title: Analysis of DNA sequence variation within marine species using Beta-coalescents.
abstract: We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweepstakes". Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta-coalescents (as opposed to Kingman's coalescent), allowing multiple mergers of genealogies. The choice of the underlying coalescent model for the genealogy has drastic implications for the estimation of the above quantities, in particular the real-time embedding of the genealogy.
authors: Department of Statistics, University of California, 367 Evans Hall MC 3860, Berkeley, CA 94720-3860, USA. steinrue@stat.berkeley.edu
authors: Matthias
authors: M
authors: Steinrücken
authors: Matthias
authors: M
authors: Birkner
authors: Jochen
authors: J
authors: Blath
mesh_terms: D000818:Animals; D008386:Marine Biology; D010125:Ostreidae / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: Beta-coalescents; Hedgecock sweepstakes; Inference of mutation rates; Population genetics; Time to the most recent common ancestor
references: Mol Ecol. 1995 Feb;4(1):79-88
references: 7711956
references: Math Biosci. 1995 May;127(1):77-98
references: 7734858
references: Genetics. 2002 Nov;162(3):1329-39
references: 12454077
references: Hereditas. 1998;129(1):37-43
references: 9868927
references: Genetics. 2001 Jan;157(1):317-30
references: 11139512
references: Genetics. 2009 Jan;181(1):341-5
references: 19001293
references: Theor Popul Biol. 2011 Jun;79(4):155-73
references: 21296095
references: Mol Mar Biol Biotechnol. 1996 Sep;5(3):203-14
references: 8817926
references: Evolution. 2005 Jul;59(7):1596-9
references: 16153045
references: Theor Popul Biol. 2011 Aug;80(1):16-28
references: 21570995
references: Genetics. 2004 Apr;166(4):1871-85
references: 15126405
references: J Math Biol. 2008 Sep;57(3):435-65
references: 18347796
references: Genetics. 1993 Mar;133(3):693-709
references: 8454210
references: Mol Biol Evol. 2003 Feb;20(2):208-13
references: 12598687
references: Theor Popul Biol. 2004 Sep;66(2):129-38
references: 15302222
references: Heredity (Edinb). 2003 Dec;91(6):557-64
references: 14560303
references: Genetics. 2005 Feb;169(2):1061-70
references: 15489538
references: Genetics. 1989 Nov;123(3):585-95
references: 2513255
references: Genetics. 2006 Apr;172(4):2621-33
references: 16452141