1. Alter S, Rynes E, Palumbi S (2007) DNA evidence for historic population size and past ecosystem impacts of gray whales. Proc Natl Acad Sci USA 104: 15162-15167. doi: 10. 1073/pnas. 0706056104.
2. Anderson E (1990) Fishery models as applied to elasmobranch fisheries. In: Pratt H, Gruber S, Taniuchi T (eds) Elasmobranchs as living resources: advances in biology, ecology, systematics and the status of fisheries. U. S. Department of Commerce, NOAA Technical Report NMFS 90, pp 473-484.
3. Ardren W, Kapuscinski A (2003) Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout. Mol Ecol 11: 35-49. doi: 10. 1046/j. 1365-294X. 2003. 01705. x.
4. Bartley D, Bagley M, Gall G, Bentley B (1992) Use of linkage disequilibrium data to estimate effective size of hatchery and natural fish populations. Conserv Biol 6: 365-375. doi: 10. 1046/j. 1523-1739. 1992. 06030365. x.
5. Bhattacharya C (1967) A simple method of resolution of a distribution into gaussian components. Biometrics 23: 115-135. doi: 10. 2307/2528285.
6. Branstetter S (1990) Early life-history implications of selected carcharhinoid and lamnoid sharks of the Northwest Atlantic. In: Pratt H, Gruber S, Taniuchi T (eds) Elasmobranchs as living resources: advances in biology, ecology, systematics and the status of fisheries. U. S. Department of Commerce, NOAA Technical Report NMFS 90, pp 17-28.
7. Branstetter S, Musick J (1993) Comparisons of shark catch rates on longlines using rope/steel (Yankee) and monofilament gangions. Mar Fish Rev 55: 4-9.
8. Caballero A (1994) Developments in the prediction of effective population size. Heredity 73: 657-679. doi: 10. 1038/hdy. 1994. 174.
9. Castro J (1993) The shark nursery of Bulls Bay, South Carolina, with a review of the shark nurseries of the southeastern coast of the United States. Environ Biol Fishes 38: 37-48. doi: 10. 1007/BF00842902.
10. Cortes E, Brooks E (2005) SEDAR doc LCS 05/06-dw15: indirect estimates of natural mortality for sandbar (Carcharhinus plumbeus) and blacktip (Carcharhinus limbatus) sharks in the western North Atlantic, pp 5: Shark SEDAR Data Workshop Document.
11. Crandall K, Posada D, Vasco D (1999) Effective population sizes: missing measures and missing concepts. Anim Conserv 2: 317-319. doi: 10. 1111/j. 1469-1795. 1999. tb00078. x.
12. Estoup A, Larigiader C, Perrot E, Chourrout D (1996) Rapid one-tube DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Mol Mar Biol Biotechnol 5: 295-298.
13. Falconer D, Mackay T (1996) Introduction to quantitative genetics, 3rd edn. Pearson Education, Harlow.
14. Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genet Res Camb 66: 95-106.
15. Franklin I (1980) Evolutionary changes in small populations. In: Soule M, Wilcox B (eds) Conservation biology: an evolutionary-ecological perspective. Sinauer Associates, Sunderland, pp 135-150.
16. Franklin I, Frankham R (1998) How large must populations be to retain evolutionary potential. Anim Conserv 1: 69-73. doi: 10. 1111/j. 1469-1795. 1998. tb00228. x.
17. Gayanilo F, Sparre P, Pauly D (2005) FAO-ICLARM Stock Assessment Tools II (FISAT II). Revised version. User's Guide, Rome: FAO Computerized Information Series (Fisheries).
18. Gomez-Uchida D, Banks M (2006) Estimation of effective size for the long-lived darkblotch rockfish Sebastes carmeri. J Hered 97: 603-606. doi: 10. 1093/jhered/esl042.
19. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices version 2. 9. 3. Available from http://www. unil. chlizea/softwares/fstat. html.
20. Grant W, Bowen B (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89: 415-426. doi: 10. 1093/jhered/89. 5. 415.
21. Grubbs R, Musick J (2007) Spatial delineation of summer nursery areas for juvenile sandbar sharks in Chesapeake Bay, Virginia. Am Fish Soc Symp 50: 63-85.
22. Grubbs R, Musick J, Conrath C, Romine J (2007) Long-term movements, migration and temporal delineation of a summer nursery for juvenile sandbar sharks in the Chesapeake Bay region. Am Fish Soc Symp 50: 87-107.
23. Guo S, Thompson E (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372. doi: 10. 2307/2532296.
24. Hauser L, Adcock G, Smith P, Ramirez J, Carvalho G (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc Natl Acad Sci USA 99: 11742-11747. doi: 10. 1073/pnas. 172242899.
25. Hedgecock D (1994) Does variance in reproductive success limit effective population sizes of marine organisms? In: Beaumont M (ed) Genetics and evolution of aquatic organisms. Chapman and Hall, London, pp 122-134.
26. Hedrick P (2005) Large variance in reproductive success and the Ne/N ratio. Evol Int J Org Evol 59: 1569-1599.
27. Heist E, Graves J, Musick J (1995) Population genetics of the sandbar shark (Carcharhinus plumbeus) in the Gulf of Mexico and Mid-Atlantic Bight. Copeia 1995: 555-562. doi: 10. 2307/1446752.
28. Hill W (1981) Estimation of effective population size from data on linkage disequilibrium. Genet Res 38: 209-216.
29. Hoarau G, Boon E, Jongma D, Ferber S, Palsson J, Veer H, Rijnsdorp A, Stam W, Olsen J (2005) Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.). Proc R Soc Lond B Biol Sci 272: 497-503. doi: 10. 1098/rspb. 2004. 2963.
30. Hoff T, Musick J (1990) Western North Atlantic shark-fishery management problems and informational requirements. In: Pratt H, Gruber S, Taniuchi T (eds) Elasmobranchs as living resources: advances in biology, ecology, systematics and the status of fisheries. U. S. Department of Commerce, NOAA Technical Report NMFS 90, pp 455-472.
31. Hutchinson W, Oosterhout C, Rogers S, Carvalho G (2003) Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). Proc R Soc Lond B Biol Sci 270: 2125-2132. doi: 10. 1098/rspb. 2003. 2493.
32. Jones M, McParland T, Hutchings J, Danzmann R (2001) Low genetic variability in lake populations of brook trout (Salvelinus fontinalis): a consequence of exploitation? Conserv Genet 2: 245-256. doi: 10. 1023/A: 1012215826057.
33. Jorde P, Ryman N (1995) Temporal allele frequency change and estimation of effective size in populations with overlapping generations. Genetics 139: 1077-1090.
34. Jorde P, Ryman N (1996) Demographic genetics of brown trout (Salmo trutta) and estimation of effective population size from temporal change of allele frequencies. Genetics 143: 1369-1381.
35. Jorde PE, Ryman N (2007) Unbiased estimator for genetic drift and effective size. Genetics 177: 927-935. doi: 10. 1534/genetics. 107. 075481.
36. Keeney D, Heist E (2003) Characterization of microsatellite loci isolated from the blacktip shark and their utility in requiem and hammerhead sharks. Mol Ecol Notes 3: 501-504. doi: 10. 1046/j. 1471-8286. 2003. 00492. x.
37. Lande R (1995) Mutation and conservation. Conserv Biol 9: 782-791. doi: 10. 1046/j. 1523-1739. 1995. 09040782. x.
38. Law R (2000) Fishing, selection, and phenotypic evolution. ICES J Mar Sci 57: 659-668. doi: 10. 1006/jmsc. 2000. 0731.
39. Lesica P, Allendorf F (1992) Are small populations of plants worth preserving? Conserv Biol 6: 135-139. doi: 10. 1046/j. 1523-1739. 1992. 610135. x.
40. Lynch M, Conery J, Burger R (1995) Mutation accumulation and the extinction of small populations. Am Nat 146: 489-518. doi: 10. 1086/285812.
41. McCandless C, Pratt H Jr, Kohler N, Merson R, Recksiek C (2007) Distribution localized abundance, movements, and migrations of juvenile sandbar sharks tagged in Delaware Bay. Am Fish Soc Symp 50: 45-62.
42. Medved R, Stillwell C, Casey J (1985) Stomach contents of young sandbar sharks, Carcharhinus plumbeus in Chincoteague Bay Virginia. Fish Bull (Wash DC) 83: 395-402.
43. Merson R (1998) Nursery grounds and maturation of the sandbar shark in the western North Atlantic. PhD thesis, University of Rhode Island, Kingston, RI.
44. Mills L, Smouse P (1994) Demographic consequences of inbreeding in remnant populations. Am Nat 144: 412-431. doi: 10. 1086/285684.
45. Musick J, Bransetter S, Colvocoresses J (1993) Trends in shark abundance from 1974 to 1991 for the Chesapeake Bight region of the U. S. Mid-Atlantic Coast. NOAA Technical Report 115, pp 1-18.
46. Musick J, Burgess G, Cailliet G, Camhi M, Fordham S (2000) Management of sharks and their relatives (Elasmobranchii). Fisheries 25: 9-13. doi: 10. 1577/1548-8446(2000)025> 0009: MOSATR< 2. 0. CO; 2.
47. Newman D, Pilson D (1997) Increased probability of extinction due to decreased genetic effective population size: experimental populations of Clarkia pulchella. Evol Int J Org Evol 51: 354-362. doi: 10. 2307/2411107.
48. Nunney L (1993) The influence of mating system and overlapping generations on effective population size. Evol Int J Org Evol 47: 1329-1341. doi: 10. 2307/2410151.
49. Nunney L, Campbell K (1993) Assessing minimum viable population size: demography meets population genetics. Trends Ecol Evol 8: 234-239. doi: 10. 1016/0169-5347(93)90197-W.
50. Nunney L, Elam D (1994) Estimating the effective population size of conserved populations. Conserv Biol 8: 175-184. doi: 10. 1046/j. 1523-1739. 1994. 08010175. x.
51. Portnoy D, McDowell J, Thompson K, Musick J, Graves J (2006) Isolation and characterization of five dinucleotide microsatellite loci in the sandbar shark, Carcharhinus plumbeus. Mol Ecol Notes 6: 431-433. doi: 10. 1111/j. 1471-8286. 2006. 01261. x.
52. Portnoy D, Piercy A, Musick J, Burgess G, Graves J (2007) Genetic polyandry and sexual conflict in the sandbar shark, Carcharhinus plumbeus, in the western North Atlantic and Gulf of Mexico. Mol Ecol 16: 187-197. doi: 10. 1111/j. 1365-294X. 2006. 03138. x.
53. Poulsen N, Nielsen E, Schierup M, Loeschcke V, Gronkjaer P (2006) Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Mol Ecol 15: 321-331. doi: 10. 1111/j. 1365-294X. 2005. 02777. x.
54. Pratt H, Carrier J (2001) A review of elasmobranch reproductive behaviour with a case study on the nurse shark, Ginglymostoma cirratum. Environ Biol Fishes 60: 157-188. doi: 10. 1023/A: 1007656126281.
55. Ralls K, Ballou J, Brownell R (1983) Genetic diversity in California sea otters: theoretical considerations and management implications. Biol Conserv 25: 209-232. doi: 10. 1016/0006-3207(83)90037-X.
56. Raymond M, Rousset F (1995) GENEPOP (version 1. 2): population genetics software for exact tests and ecumenicism. Heredity 86: 248-249.
57. Roman J, Palumbi S (2003) Whales before whaling in the North Atlantic. Science 301: 508-510. doi: 10. 1126/science. 1084524.
58. Ruzzante D, Taggart C, Doyle R, Cook D (2001) Stability in the historical pattern of genetic structure of Newfoundland cod (Gadus morhua) despite the catastrophic decline in population size from 1964 to 1994. Conserv Genet 2: 257-259. doi: 10. 1023/A: 1012247213644.
59. Ryman N, Utter F, Laikre L (1995) Protection of intraspecific biodiversity of exploited fishes. Rev Fish Biol Fish 5: 417-446. doi: 10. 1007/BF01103814.
60. Schwartz M, Tallmon D, Luikart G (1999) Using genetics to estimate the size of wild populations: many methods, much potential, uncertain utility. Anim Conserv 2: 321-323. doi: 10. 1111/j. 1469-1795. 1999. tb00079. x.
61. Seutin G, White B, Boag P (1991) Preservation of avian blood and tissue samples for DNA analyses. Can J Zool 69: 82-90. doi: 10. 1139/z91-013.
62. Shelden K, DeMaster D, Rugh D, Olson A (2001) Developing classification criteria under the U. S. Endangered Species Act: bowhead whales as a case study. Conserv Biol 15: 1300-1307. doi: 10. 1046/j. 1523-1739. 2001. 99380. x.
63. Sminkey T, Musick J (1996) Demographic analysis of the sandbar shark, Carcharhinus plumbeus, in the western North Atlantic. Fish Bull (Wash DC) 94: 341-347.
64. Smith S, Au D, Show C (1998) Intrinsic rebound potentials of 26 species of Pacific sharks. Mar Freshw Res 49: 663-678. doi: 10. 1071/MF97135.
65. Springer S (1960) Natural history of the sandbar shark, Eulamia milberti. Fish Bull (Wash DC) 61: 1-38.
66. Stevens J, Bonfil R, Dulvy N, Walker P (2000) The effects of fishing on sharks, rays and chimaeras (chondricthyans) and the implications for marine ecosystems. ICES J Mar Sci 57: 476-494. doi: 10. 1006/jmsc. 2000. 0724.
67. Turner T, Wares J, Gold J (2002) Genetic effective size is three orders of magnitude smaller than adult census size in abundant, estuarine-dependent marine fish (Sciaenops ocellatus). Genetics 162: 1329-1339.
68. van Oosterhout C, Hutchinson W, Wills D, Shipley P (2004) MICRO-CHECKER: software for identifying genotyping errors in microsatellite data. Mol Ecol Notes 4: 535-538. doi: 10. 1111/j. 1471-8286. 2004. 00684. x.
69. Walker T (1998) Can shark resources be harvested sustainably? A question revisited with a review of shark fisheries. Mar Freshw Res 49: 553-572. doi: 10. 1071/MF98017.
70. Wang J (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genet Res Camb 78: 243-257.
71. Wang J (2005) Estimation of effective population sizes from data on genetic markers. Philos Trans R Soc Lond B 360: 1395-1409. doi: 10. 1098/rstb. 2005. 1682.
72. Waples R (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121: 379-391.
73. Waples R (1991) Genetic methods for estimating the effective size of cetacean populations. Rep Int Whaling Comm 13: 279-300.
74. Waples R (2005) Genetic estimates of contemporary effective population size: to what time periods do estimates apply? Mol Ecol 14: 3335-3352. doi: 10. 1111/j. 1365-294X. 2005. 02673. x.
75. Waples R (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conserv Genet 7: 167-184. doi: 10. 1007/s10592-005-9100-y.
76. Waples R, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8: 753-756.
77. Waples R, Masuda M, Pella J (2007) SalmonNb: a program fro computing cohort-specific effective populations sizes (Nb) in Pacific salmon and other semelparous species using the temporal method. Mol Ecol Notes 7: 21-24. doi: 10. 1111/j. 1471-8286. 2006. 01567. x.
78. Williamson E, Slatkin M (1999) Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152: 755-761.
79. Wright S (1931) Evolution in Mendelian populations. Genetics 16: 97-159.