Molecular Biology and Evolution, Vol 13, 895-902, Copyright © 1996 by Society for Molecular Biology and Evolution
AR Rogers, AE Fraley, MJ Bamshad, WS Watkins and LB Jorde
Mismatch distributions are histograms showing the pattern of nucleotide (or
restriction) site differences between pairs of individuals in a sample.
They can be used to test hypotheses about the history of population size
and subdivision (if selective neutrality is assumed) or about selection (if
a constant population size is assumed). Previous work has assumed that
mutations never strike the same site twice, an assumption that is called
the model of infinite sites. Fortunately, the results are surprisingly
robust even when this assumption is violated. We show here that (1)
confidence regions inferred using the infinite- sites model differ little
from those inferred using a model of finite sites with uniform
site-specific mutation rates, and (2) even when site- specific mutation
rates follow a gamma distribution, confidence regions are little changed
until the gamma shape parameter falls well below its plausible range, to
roughly 0.01. In addition, we evaluate and reject the proposition that
mismatch waves are produced by pooling data from several subdivisions of a
structured population.
ORIGINAL ARTICLE
Mitochondrial mismatch analysis is insensitive to the mutational process
Department of Anthropology, University of Utah, Salt Lake City 84112, USA. rogers@anthro.utah.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. S. Weber, B. S. Stewart, and N. Lehman Genetic Consequences of a Severe Population Bottleneck in the Guadalupe Fur Seal (Arctocephalus townsendi) J. Hered., March 1, 2004; 95(2): 144 - 153. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. E. Ramos-Onsins and J. Rozas Statistical Properties of New Neutrality Tests Against Population Growth Mol. Biol. Evol., December 1, 2002; 19(12): 2092 - 2100. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. F. Storz, M. A. Beaumont, and S. C. Alberts Genetic Evidence for Long-Term Population Decline in a Savannah-Dwelling Primate: Inferences from a Hierarchical Bayesian Model Mol. Biol. Evol., November 1, 2002; 19(11): 1981 - 1990. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Pereira, I. Dupanloup, Z. H. Rosser, M. A. Jobling, and G. Barbujani Y-Chromosome Mismatch Distributions in Europe Mol. Biol. Evol., July 1, 2001; 18(7): 1259 - 1271. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Walton, J. M. Handley, F. H. Collins, R. E. Harbach, V. Baimai, and R. K. Butlin Population Structure and Population History of Anopheles dirus Mosquitoes in Southeast Asia Mol. Biol. Evol., June 1, 2000; 17(6): 962 - 974. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Excoffier and S. Schneider Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions PNAS, September 14, 1999; 96(19): 10597 - 10602. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Schneider and L. Excoffier Estimation of Past Demographic Parameters From the Distribution of Pairwise Differences When the Mutation Rates Vary Among Sites: Application to Human Mitochondrial DNA Genetics, July 1, 1999; 152(3): 1079 - 1089. [Abstract] [Full Text]
|
|
|
|
|
|
G. Weiss and A. von Haeseler Inference of Population History Using a Likelihood Approach Genetics, July 1, 1998; 149(3): 1539 - 1546. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Polanski, M. Kimmel, and R. Chakraborty Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data PNAS, May 12, 1998; 95(10): 5456 - 5461. [Abstract] [Full Text] [PDF]
|
|