Modified SLCA algorithm for full-sib reconstruction of haplodiploid species

Environmental Entomology

Volumn 36, Issue 6, 2007, Pages 1523-1528

  Kokuvo, Nozomu ^a   Yoshimura, Shinya ^a   Mano, Hiroyuki ^b   Toquenaga, Yukihiko ^a   Goka, Koichi ^b  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b NATIONAL INSTITUTE FOR ENVIRONMENTAL STUDIES   (Japan)

Author keywords

Kinship; Microsatellites; mSLCA; Pedigree reconstruction; Shared Loci Correspondence Analysis; Social insects

Indexed keywords

MICROSATELLITE DNA;

ALLELE; BEE; CORRESPONDENCE ANALYSIS; DNA; GENE FLOW; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC MARKER; KINSHIP; MOLECULAR ANALYSIS; POPULATION ESTIMATION; POPULATION SIZE; RECONSTRUCTION; REPRODUCTIVE STRATEGY; SOCIAL INSECT;

ALGORITHM; ANIMAL; ARTICLE; BEE; COMPUTER SIMULATION; FAMILY SIZE; GENE FREQUENCY; GENETICS; HETEROZYGOTE;

ALGORITHMS; ANIMALS; BEES; COMPUTER SIMULATION; FAMILY CHARACTERISTICS; GENE FREQUENCY; HETEROZYGOTE; MICROSATELLITE REPEATS;

BOMBUS TERRESTRIS; HEXAPODA;

EID: 40549107093     PISSN: 0046225X     EISSN: None     Source Type: Journal    
DOI: 10.1603/0046-225X(2007)36[1523:MSAFFR]2.0.CO;2     Document Type: Article

References (26)

1. Almudevar, A., and C. Field. 1999. Estimation of single-generation sibling relationships based on DNA markers. J. Agric. Biol. Environ. Stat. 4: 136-165.
2. Beyer, J., and B. May. 2003. A graph-theoretic approach to the partition of individuals into full-sib families. Molec. Ecol. 12: 2243-2250.
3. Blouin, M. S. 2003. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends. Ecol. Evol. 18: 503-511.
4. Blouin, M. S., M. Parsons, V. Lacaille, and S. Lotz. 1996. Use of microsatellite loci to classify individuals by relatedness. Molec. Ecol. 5: 394-401.
5. Butler, K., C. Field, C. M. Herbinger, and B. R. Smith. 2004. Accuracy, efficiency and robustness of four algorithms allowing full sibship reconstruction from DNA marker data. Molec. Ecol. 13: 1589-1600.
6. Cameron, E. C., P. Franck, and P. Oldroyd. 2004. Genetic structure of nest aggregations and drone congregations of the southeast Asian stingless bee Trigona collina. Molec. Ecol. 13: 2357-2364.
7. Chapman, R. E., J. Wang, and A.F.G. Bourke. 2003. Genetic analysis of spatial foraging patterns and resource sharing in bumblebee pollinators. Molec. Ecol. 12: 2801-2808.
8. Darvill, B., M. E. Knight, and D. Goulson. 2004. Use of genetic markers to quantify bumblebee foraging range and nest density. Oikos 107: 471-478.
9. Ellis, J. S., E. Knight, B. Darvill, and D. Goulson. 2006. Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae). Molec. Ecol. 15: 4375-4386.
10. Estoup, A., M. Solignac, J. M. Cornuet, J. Goudet, and A. Scholl. 1996. Genetic differentiation of continental and island populations of Bombus terrestris (Hymenoptera; Apidae) in Europe. Molec. Ecol. 5: 19-31.
11. Goodnight, K. F., and D. C. Queller. 1999. Computer software for performing likelihood tests of pedigree relationship using genetic markers. Molec. Ecol. 8: 1231-1234.
12. Goulson, D. 2003. Bumblebees: their behaviour and ecology. Oxford University Press, Oxford, UK.
13. Hamilton, W. D. 1964. The genetical evolution of social behaviour. J. Theor. Biol. 7: 1-52.
14. Herbinger, C. M., P. T. O'Reilly, and E. Verspoor. 2006. Unravelling first-generation pedigrees in wild endangered salmon populations using molecular genetic markers. Mol. Ecol. 15: 2261-2275.
15. Knight, M. E., A. P. Martin, S. Bishop, J.J.L. Osborne, R. J. Hale, and A. Sanderson. 2005. An interspecific comparison of foraging range and nest density of four bumblebee (Bombus) species. Molec. Ecol. 14: 1811-1820.
16. Kokuvo, N., Y. Toquenaga, and K. Goka. 2007a. A simple visualization method to reconstruct nest-mate patterns among bumble bees (hymenoptera, Apidae) using genetic data. Appl. Entomol. Zool. 42: 137-141.
17. Kokuvo, N., Y. Toquenaga, and K. Goka. 2008. Estimating colony number of Bombus terrestris (Hymenoptera, Apidae) queens foraging at Biratori, Hokkaido, Japan. Appl. Entomol. Zool. (in press).
18. Konovalov, D., C. Manning, and M. Henshaw. 2004. KIN-GROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers. Molec. Ecol. Note 4: 779-782.
19. 3) algorithm for the full sibship reconstruction problem. Bioinformatics 21: 3912-3917.
20. Painter, I. 1997. Sibship reconstruction without parental information. J. Agric. Biol. Environ. Stat. 2: 212-229.
21. Paxton, R. J., M. Ayasse, J. Field, and A. Soro. 2002. Complex sociogenetic organization and reproductive skew in a primitively eusocial sweat bee, Laioglossum malachurum, as revealed by microsatellites. Molec. Ecol. 11: 2405-2416.
22. R Development Core Team. 2004. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austaria.
23. Schmid-Hempel, R., and P. Schmid-Hempel. 2000. Female mating frequencies in Bombus spp. from Central Europe. Insectes. Soc. 47: 36-41.
24. Smith, B. R., C. Herbinger, and H. Merry. 2001. Accurate partition of individuals into full-sib families from genetic data without parental information. Genetics 158: 1329-1338.
25. Thomas, S. C., and W. G. Hill. 2000. Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics 155: 1961-1972.
26. Wang, J. 2004. Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963-1979.