Bayesian spatial modeling of genetic population structure

Computational Statistics - Tập 23 Số 1 - Trang 111-129 - 2008
Jukka Corander1, Jukka Sirén1, Elja Arjas1
1Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland

Tóm tắt

Từ khóa


Tài liệu tham khảo

Andrieu C, Doucet A and Robert CP (2004). Computational advances for and from Bayesian Analysis. Stat Sci 19: 120–129

Balding DJ and Nichols RA (1997). Significant genetic correlations among Caucasians at forensic DNA loci. Heredity 78: 583–589

Barber CB, Dobkin DP and Huhdanpaa HT (1996). The Quickhull algorithm for convex hulls. ACM Trans Math Software 22: 469–483

Berry A (1999) A wide-range efficient algorithm for minimal triangulation. Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms, Philadelphia, SIAM, pp 860–861

Cegelski CC, Waits LP and Anderson NJ (2003). Assessing population structure and gene flow in Montana wolverines (Gulo gulo) using assignment-based approaches. Mol Ecol 12: 2907–2918

Corander J, Waldmann P and Sillanpää MJ (2003). Bayesian analysis of genetic differentiation between populations. Genetics 163: 367–374

Corander J, Waldmann P, Marttinen P and Sillanpää MJ (2004). BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20: 2363–2369

Corander J, Marttinen P and Mäntyniemi S (2006). Bayesian identification of stock mixtures from molecular marker data. Fish Bull 104: 550–558

Corander J, Gyllenberg M, Koski T (2007) Bayesian unsupervised classification framework based on stochastic partitions of data and a parallel search strategy. Adv Data Analysis Classification, under review

Denison DGT and Holmes CC (2001). Bayesian partitioning for estimating disease risk. Biometrics 57: 143–149

Duda RO, Hart PE and Stork DG (2000). Pattern classification, 2nd edn. Wiley, New York

Falush D, Stephens M and Pritchard JK (2003). Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164: 1567–1587

Gelfand AE and Vounatsou P (2003). Proper multivariate conditional autoregressive models for spatial data analysis. Biostatistics 4: 11–25

Guillot G, Estoup A, Mortier F and Cosson JF (2005). A spatial statistical model for landscape genetics. Genetics 170: 1261–1280

Hartl DL and Clark AG (1997). Principles of population genetics, 3rd edn. Sinauer Associates, Sunderland

Heikkinen J and Arjas E (1998). Non-parametric Bayesian estimation of a spatial Poisson intensity. Scand J Statist 25: 435–450

Heikkinen J and Arjas E (1999). Modeling a poisson forest in variable elevations: a nonparametric Bayesian approach. Biometrics 55: 738–745

Kimura M and Weiss GH (1964). The stepping-stone model of population structure and the decrease of genetic correlation with distance. Genetics 49: 561–576

Lauritzen SL (1996). Graphical models. Oxford University Press, Oxford

Manni F, Guérard E and Heyer E (2004). Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by “Monmonier’s algorithm”. Hum Biol 76: 173–190

Pella J and Masuda M (2001). Bayesian methods for analysis of stock mixtures from genetic characters. Fish Bull 99: 151–167

Perks W (1947). Some observations on inverse probability including a new indifference rule. J Inst Actuaries 73: 285–334

Pritchard JK, Stephens M and Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945–959

Rannala B and Mountain JL (1997). Detecting immigration by using multilocus genotypes. PNAS 94: 9197–9201

Seppä P, Gyllenstrand M, Corander J and Pamilo P (2004). Coexistence of the social types: Genetic population structure in the ant Formica exsecta. Evolution 58: 2462–2471

Sawyer S (1977). Asymptotic properties of the equilibrium probability of identity in a geographically structured population. Adv Appl Prob 9: 268–282

Vounatsou P, Smith T and Gelfand AE (2000). Spatial modeling of multinomial data with latent structure; an application to geographical mapping of human gene and haplotype frequencies. Biostatistics 1: 177–189

Wasser SK, Shedlock AM, Comstock K, Ostrander EA, Mutayoba B and Stephens M (2004). Assigning African elephant DNA to geographic region of origin: Applications to the ivory trade. PNAS 101: 14847–14852

Wright S (1943). Isolation by distance. Genetics 28: 139–156

Wright S (1951). The genetical structure of populations. Ann Eugen 15: 323–354

Wright S (1965). The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 52: 950–956