An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta)

American Journal of Primatology

Volumn 76, Issue 4, 2014, Pages 313-324

  Ross, Cody T ^a,b   Weise, Jessica A ^a   Bonnar, Sarah ^a   Nolin, David ^c   Satkoski Trask, Jessica ^a   Smith, David Glenn ^a,b   Ferguson, Betsy ^d   Ha, James ^e   Kubisch, H Michael ^f   Vinson, Amanda ^d   Kanthaswamy, Sree ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c BOISE STATE UNIVERSITY   (United States)

^d OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^e UNIVERSITY OF WASHINGTON   (United States)

^f TULANE NATIONAL PRIMATE RESEARCH CENTER   (United States)

Author keywords

Colony management; Kinship; Macaca; Relatedness estimation; SNP; STR

Indexed keywords

ALGORITHM; CAPTIVE POPULATION; COLONY; DATA SET; EMPIRICAL ANALYSIS; GENOTYPE; POLYMORPHISM; PRIMATE; RELATEDNESS; RESEARCH;

CALIFORNIA; UNITED STATES;

MACACA; MACACA MULATTA; PRIMATES;

MICROSATELLITE DNA;

ALGORITHM; ANIMAL; ARTICLE; COLONY MANAGEMENT; EXPERIMENTAL ANIMAL; GENETIC VARIABILITY; GENETICS; GENOTYPING TECHNIQUE; KINSHIP; LABORATORY; MACACA; PEDIGREE; RELATEDNESS ESTIMATION; RHESUS MONKEY; SINGLE NUCLEOTIDE POLYMORPHISM; SNP; STANDARD; STR;

COLONY MANAGEMENT; KINSHIP; MACACA; RELATEDNESS ESTIMATION; SNP; STR;

ALGORITHMS; ANIMALS; ANIMALS, LABORATORY; GENETIC VARIATION; GENOTYPING TECHNIQUES; LABORATORY ANIMAL SCIENCE; MACACA MULATTA; MICROSATELLITE REPEATS; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84895930779     PISSN: 02752565     EISSN: 10982345     Source Type: Journal    
DOI: 10.1002/ajp.22235     Document Type: Article

References (27)

1. Bolker B. 2012. bbmle: tools for general maximum likelihood estimation. R package version 1.0.4. 1.
2. Burnham K, Anderson D. 2002. Model selection and multimodel inference: a practical information-theoretic approach. 2nd edition. New York: Springer-Verlag.
3. Butler JM, Coble MD, Vallone PM. 2007. STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci Med Pathol 200-205.
4. Butts CT. 2010. sna: tools for social network analysis. R package version 2.1.
5. Csilléry K, Johnson T, Beraldi D, et al. 2006. Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics 173:2091-2101.
6. Dario P, Ribeiro T, Espinheira R, et al. 2009. SNPs in paternity investigation: the simple future. Forensic Sci Int Genet Suppl Ser 2:127-128.
7. Eding H, Meuwissen T. 2001. Marker-based estimates of between and within population kinships for the conservation of genetic diversity. Anim Breed Genet 118:141-159.
8. Estoup A, Jarne P, Cornuet JM. 2002. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol 11:1591-1604.
9. Glover KA, Hansen MM, Lien S, et al. 2010. A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment. BMC Genet 11:1-12.
10. Hagen EH. 2005. Descent. Version 2.0. Available online at: http://itb.biologie.hu-berlin.de/hagen/Descent/ [accessed January 2013].
11. Hardy OJ, Vekemans X. 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618-620.
12. Hauser L, Baird M, Hilborn R, et al. 2011. An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Mol Ecol Resour 11:150-161.
13. Kalinowski ST, Wagner AP, Taper ML. 2006. ML-RELATE: a computer program for maximum likelihood estimation of relatedness and relationship. Mol Ecol Notes 6:576-579.
14. Kanthaswamy S, von Dollen A, Kurushima JD, et al. 2006. Microsatellite markers for standardized genetic management of captive colonies of rhesus macaques (Macaca mulatta). Am J Primatol 68:73-95.
15. Kanthaswamy S, Capitanio JP, Dubay CJ, et al. 2009. Resources for genetic management and genomics research on non-human primates at the National Primate Research Centers (NPRCs). J Med Primatol 38:17-23.
16. Krackhardt D. 1987. QAP partialling as a test of spuriousness. Soc Netw 9:171-186.
17. Li M, Ismo S, Timo T, et al. 2011. A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population. PLoS ONE 6:e26256.
18. Lynch M, Ritland K. 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152:1753-1766.
19. McElreath R. 2011. Statistical rethinking: a mostly Bayesian course in mostly non-Bayesian statistics. Available online at: xcelab.net/rm/?page_id=598 [accessed June 2013].
20. McElreath R. 2012. Rethinking. R package version 1.02.
21. Morin P, Luikart G, Wayne RK, et al. 2004. SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208-216.
22. Queller DC, Goodnight KF. 1989. Estimating relatedness using genetic markers. Evolution 43:258-275.
23. R Development Core Team. 2010. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Available online at: http://www.R-project.org/ [accessed June 2013].
24. Rousset F. 2008. Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103-106.
25. Satkoski Trask JA, Garnica WT, Kanthaswamy S, et al. 2011. 4040 novel SNPs for genomic analysis in the rhesus macaque (Macaca mulatta). Genomics 98:352-358.
26. Wang, J. 2002. An estimator for pairwise relatedness using molecular markers. Genetics 160:1203-1215.
27. Wang J. 2011. COANCESTRY: a program for simulating, estimating, and analyzing relatedness and inbreeding coefficients. Mol Ecol Resour 11:141-145.