The SMC' is a highly accurate approximation to the ancestral recombination graph

Genetics

Volumn 200, Issue 1, 2015, Pages 343-355

  Wilton, Peter R ^a   Carmi, Shai ^b   Hobolth, Asger ^c  

^a HARVARD UNIVERSITY   (United States)

^b Department of Earth and Environmental Sciences   (United States)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

Ancestral recombination graph; Consistency; Ergodicity; Markov approximation; Sequentially markov coalescent

Indexed keywords

ANCESTRAL RECOMBINATION GRAPH; ARTICLE; BIRTH RATE; CHROMOSOME; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETIC VARIABILITY; HETEROZYGOSITY; HIDDEN MARKOV MODEL; HUMAN; MACHINE LEARNING; MAXIMUM LIKELIHOOD METHOD; MORTALITY; PLESIOMORPHY; POPULATION SIZE; POPULATION STRUCTURE; PRIORITY JOURNAL; PROBABILITY; SEQUENTIALLY MARKOV COALESCENT MODEL; ALGORITHM; BIOLOGICAL MODEL; GENETIC VARIATION; MARKOV CHAIN; MOLECULAR EVOLUTION; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; EVOLUTION, MOLECULAR; GENETIC VARIATION; MARKOV CHAINS; MODELS, GENETIC; RECOMBINATION, GENETIC; SENSITIVITY AND SPECIFICITY;

EID: 84929000162     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.173898     Document Type: Article

References (33)

1. Carmi, S., P. R. Wilton, J. Wakeley, and I. Peer, 2014 A renewal theory approach to IBD sharing. Theor. Popul. Biol. 97: 35-48.
2. Chen, G. K., P. Marjoram, and J. D. Wall, 2009 Fast and flexible simulation of DNA sequence data. Genome Res. 19: 136-142.
3. Dutheil, J. Y., G. Ganapathy, A. Hobolth, T. Mailund, M. K. Uyenoyama et al., 2009 Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 183: 259-274.
4. Eriksson, A., and B. Mehlig, 2004 Gene-history correlation and population structure. Phys. Biol. 1: 220.
5. Eriksson, A., B. Mahjani, and B. Mehlig, 2009 Sequential Markov coalescent algorithms for population models with demographic structure. Theor. Popul. Biol. 76: 84-91.
6. Fernandez, R., and A. Galves, 2002 Markov approximations of chains of infinite order. Bull. Braz. Math. Soc. 33: 1-12.
7. Gallo, S., M. Lerasle, and D. Takahashi, 2013 Markov approximation of chains of infinite order in the d-metric. Markov Processes and Related Fields 19: 51-82.
8. Griffiths, R., and P. Marjoram, 1997 An ancestral recombination graph, pp. 257-270 in Progress in Population Genetics and Human Evolution IMA Volumes in Mathematics and Its Application, Vol. 87, edited by P. Donnelly and S. Tavare. Springer-Verlag, New York.
9. Harris, K., and R. Nielsen, 2013 Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genet. 9: e1003521.
10. Hobolth, A., and J. L. Jensen, 2014 Markovian approximation to the finite loci coalescent with recombination along multiple sequences. Theor. Popul. Biol. 48: 48-58.
11. Hobolth, A., O. F. Christensen, T. Mailund, and M. H. Schierup, 2007 Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 3: e7.
12. Hudson, R., 1991 Gene genealogies and the coalescent process, pp. 1-44 in Oxford Surveys in Evolutionary Biology, Vol. 7, edited by D. Futuyma, and J. Antonovics. University Press, Oxford, UK.
13. Kaplan, N., and R. R. Hudson, 1985 The use of sample genealogies for studying a selectively neutral m-loci model with recombination. Theor. Popul. Biol. 28: 382-396.
14. Kim, J., E. Mossel, M. Z. Racz, and N. Ross, 2015 Can one hear the shape of a population history? Theor. Popul. Biol. 100: 26-38.
15. Lessard, S., and J. Wakeley, 2003 The two-locus ancestral graph in a subdivided population: convergence as the number of demes grows in the island model. J. Math. Biol. 48: 275-292.
16. Li, H., and R. Durbin, 2011 Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
17. Lipson, M., P.-R. Loh, S. Sankararaman, N. Patterson, B. Berger, et al., 2015 Calibrating the human mutation rate via ancestral recombination density in diploid genomes. bioRxiv DOI: http:// dx.doi.org/10.1101/015560
18. Mailund, T., J. Y. Dutheil, A. Hobolth, G. Lunter, and M. H. Schierup, 2011, Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet. 7: e1001319.
19. Marjoram, P., and J. D. Wall, 2006 Fast “coalescent” simulation. BMC Genet. 7: 16.
20. Mc Vean, G. A. T., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
21. Mc Vean, G. A. T., and N. J. Cardin, 2005 Approximating the coales- cent with recombination. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360: 1387-1393.
22. Palamara, P. F., T. Lencz, A. Darvasi, and I. Pe’er, 2012 Length distributions of identity by descent reveal fine-scale demographic history. Am. J. Hum. Genet. 91: 809-822.
23. Rasmussen, M. D., M. J. Hubisz, I. Gronau, and A. Siepel, 2014 Genome-wide inference of ancestral recombination graphs. PLoS Genet. 10: e1004342.
24. Schaper, E., A. Eriksson, M. Rafajlovic, S. Sagitov, and B. Mehlig, Linkage disequilibrium under recurrent bottlenecks. Genetics 190: 217-229.
25. Schiffels, S., and R. Durbin, 2014 Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46: 919-925.
26. Schwarz, G., 1976 Noninvariance of d-convergence of k-step Markov approximations. Ann. Probab. 4: 1033-1035.
27. Sheehan, S., K. Harris, and Y. S. Song, 2013 Estimating variable effective population sizes from multiple genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194: 647-662.
28. Simonsen, K. L., and G. A. Churchill, 1997 A Markov chain model of coalescence with recombination. Theor. Popul. Biol. 52: 43-59.
29. Slatkin, M., and J. L. Pollack, 2006 The concordance of gene trees and species trees at two linked loci. Genetics 172: 1979-1984.
30. van Doorn, E. A., and A. I. Zeifman, 2005 Birth-death processes with killing. Stat. Probab. Lett. 72: 33-42.
31. Wiuf, C., 2006 Consistency of estimators of population scaled parameters using composite likelihood. J. Math. Biol. 53: 821-841.
32. Wiuf, C., and J. Hein, 1999 Recombination as a point process along sequences. Theor. Popul. Biol. 55: 248-259.
33. Zheng, C., M. K. Kuhner, and E. A. Thompson, 2014 Bayesian inference of local trees along chromosomes by the sequential Markov coalescent. J. Mol. Evol. 78: 279-292.