scholarly journals Mathematical constraints on FST: multiallelic markers in arbitrarily many populations

2021 ◽  
Author(s):  
Nicolas Alcala ◽  
Noah A Rosenberg
Keyword(s):  
Genetic Differentiation ◽  
Joint Distribution ◽  
Island Model ◽  
General Description ◽  
Multiple Populations ◽  
Mutation Model ◽  
Coalescent Simulations ◽  
And Migration ◽  
Interspecific Comparisons ◽  
Frequent Allele

Interpretations of values of the FST measure of genetic differentiation rely on an understanding of its mathematical constraints. Previously, it has been shown that FST values computed from a biallelic locus in a set of multiple populations and FST values computed from a multiallelic locus in a pair of populations are mathematically constrained by the frequency of the allele that is most frequent across populations. We report here the mathematical constraint on FST given the frequency M of the most frequent allele at a multiallelic locus in a set of multiple populations, providing the most general description to date of mathematical constraints on FST in terms of M. Using coalescent simulations of an island model of migration with an infinitely-many-alleles mutation model, we argue that the joint distribution of FST and M helps in disentangling the separate influences of mutation and migration on FST. Finally, we show that our results explain puzzling patterns of microsatellite differentiation, such as the lower FST values in interspecific comparisons between humans and chimpanzees than in the intraspecific comparison of chimpanzee populations. We discuss the implications of our results for the use of FST.

scholarly journals A New Statistic for Detecting Genetic Differentiation

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 2011-2014 ◽  
Author(s):  
Richard R Hudson
Keyword(s):  
Genetic Differentiation ◽  
Dna Sequences ◽  
Genetic Data ◽  
Island Model ◽  
Wide Range ◽  
Infinite Sites Model ◽  
Parameter Values

Abstract A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.

scholarly journals Population differentiation and migration: Coalescence times in a two-sex island model for autosomal and X-linked loci

2008 ◽  
Vol 74 (4) ◽  
pp. 291-301 ◽  
Author(s):  
Sohini Ramachandran ◽  
Noah A. Rosenberg ◽  
Marcus W. Feldman ◽  
John Wakeley
Keyword(s):  
Population Differentiation ◽  
Island Model ◽  
And Migration ◽  
Coalescence Times

scholarly journals The evolution of altruism through war is highly sensitive to population structure and to civilian and fighter mortality

2021 ◽  
Vol 118 (11) ◽  
pp. e2011142118
Author(s):  
Mark Dyble
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Computational Models ◽  
Original Model ◽  
Empirical Estimates ◽  
Highly Sensitive ◽  
Cast Doubt ◽  
Human Social Behavior ◽  
And Migration ◽  
Parameter Values

The importance of warfare in the evolution of human social behavior remains highly debated. One hypothesis is that intense warfare between groups favored altruism within groups, a hypothesis given some support by computational modeling and, in particular, the work of Choi and Bowles [J.-K. Choi, S. Bowles, Science 318, 636–640 (2007)]. The results of computational models are, however, sensitive to chosen parameter values and a deeper assessment of the plausibility of the parochial altruism hypothesis requires exploring this model in more detail. Here, I use a recently developed method to reexamine Choi and Bowles’ model under a much broader range of conditions to those used in the original paper. Although the evolution of altruism is robust to perturbations in most of the default parameters, it is highly sensitive to group size and migration and to the lethality of war. The results show that the degree of genetic differentiation between groups (FST) produced by Choi and Bowles’ original model is much greater than empirical estimates of FST between hunter-gatherer groups. When FST in the model is close to empirically observed values, altruism does not evolve. These results cast doubt on the importance of war in the evolution of human sociality.

scholarly journals GENE FLOW AND GENETIC DIFFERENTIATION

Genetics ◽  
1974 ◽  
Vol 78 (3) ◽  
pp. 961-965
Author(s):  
P T Spieth
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Size ◽  
Local Population ◽  
Biological Significance ◽  
Island Model ◽  
Genetic Identity ◽  
Biological Interpretation ◽  
Different Populations ◽  
Stepping Stone Model

ABSTRACT A brief analysis is presented for the effects of gene flow upon genetic differentiation within and between populations generated by mutation and drift. Previous results obtained with the "island" model are developed into a form that lends itself to biological interpretation. Attention is focused upon the effective local population size and the ratio of the genetic identity of two genes in different populations to that of two genes in the same population. The biological significance of this ratio, which is independent of population size, is discussed. Similarities between the results of this model and those of the "stepping-stone" model are noted.

EXTRANUCLEAR DIFFERENTIATION AND GENE FLOW IN THE FINITE ISLAND MODEL

Genetics ◽  
1985 ◽  
Vol 109 (2) ◽  
pp. 441-457
Author(s):  
Naoyuki Takahata ◽  
Stephen R Palumbi
Keyword(s):  
Gene Flow ◽  
Natural Populations ◽  
Island Model ◽  
Published Data ◽  
Sequence Information ◽  
Restriction Maps ◽  
Mt Dna ◽  
Sequence Relatedness ◽  
And Migration ◽  
The Relationship

ABSTRACT Use of sequence information from extranuclear genomes to examine deme structure in natural populations has been hampered by lack of clear linkage between sequence relatedness and rates of mutation and migration among demes. Here, we approach this problem in two complementary ways. First, we develop a model of extranuclear genomes in a population divided into a finite number of demes. Sex-dependent migration, neutral mutation, unequal genetic contribution of separate sexes and random genetic drift in each deme are incorporated for generality. From this model, we derive the relationship between gene identity probabilities (between and within demes) and migration rate, mutation rate and effective deme size. Second, we show how within- and between-deme identity probabilities may be calculated from restriction maps of mitochondrial (mt) DNA. These results, when coupled with our results on gene flow and genetic differentiation, allow estimation of relative interdeme gene flow when deme sizes are constant and genetic variants are selectively neutral. We illustrate use of our results by reanalyzing published data on mtDNA in mouse populations from around the world and show that their geographic differentiation is consistent with an island model of deme structure.

scholarly journals Inference of complex population histories using whole-genome sequences from multiple populations

2019 ◽  
Vol 116 (34) ◽  
pp. 17115-17120 ◽  
Author(s):  
Matthias Steinrücken ◽  
Jack Kamm ◽  
Jeffrey P. Spence ◽  
Yun S. Song
Keyword(s):  
Sequence Data ◽  
Model Complexity ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
East Asians ◽  
Multiple Populations ◽  
Demographic Models ◽  
Dna Sequence Data ◽  
Complex Population ◽  
And Migration

There has been much interest in analyzing genome-scale DNA sequence data to infer population histories, but inference methods developed hitherto are limited in model complexity and computational scalability. Here we present an efficient, flexible statistical method, diCal2, that can use whole-genome sequence data from multiple populations to infer complex demographic models involving population size changes, population splits, admixture, and migration. Applying our method to data from Australian, East Asian, European, and Papuan populations, we find that the population ancestral to Australians and Papuans started separating from East Asians and Europeans about 100,000 y ago, and that the separation of East Asians and Europeans started about 50,000 y ago, with pervasive gene flow between all pairs of populations.

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