Sequence diversity under the multispecies coalescent with Yule process and constant population size

2012 ◽  
Vol 81 (2) ◽  
pp. 97-101 ◽  
Author(s):  
Joseph Heled
Keyword(s):  
Population Size ◽  
Sequence Diversity ◽  
Constant Population Size ◽  
Multispecies Coalescent ◽  
Yule Process

scholarly journals Inferences About Human Demography Based on Multilocus Analyses of Noncoding Sequences

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1209-1218 ◽  
Author(s):  
Anna Pluzhnikov ◽  
Anna Di Rienzo ◽  
Richard R Hudson
Keyword(s):  
Population Size ◽  
Italian Population ◽  
Chinese Sample ◽  
Constant Population Size ◽  
Human Demography ◽  
Multilocus Analysis ◽  
Simple Expansion ◽  
Size Model ◽  
Expansion Model ◽  
Tajima’S D

Abstract Data from 10 unlinked autosomal noncoding regions, resequenced in 15 individuals from each of three populations, were used in a multilocus analysis to test models of human demography. Each of the 10 regions consisted of ~2500 bp. The multilocus analysis, based on summary statistics (average and variance of Tajima's D and Fu and Li's D*), was used to test a family of models with recent population expansion. The African sample (Hausa of Cameroon) is compatible with a constant population size model and a range of models with recent expansion. For this population sample, we estimated confidence sets that showed the limited range of parameter values compatible with growth. For an exponential growth rate as low as 1 × 10−3/generation, population growth is unlikely to have started prior to 50,000 years ago. For higher growth rates, the onset of growth must be more recent. On the basis of the average value of Tajima's D, our sample from an Italian population was found to be incompatible with a constant population size model or any simple expansion model. In the Chinese sample, the variance of Tajima's D was too large to be compatible with the constant population size model or any simple expansion model.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: a Correlation Between the Effective and Census Population Sizes

2020 ◽  
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Diversity ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

AbstractWhat determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Since, neutral diversity depends upon the product of the effective population size and mutation rate there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest dataset to date from 639 mammalian species. In a multiple regression we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of non-synonymous to synonymous diversity, is also significantly negatively correlated to both range and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12 to 20%, providing one of the first quantifications of the relationship between effective and census population sizes.

scholarly journals Real royal road functions for constant population size

2004 ◽  
Vol 320 (1) ◽  
pp. 123-134 ◽  
Author(s):  
Tobias Storch ◽  
Ingo Wegener
Keyword(s):  
Population Size ◽  
Constant Population Size ◽  
Royal Road

Heterogeneity of Microsatellite Mutations Within and Between Loci, and Implications for Human Demographic Histories

Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 1269-1284 ◽  
Author(s):  
Anna Di Rienzo ◽  
Peter Donnelly ◽  
Chris Toomajian ◽  
Bronwyn Sisk ◽  
Adrian Hill ◽  
...  
Keyword(s):  
Population Size ◽  
Cancer Patients ◽  
Somatic Mutations ◽  
Repeat Unit ◽  
Population Expansion ◽  
Population Variation ◽  
Rapid Expansion ◽  
Constant Population Size ◽  
Time Estimates ◽  
Novel Approach

Abstract Microsatellites have been widely used to reconstruct human evolution. However, the efficient use of these markers relies on information regarding the process producing the observed variation. Here, we present a novel approach to the locus-by-locus characterization of this process. By analyzing somatic mutations in cancer patients, we estimated the distributions of mutation size for each of 20 loci. The same loci were then typed in three ethnically diverse population samples. The generalized stepwise mutation model was used to test the predicted relationship between population and mutation parameters under two demographic scenarios: constant population size and rapid expansion. The agreement between the observed and expected relationship between population and mutation parameters, even when the latter are estimated in cancer patients, confirms that somatic mutations may be useful for investigating the process underlying population variation. Estimated distributions of mutation size differ substantially amongst loci, and mutations of more than one repeat unit are common. A new statistic, the normalized population variance, is introduced for multilocus estimation of demographic parameters, and for testing demographic scenarios. The observed population variation is not consistent with a constant population size. Time estimates of the putative population expansion are in agreement with those obtained by other methods.

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