The site-frequency spectrum associated with Ξ-coalescents

Theoretical Population Biology

Volumn 110, Issue , 2016, Pages 36-50

  Blath, Jochen ^a   Cronjäger, Mathias Christensen ^b   Eldon, Bjarki ^c   Hammer, Matthias ^a  

^a TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c LEIBNIZ INSTITUTE FOR EVOLUTION AND BIODIVERSITY SCIENCE   (Germany)

Author keywords

Atlantic cod; Diploidy; Simultaneous mergers; Site frequency spectrum; Xi coalescents

Indexed keywords

AQUACULTURE; COALESCENCE; MUTATION; OFFSHORING; PELAGIC FISH; POLYPLOIDY; SPECTRUM;

GADUS MORHUA;

BIOLOGICAL MODEL; COMPUTER SIMULATION; DIPLOIDY; FERTILITY; GENETICS; MUTATION; POPULATION GENETICS; PROCEDURES; REPRODUCTION;

COMPUTER SIMULATION; DIPLOIDY; FERTILITY; GENETICS, POPULATION; MODELS, GENETIC; MUTATION; REPRODUCTION;

EID: 84966569772     PISSN: 00405809     EISSN: 10960325     Source Type: Journal    
DOI: 10.1016/j.tpb.2016.04.002     Document Type: Article

References (46)

1. Árnason E. Mitochondrial cytochrome b variation in the high-fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy. Genetics 2004, 166:1871-1885.
2. Árnason Einar, Halldórsdóttir Katrín Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models. PeerJ 2015, 3:e786.
3. Barton N.H., Etheridge A.M., Véber A. A new model for evolution in a spatial continuum. Electron. J. Probab. 2010, 15:162-216.
4. Basdevant A.-L., Goldschmidt C. Asymptotics of the allele frequency spectrum associated with the Bolthausen-Sznitman coalescent. Electron. J. Probab. 2008, 13:486-512.
5. Berestycki N. Recent progress in coalescent theory. Ens. Math. 2009, 16:1-193.
6. Berestycki J., Berestycki N., Schweinsberg J. Beta-coalescents and continuous stable random trees. Ann. Probab. 2007, 35:1835-1887.
7. Berestycki J., Berestycki N., Schweinsberg J. Small-time behavior of beta coalescents. Ann. Inst. Henri Poincaré Probab. Stat. 2008, 44:214-238.
8. Birkner M., Blath J. Computing likelihoods for coalescents with multiple collisions in the infinitely many sites model. J. Math. Biol. 2008, 57:435-465.
9. Birkner M., Blath J., Eldon B. An ancestral recombination graph for diploid populations with skewed offspring distribution. Genetics 2013, 193:255-290.
10. Birkner M., Blath J., Eldon B. Statistical properties of the site-frequency spectrum associated with Λ-coalescents. Genetics 2013, 195:1037-1053.
11. Birkner M., Blath J., Möhle M., Steinrücken M., Tams J. A modified lookdown construction for the Xi-Fleming-Viot process with mutation and populations with recurrent bottlenecks. ALEA Lat. Am. J. Probab. Math. Stat. 2009, 6:25-61.
12. Birkner M., Blath J., Steinrücken M. Importance sampling for Lambda-coalescents in the infinitely many sites model. Theor. Popul. Biol. 2011, 79:155-173.
13. Birkner M., Blath J., Steinrücken M. Analysis of DNA sequence variation within marine species using Beta-coalescents. Theor. Popul. Biol. 2013, 87:15-24.
14. Birkner, M., Liu, H., Sturm, A., A note on coalescent results for diploid exchangeable population models. Preprint, 2015.
15. Cronjäger M.C. On the expected site-frequency spectrum associated with Ξ-coalescents 2014, (Master's thesis), TU Berlin, Berlin.
16. Dahmer I., Kersting G. The internal branch lengths of the Kingman coalescent. Ann. Appl. Probab. 2015, 25:1325-1348.
17. Donnelly P., Kurtz T.G. Particle representations for measure-valued population models. Ann. Probab. 1999, 27:166-205.
18. Durrett R. Probability Models for DNA Sequence Evolution 2008, Springer, New York. second ed.
19. Durrett R., Schweinsberg J. Approximating selective sweeps. Theor. Popul. Biol. 2004, 66:129-138.
20. Durrett R., Schweinsberg J. A coalescent model for the effect of advantageous mutations on the genealogy of a population. Stochastic Process. Appl. 2005, 115:1628-1657.
21. Eldon B. Structured coalescent processes from a modified Moran model with large offspring numbers. Theor. Popul. Biol. 2009, 76:92-104.
22. Eldon B., Birkner M., Blath J., Freund F. Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents. Genetics 2015, 199:841-856.
23. Eldon B., Wakeley J. Coalescent processes when the distribution of offspring number among individuals is highly skewed. Genetics 2006, 172:2621-2633.
24. Fu Y.-X. Statistical properties of segregating sites. Theor. Popul. Biol. 1995, 48:172-197.
25. Fu Y.-X. New statistical tests of neutrality for DNA samples from a population. Genetics 1996, 143:557-570.
26. Hedgecock D. Does variance in reproductive success limit effective population sizes of marine organisms?. Genetics and Evolution of Aquatic Organisms 1994, 1222-1344. Chapman and Hall, London. A. Beaumont (Ed.).
27. Hedgecock D., Pudovkin A.I. Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bull. Mar. Sci. 2011, 87:971-1002.
28. Kingman J.F.C. Exchangeability and the evolution of large populations. Exchangeability in Probability and Statistics 1982, 97-112. North-Holland, Amsterdam. G. Koch, F. Spizzichino (Eds.).
29. Kingman J.F.C. On the genealogy of large populations. J. Appl. Probab. 1982, 19A:27-43.
30. Kingman J.F.C. The coalescent. Stochastic Process. Appl. 1982, 13:235-248.
31. Limic V., Sturm A. The spatial Λ-coalescent. Electron. J. Probab. 2006, 11:363-393.
32. McCombie H., Lapègue S., Cornette F., Ledu C., Boudry P. Chromosome loss in bi-parental progenies of tetraploid Pacific oysters Crassostrea gigas. Aquaculture 2005, 247:97-105.
33. Möhle M., Sagitov S. A classification of coalescent processes for haploid exchangeable population models. Ann. Probab. 2001, 29:1547-1562.
34. Möhle M., Sagitov S. Coalescent patterns in diploid exchangeable population models. J. Math. Biol. 2003, 47:337-352.
35. Pitman J. Coalescents with multiple collisions. Ann. Probab. 1999, 27:1870-1902.
36. Sagitov S. The general coalescent with asynchronous mergers of ancestral lines. J. Appl. Probab. 1999, 36:1116-1125.
37. Sagitov S. Convergence to the coalescent with simultaneous mergers. J. Appl. Probab. 2003, 40:839-854.
38. Sargsyan O., Wakeley J. A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms. Theor. Popul. Biol. 2008, 74:104-114.
39. Sawyer S.A., Hartl D.L. Population genetics of polymorphism and divergence. Genetics 1992, 132:1161-1176.
40. Schweinsberg J. Coalescents with simultaneous multiple collisions. Electron. J. Probab. 2000, 5:1-50.
41. Schweinsberg J. Coalescent processes obtained from supercritical Galton-Watson processes. Stochastic Process. Appl. 2003, 106:107-139.
42. Schweinsberg J., Durrett R. Random partitions approximating the coalescence of lineages during a selective sweep. Ann. Appl. Probab. 2005, 1591-1651.
43. Spence Jeffrey P., Kamm John A., Song Yun S. The site frequency spectrum for general coalescents. Genetics 2016, 202(4):1549-1561.
44. Stanley R.P. Enumerative Combinatorics, Vol. 2 2001, Cambridge University Press, New York.
45. Wakeley J. Coalescent Theory 2007, Roberts & Co.
46. Watterson G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 1975, 7:256-276.