Extensions of the Coalescent Effective Population Size

We suggest two extensions of the coalescent effective population size of Sjödin et al. (2005) and make a third, practical point. First, to bolster its relevance to data and allow comparisons between models, the coalescent effective size should be recast as a kind of mutation effective size. Second, the requirement that the coalescent effective population size must depend linearly on the actual population size should be lifted. Third, even if the coalescent effective population size does not exist in the mathematical sense, it may be difficult to reject Kingman's coalescent using genetic data.

[1]  R. Paine,et al.  Intertidal Landscapes: Disturbance and the Dynamics of Pattern , 1981 .

[2]  B. Charlesworth The effect of life-history and mode of inheritance on neutral genetic variability. , 2001, Genetical research.

[3]  Mitochondrial Haplotype Frequencies in Oysters: Neutral Alternatives to Selection Models , 1994 .

[4]  J. Kingman On the genealogy of large populations , 1982, Journal of Applied Probability.

[5]  M. Whitlock,et al.  The effective size of a subdivided population. , 1997, Genetics.

[6]  G. A NOTE ON EFFECTIVE POPULATION SIZE WITH OVERLAPPING GENERATIONS , 2003 .

[7]  John Wakeley,et al.  Gene genealogies when the sample size exceeds the effective size of the population. , 2003, Molecular biology and evolution.

[8]  Stephen M. Krone,et al.  Separation of time scales and convergence to the coalescent in structured populations ∗ , 2001 .

[9]  Jason Schweinsberg A Necessary and Sufficient Condition for the $\Lambda$-Coalescent to Come Down from Infinity. , 2000 .

[10]  M. Kimura,et al.  An introduction to population genetics theory , 1971 .

[11]  Warren J. Ewens,et al.  On the concept of the effective population size , 1982 .

[12]  M. Kimura,et al.  Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Jason Schweinsberg Coalescents with Simultaneous Multiple Collisions , 2000 .

[14]  G. A. Watterson On the number of segregating sites in genetical models without recombination. , 1975, Theoretical population biology.

[15]  John R Pannell COALESCENCE IN A METAPOPULATION WITH RECURRENT LOCAL EXTINCTION AND RECOLONIZATION , 2003, Evolution; international journal of organic evolution.

[16]  P. A. P. Moran,et al.  Random processes in genetics , 1958, Mathematical Proceedings of the Cambridge Philosophical Society.

[17]  Stephen M. Krone,et al.  On the Meaning and Existence of an Effective Population Size , 2005, Genetics.

[18]  A. Beaumont,et al.  Genetics and evolution of aquatic organisms , 2004, Reviews in Fish Biology and Fisheries.

[19]  Serik Sagitov,et al.  The general coalescent with asynchronous mergers of ancestral lines , 1999 .

[20]  P. E. Kopp,et al.  Convergence in Incomplete Market Models , 2000 .

[21]  J. Wakeley,et al.  A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms. , 2008, Theoretical population biology.

[22]  P. Dayton Competition, Disturbance, and Community Organization: The Provision and Subsequent Utilization of Space in a Rocky Intertidal Community , 1971 .

[23]  J. Pitman Coalescents with multiple collisions , 1999 .

[24]  R. A. Fisher,et al.  The Genetical Theory of Natural Selection , 1931 .

[25]  J. Felsenstein,et al.  Inbreeding and variance effective numbers in populations with overlapping generations. , 1971, Genetics.

[26]  Richard R. Hudson,et al.  TESTING THE CONSTANT‐RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA , 1983, Evolution; international journal of organic evolution.

[27]  S. Sagitov CONVERGENCE TO THE COALESCENT WITH SIMULTANEOUS MULTIPLE MERGERS , 2003 .

[28]  M. Dickie On The Meaning of ε̉φήμερος , 1976 .

[29]  N. Joshi Mathematical evolutionary theory , 1995, Journal of Genetics.

[30]  John Wakeley,et al.  Coalescent Processes When the Distribution of Offspring Number Among Individuals Is Highly Skewed , 2006, Genetics.

[31]  S. Wright,et al.  Evolution in Mendelian Populations. , 1931, Genetics.

[32]  F. Tajima Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[33]  Martin Möhle,et al.  Forward and backward diffusion approximations for haploid exchangeable population models , 2001 .

[34]  F. Tajima Evolutionary relationship of DNA sequences in finite populations. , 1983, Genetics.

[35]  Robustness results for the coalescent , 1998 .

[36]  Martin Möhle,et al.  A Classification of Coalescent Processes for Haploid Exchangeable Population Models , 2001 .