Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent-offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

Molecular Ecology Resources

Volumn 12, Issue 6, 2012, Pages 1114-1123

  Hess, Maureen A ^a,d   Rhydderch, James G ^a   Leclair, Larry L ^a,b   Buckley, Raymond M ^b   Kawase, Mitsuhiro ^c   Hauser, Lorenz ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b WASHINGTON DEPARTMENT OF FISH AND WILDLIFE   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d NONE   (United States)

Author keywords

Genotyping error; Mendelian inheritance; Microsatellites; Rockfish; Sebastes auriculatus

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; CHORDATA; CLASSIFICATION; DIAGNOSTIC ERROR; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOTYPE; METHODOLOGY; MOLECULAR BIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; STATISTICS;

ANIMALS; CHORDATA; DIAGNOSTIC ERRORS; GENETIC VARIATION; GENOTYPE; MICROSATELLITE REPEATS; MOLECULAR BIOLOGY; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA;

SEBASTES AURICULATUS;

EID: 84867524957     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12002     Document Type: Article

References (40)

1. Bonin A, Bellemain E, Eidesen PB, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13, 3261-3273.
2. Broquet T, Petit E (2004) Quantifying genotyping errors in noninvasive population genetics. Molecular Ecology, 13, 3601-3608.
3. Bulut Z, McCormick CR, Gopurenko D, Williams RN, Bos DH, DeWoody AJ (2009) Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci. Genetica, 136, 501-504.
4. Campbell NR, Narum SR (2009) Quantitative PCR assessment of microsatellite and SNP genotyping with variable quality DNA extracts. Conservation Genetics, 10, 779-784.
5. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24, 621-631.
6. Copeland T, Kozfkay CC, Johnson J, Campbell MR (2009) Do Dead Fish Tell Tales? DNA degradation in Chinook Salmon (Oncorhynchus tshawytscha) Carcasses Northwest Science, 83, 140-147.
7. Creel S, Spong G, Sands JL et al. (2003) Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Molecular Ecology, 12, 2003-2009.
8. Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity, 93, 504-509.
9. DeWoody J, Nason JD, Hipkins VD (2006) Mitigating scoring errors in microsatellite data from wild populations. Molecular Ecology Notes, 6, 951-957.
10. Douglas JA, Skol AD, Boehnke M (2002) Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data. American Journal of Human Genetics, 70, 487-495.
11. Ellis J, Gilbey J, Armstrong A et al. (2011) Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.). Genetica, 139, 353-367.
12. Ewen KR, Bahlo M, Treloar SA et al. (2000) Identification and analysis of error types in high-throughput genotyping. American Journal of Human Genetics, 67, 727-736.
13. Gagneux P, Woodruff DS, Boesch C (1997) Furtive mating in female chimpanzees. Nature, 387, 358.
14. Gagneux P, Woodruff DS, Boesch C (2001) Retraction: furtive mating in female chimpanzees. Nature, 414, 508.
15. Garner T (2000) Construction and Screening of a Subgenomic Library Highly Enriched for Microsatellite Regions, pp. 1-13. Zoologisches Institut, Universität Zürich, Zürich, Switzerland.
16. Gomez-Uchida D, Hoffman EA, Ardren WR, Banks MA (2003) Microsatellite markers for the heavily exploited canary (Sebastes pinniger) and other rockfish species. Molecular Ecology Notes, 3, 387-389.
17. Goudet J (1995) FSTAT (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
18. Hamilton MB, Pincus EL, Di FioreA, Fleischer RC (1999) Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. BioTechniques, 27, 500-507.
19. Hoffman JI, Amos W (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Molecular Ecology, 14, 599-612.
20. Johnson PCD, Haydon DT (2007) Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data. Genetics, 175, 827-842.
21. Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Molecular Ecology, 12, 2511-2523.
22. Kalinowski ST, Taper ML (2006) Maximum likelihood estimation of the frequency of null alleles at microsatellite loci. Conservation Genetics, 7, 991-995.
23. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16, 1099-1106.
24. Kuroki M, Buckley RM, LeClair LL, Hauser L (2010) Validation and efficacy of transgenerational mass marking of otoliths in viviparous fish larvae. Journal of Fish Biology, 77, 292-298.
25. Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7, 639-655.
26. Miller KM, Schulze AD, Withler RE (2000) Characterization of microsatellite loci in Sebastes alutus and their conservation in congeneric rockfish species. Molecular Ecology, 9, 240-242.
27. Okello JBA, Wittemyer G, Rasmussen HB et al. (2005) Noninvasive genotyping and Mendelian analysis of microsatellites in African Savannah Elephants. Journal of Heredity, 96, 679-687.
28. Palsboll PJ, Allen J, Berube M et al. (1997) Genetic tagging of humpback whales. Nature, 388, 767-769.
29. Park S (2001) Microsatellite Toolkit. Department of Genetics, Trinity College, Dublin, Ireland.
30. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nature Reviews Genetics, 6, 847-859.
31. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds Krawetz S, Misener S), Humana Press, Totowa, New Jersey.
32. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18, 233-234.
33. Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters, 9, 615-629.
34. Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society, 68, 41-55.
35. Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends in Ecology & Evolution, 14, 323-327.
36. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535-538.
37. Waits JL, Leberg PL (2000) Biases associated with population estimation using molecular tagging. Animal Conservation, 3, 191-199.
38. Weetman D, Hauser L, Carvalho GR (2006) Heterogeneous evolution of microsatellites revealed by reconstruction of recent mutation history in an invasive apomictic snail, Potamopyrgus antipodarum. Genetica, 127, 285-293.
39. Westerman ME, Buonaccorsi VP, Stannard JA et al. (2005) Cloning and characterization of novel microsatellite DNA markers for the grass rockfish, Sebastes rastrelliger, and cross-species amplification in 10 related Sebastes spp. Molecular Ecology Notes, 5, 74-76.
40. Whittaker JC, Harbord RM, Boxall N, Mackay I, Dawson G, Sibly RM (2003) Likelihood-based estimation of microsatellite mutation rates. Genetics, 164, 781-787.