An ancestral recombination graph for diploid populations with skewed offspring distribution

Genetics

Volumn 193, Issue 1, 2013, Pages 255-290

  Birkner, Matthias ^a   Blath, Jochen ^b   Eldon, Bjarki ^b  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

^b TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; DIPLOIDY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENEALOGY; GENETIC RECOMBINATION; HUMAN; NONHUMAN; PARENT; POPULATION MODEL; POPULATION SIZE; PRIORITY JOURNAL; PROGENY; REPRODUCTION; REVIEW; SEX;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; DIPLOIDY; EVOLUTION, MOLECULAR; FEMALE; GENETIC LOCI; GENETICS, POPULATION; HUMANS; MALE; MODELS, GENETIC; RECOMBINATION, GENETIC;

EID: 84871723554     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.144329     Document Type: Review

References (55)

1. Árnason, E., 2004 Mitochondrial cytochrome b variation in the high-fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy. Genetics 166: 1871-1885.
2. Avise, J. C., R. M. Ball, and J. Arnold, 1988 Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations. Mol. Biol. Evol. 5: 331-344.
3. Beckenbach, A. T., 1994 Mitochondrial haplotype frequencies in oysters: neutral alternatives to selection models, pp. 188-198 in Non-Neutral Evolution, edited by B. Golding. Chapman & Hall, New York.
4. Berestycki, J., N. Berestycki, and J. Schweinsberg, 2007 Beta-coalescents and continuous stable random trees. Ann. Probab. 35: 1835-1887.
5. Berestycki, J., N. Berestycki, and J. Schweinsberg, 2008 Small-time behavior of beta coalescents. Ann. Inst. H. Poincaré. Probab. Stat. 44:214-238.
6. Birkner, M., and J. Blath, 2008 Computing likelihoods for coalescents with multiple collisions in the infinitely many sites model. J. Math. Biol. 57: 435-465.
7. Birkner, M., and J. Blath, 2009 Measure-valued diffusions, general coalescents and population genetic inference, pp. 329-363 in Trends in Stochastic Analysis, edited by J. Blath, P. Mörters, and M. Scheutzow. Cambridge University Press, Cambridge/ London/New York.
8. Birkner, M., J. Blath, M. Möhle, M. Steinrücken, and J. Tams, 2009 A modified lookdown construction for the Xi-Fleming-Viot process with mutation and populations with recurrent bottlenecks. ALEA Lat. Am. J. Probab. Math. Stat. 6: 25-61.
9. Birkner, M., J. Blath, and M. Steinrücken, 2011 Importance sampling for Lambda-coalescents in the infinitely many sites model. Theor. Popul. Biol. 79: 155-173.
10. Cannings, C., 1974 The latent roots of certain Markov chains arising in genetics: a new approach, I. Haploid models. Adv. Appl. Probab. 6: 260-290.
11. Davies, J. L., F. Simančík, R. Lyngsø, T. Mailund, and J. Hein, 2007 On recombination-induced multiple and simultaneous coalescent events. Genetics 177: 2151-2160.
12. Donnelly, P., and T. G. Kurtz, 1999 Particle representations for measure-valued population models. Ann. Probab. 27: 166-205.
13. Durrett, R., 2002 Probability Models for DNA Sequence Evolution. Springer-Verlag, New York.
14. Eldon, B., 2011 Estimation of parameters in large offspring number models and ratios of coalescence times. Theor. Popul. Biol. 80: 16-28.
15. Eldon, B., and J. Wakeley, 2006 Coalescent processes when the distribution of offspring number among individuals is highly skewed. Genetics 172: 2621-2633.
16. Eldon, B., and J. Wakeley, 2008 Linkage disequilibrium under skewed offspring distribution among individuals in a population. Genetics 178: 1517-1532.
17. Etheridge, A. M., R. C. Griffiths, and J. E. Taylor, 2010 A coalescent dual process in a Moran model with genic selection, and the Lambda coalescent limit. Theor. Popul. Biol. 78: 77-92.
18. Fearnhead, P., and P. Donnelly, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
19. Griffiths, R. C., 1991 The two-locus ancestral graph, pp. 100-117 in Selected Proceedings of the Symposium on Applied Probability, edited by I. V. Basawa and R. L. Taylor. Institute of Mathematical Statistics, Hayward, CA.
20. Griffiths, R. C., 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 Applications 87), edited by P. Donnelly, and S. Tavaré. Springer-Verlag, New York.
21. Hartl, D. L., and A. G. Clark, 1989 Principles of Population Genetics, Ed. 2. Sinauer Associates, Sunderland, MA.
22. Hedgecock, D., 1994 Does variance in reproductive success limit effective population sizes of marine organisms? pp. 1222-1344 in Genetics and Evolution of Aquatic Organisms, edited by A. Beaumont. Chapman & Hall, London.
23. Hedgecock, D., and A. I. Pudovkin, 2011 Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bull. Mar. Sci. 87: 971-1002.
24. Hedgecock, D., M. Tracey, and K. Nelson, 1982 Genetics, pp. 297-403 in The Biology of Crustacea, Vol. 2, edited by L. G. Abele. Academic Press, New York.
25. Herbots, H. M., 1997 The structured coalescent, pp. 231-255 in Progress of Population Genetics and Human Evolution, edited by P. Donnelly and S. Tavaré. Springer-Verlag, Berlin/Heidelberg, Germany/New York.
26. Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
27. Hudson, R. R., 1983a Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
28. Hudson, R. R., 1983b Testing the constant-rate neutral allele model with protein sequence data. Evolution 37: 203-217.
29. Huillet, T., and M. Möhle, 2011 On the extended Moran model and its relation to coalescents with multiple collisions. Theor. Popul. Biol. (in press).
30. Hutchings, J. A., T. D. Bishop, and C. R. McGregor-Shaw, 1999 Spawning behaviour of Atlantic cod, Gadus morhua: evidence of mate competition and mate choice in a broadcast spawning. Can. J. Fish. Aquat. Sci. 56: 97-104.
31. Kingman, J. F. C., 1982a The coalescent. Stoch. Proc. Appl. 13: 235-248.
32. Kingman, J. F. C., 1982b On the genealogy of large populations. J. Appl. Probab. 19A: 27-43.
33. Krone, S. M., and C. Neuhauser, 1997 Ancestral processes with selection. Theor. Popul. Biol. 51: 210-237.
34. McVean, G. A., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
35. Möhle, M., 1998 A convergence theorem for Markov chains arising in population genetics and the coalescent with selfing. Adv. Appl. Probab. 30: 493-512.
36. Möhle, M., and S. Sagitov, 2001 A classification of coalescent processes for haploid exchangeable population models. Ann. Probab. 29: 1547-1562.
37. M̈hle, M., and S. Sagitov, 2003 Coalescent patterns in diploid exchangeable population models. J. Math. Biol. 47: 337-352.
38. Neuhauser, C., and S. M. Krone, 1997 The genealogy of samples in models with selection. Genetics 145: 519-534.
39. Nordeide, J. T., and I. Folstad, 2000 Is cod lekking or a promiscuous group spawner? Fish Fish. 1: 90-93.
40. Notohara, M., 1990 The coalescent and the genealogical process in geographically structured population. J. Math. Biol. 29: 59-75.
41. Ohta, T., and M. Kimura, 1971 Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68: 571-580.
42. Palumbi, S. R., and A. C. Wilson, 1990 Mitochondrial DNA diversity in the sea-urchins Strongylocentrotus purpuratus and Strongylocentrotus droebachiensis. Evolution 44: 403-415.
43. Pitman, J., 1999 Coalescents with multiple collisions. Ann. Probab. 27: 1870-1902.
44. Sagitov, S., 1999 The general coalescent with asynchronous mergers of ancestral lines. J. Appl. Probab. 36: 1116-1125.
45. Sagitov, S., 2003 Convergence to the coalescent with simultaneous mergers. J. Appl. Probab. 40: 839-854.
46. Sargsyan, O., and J. Wakeley, 2008 A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms. Theor. Popul. Biol. 74: 104-114.
47. Schweinsberg, J., 2000a Coalescents with simultaneous multiple collisions. Electron. J. Probab. 5: 1-50.
48. Schweinsberg, J., 2000b A necessary and sufficient condition for the l-coalescent to come down from infinity. Electron. Comm. Probab. 5: 1-11.
49. Schweinsberg, J., 2003 Coalescent processes obtained from supercritical Galton-Watson processes. Stoch. Proc. Appl. 106: 107-139.
50. Star, B., A. J. Nederbragt, and S. Jentoft, U. Grimholt, M. Malstrøm et al., 2011 The genomic sequence of Atlantic cod reveals a unique immune system. Nature 477: 207-210.
51. Steinrücken, M., M. Birkner, and J. Blath, 2013 Analysis of DNA sequence variation within marine species using Beta-coalescents. Theor. Popul. Biol. 83: 20-29.
52. Tajima, F., 1983 Evolutionary relationships of DNA sequences in finite populations. Genetics 105: 437-460.
53. Taylor, J., and A. Véber, 2009 Coalescent processes in subdivided populations subject to recurrent mass extinctions. Electron. J. Probab. 14: 242-288.
54. Taylor, J. E., 2009 The genealogical consequences of fecundity variance polymorphism. Genetics 182: 813-837.
55. Wakeley, J., 1997 Using the variance of pairwise differences to estimate the recombination rate. Genet. Res. 69: 45-48.