Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models.

Abstract Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population x loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites).

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Equilibrium Values of Measures of Population Subdivision for Stepwise Mutation Processes

Genetics ◽

10.1093/genetics/142.4.1357 ◽

1996 ◽

Vol 142 (4) ◽

pp. 1357-1362

Author(s):

François Rousset

Keyword(s):

Population Structure ◽

Population Subdivision ◽

Identity By Descent ◽

Infinite Allele Model ◽

Coalescence Time ◽

Stepwise Mutation ◽

Expected Values ◽

The Relationship ◽

Allele Model ◽

Coalescence Times

Abstract Expected values of Wright'sF-statistics are functions of probabilities of identity in state. These values may be quite different under an infinite allele model and under stepwise mutation processes such as those occurring at microsatellite loci. However, a relationship between the probability of identity in state in stepwise mutation models and the distribution of coalescence times can be deduced from the relationship between probabilities of identity by descent and the distribution of coalescence times. The values of FIS and FST can be computed using this property. Examination of the conditional probability of identity in state given some coalescence time and of the distribution of coalescence times are also useful for explaining the properties of FIS and FST at high mutation rate loci, as shown here in an island model of population structure.

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Genetic diversity of long-established populations of Elaeis guineensis jacquin (Arecaceae)

Revista Brasileira de Fruticultura ◽

10.1590/0100-29452019023 ◽

2019 ◽

Vol 41 (4) ◽

Author(s):

Kyvia Pontes Teixeira das Chagas ◽

Ageu da Silva Monteiro Freire ◽

Luciana Gomes Pinheiro ◽

Cristiane Gouvêa Fajardo ◽

Fábio de Almeida Vieira

Keyword(s):

Genetic Diversity ◽

Elaeis Guineensis ◽

Sustainable Use ◽

Diversity Indices ◽

Ex Situ ◽

Effective Population ◽

Infinite Allele Model ◽

Population Decrease ◽

Stepwise Mutation ◽

Conservation Projects

Abstract This study aimed to estimate the genetic diversity of three Elaeis guineensis populations in Rio Grande do Norte state, as well as to verify the decreases in effective population size. The population with the highest polymorphism was MAT (Mata) with+ 57 loci (72%), followed by RIA (Riacho) with 54 loci (68%) and HOR (Horta) with 34 loci (43.03%). The RIA population was shown to be the most genetically diverse, with Nei (h = 0.28) and Shannon (I = 0.41) diversity indices. There was high genetic differentiation among populations (AMOVA, analysis of molecular variance = 42%), which was separated into three distinct genetic groups according to a Bayesian analysis. There was a significant population decrease (P < 0.05) for the HOR population in the IAM (infinite allele model) and SMM (stepwise mutation model), and for the RIA population in the IAM. The data obtained in this study may support ex-situ conservation projects for Elaeis guineensis, contributing to the selection of genotypes and their sustainable use.

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THE SAMPLING DISTRIBUTION OF LINKAGE DISEQUILIBRIUM

Genetics ◽

10.1093/genetics/108.1.257 ◽

1984 ◽

Vol 108 (1) ◽

pp. 257-274 ◽

Cited By ~ 2

Author(s):

G B Golding

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Effective Population Size ◽

Correlation Coefficient ◽

Bimodal Distribution ◽

Test Statistic ◽

Effective Population ◽

Chi Square ◽

Infinite Allele Model ◽

Allele Model

ABSTRACT The probabilities of obtaining particular samples of gametes with two completely linked loci are derived. It is assumed that the population consists of N diploid, randomly mating individuals, that each of the two loci mutate according to the infinite allele model at a rate µ and that the population is at equilibrium. When 4Nµ is small, the most probable samples of gametes are those that segregate only two alleles at either locus. The probabilities of various samples of gametes are discussed. The results show that most samples with completely linked loci have either a very small or a very large association between the alleles of each locus. This causes the distribution of linkage disequilibrium to be skewed and the distribution of the correlation coefficient to be bimodal. The correlation coefficient is commonly used as a test statistic with a chi square distribution and yet has a bimodal distribution when the loci are completely linked. Thus, such a test is not likely to be accurate unless the rate of recombination between the loci and/or the effective population size are sufficiently large enough so that the loci can be treated as unlinked.

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LINKAGE DISEQUILIBRIUM IN A FINITE POPULATION THAT IS PARTIALLY SELFING

Genetics ◽

10.1093/genetics/94.3.777 ◽

1980 ◽

Vol 94 (3) ◽

pp. 777-789 ◽

Cited By ~ 4

Author(s):

G B Golding ◽

C Strobeck

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Finite Population ◽

Random Mating ◽

Effective Population ◽

Infinite Allele Model ◽

Inbreeding Coefficients ◽

Linkage Disequilibria ◽

Recombination Value ◽

Allele Model

ABSTRACT The linkage disequilibrium expected in a finite, partially selfing population is analyzed, assuming the infinite allele model. Formulas for the expected sum of squares of the linkage disequilibria and the squared standard linkage disequilibrium are derived from the equilibrium values of sixteen inbreeding coefficients required to describe the behavior of the system. These formulas are identical to those obtained with random mating if the effective population size Ne = (l—½S)N and the effective recombination value re = (l-S)r/(l-½S), where S is the proportion of selfing, are substituted for the population size and the recombination value, Therefore, the effect of partial selfing at equilibrium is to reduce the population size by a factor 1 — ½S and the recombination value by a factor (l-S)/(l—½S).

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Genetic variation in the greenback flounder Rhombosolea tapirina GÜnther (Teleostei, Pleuronectidae) and the implications for aquaculture

Marine and Freshwater Research ◽

10.1071/mf99022 ◽

2000 ◽

Vol 51 (1) ◽

pp. 23 ◽

Cited By ~ 2

Author(s):

Tony van den Enden ◽

Robert W. G. White ◽

Nicholas G. Elliott

Keyword(s):

Genetic Variation ◽

New Zealand ◽

Genetic Distance ◽

West Coast ◽

Gel Electrophoresis ◽

Effective Population ◽

Average Heterozygosity ◽

The West ◽

Order Of Magnitude ◽

Population Sizes

Samples of the greenback flounder, Rhombosolea tapirina, were collected from five Tasmanian sites and from one site each off Victoria and New Zealand. Thirty enzyme-coding loci were analysed by gel electrophoresis. Seventeen loci were variable, nine of which were polymorphic in at least four samples. Average heterozygosity across all 30 loci was relatively high at 0.086 ± 0.032. There were significant genetic differences between the Australian and New Zealand samples, with a genetic distance of 0.041, which was an order of magnitude larger than that observed between any Australian samples. Samples from the west coast of Tasmania and from Victoria were genetically isolated from each other and from the remaining four Tasmanian samples; the latter showed little variation among themselves. Reductions in genetic variation (heterozygosity and alleles) were observed in two cultured cohorts when compared with the wild-caught samples, with corresponding low estimates of effective population sizes compared with putative breeding numbers. No genetic variation was detected between normal and malpigmented individuals from the same culture cohort.

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A View of Modern Human Origins from Y Chromosome Microsatellite Variation

Genome Research ◽

10.1101/gr.9.6.558 ◽

1999 ◽

Vol 9 (6) ◽

pp. 558-567 ◽

Cited By ~ 3

Author(s):

Mark Seielstad ◽

Endashaw Bekele ◽

Muntaser Ibrahim ◽

Amadou Touré ◽

Mamadou Traoré

Keyword(s):

Y Chromosome ◽

Phylogenetic Trees ◽

Distance Measure ◽

Modern Human ◽

African Origin ◽

Effective Population ◽

Modern Humans ◽

Microsatellite Variation ◽

Modern Human Origins ◽

African Populations

The idea that all modern humans share a recent (within the last 150,000 years) African origin has been proposed and supported on the basis of three observations. Most genetic loci examined to date have (1) shown greater diversity in African populations than in others, (2) placed the first branch between African and all non-African populations in phylogenetic trees, and (3) indicated recent dates for either the molecular coalescence (with the exception of some autosomal and X-chromosomal loci) or for the time of separation between African and non-African populations. We analyze variation at 10 Y chromosome microsatellite loci that were typed in 506 males representing 49 populations and every inhabited continent and find significantly greater Y chromosome diversity in Africa than elsewhere, find the first branch in phylogenetic trees of the continental populations to fall between African and all non-African populations, and date this branching with the (δμ)2 distance measure to 5800–17,400 or 12,800–36,800 years BP depending on the mutation rate used. The magnitude of the excess Y chromosome diversity in African populations appears to result from a greater antiquity of African populations rather than a greater long-term effective population size. These observations are most consistent with a recent African origin for all modern humans.

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Estimation of Effective Population Size and Migration Rate From One- and Two-Locus Identity Measures

Genetics ◽

10.1093/genetics/157.2.911 ◽

2001 ◽

Vol 157 (2) ◽

pp. 911-925

Author(s):

Renaud Vitalis ◽

Denis Couvet

Keyword(s):

Population Size ◽

Effective Population Size ◽

Joint Estimation ◽

Demographic Parameters ◽

Effective Population ◽

Mutation Bias ◽

Infinite Allele Model ◽

Immigration Rate ◽

And Migration ◽

Allele Model

Abstract Standard methods for inferring demographic parameters from genetic data are based mainly on one-locus theory. However, the association of genes at different loci (e.g., two-locus identity disequilibrium) may also contain some information about demographic parameters of populations. In this article, we define one- and two-locus parameters of population structure as functions of one- and two-locus probabilities for the identity in state of genes. Since these parameters are known functions of demographic parameters in an infinite island model, we develop moment-based estimators of effective population size and immigration rate from one- and two-locus parameters. We evaluate this method through simulation. Although variance and bias may be quite large, increasing the number of loci on which the estimates are derived improves the method. We simulate an infinite allele model and a K allele model of mutation. Bias and variance are smaller with increasing numbers of alleles per locus. This is, to our knowledge, the first attempt of a joint estimation of local effective population size and immigration rate.

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A MIXED MODEL OF MUTATION FOR ELECTROPHORETIC IDENTITY OF PROTEINS WITHIN AND BETWEEN POPULATIONS

Genetics ◽

10.1093/genetics/83.2.423 ◽

1976 ◽

Vol 83 (2) ◽

pp. 423-432

Author(s):

Wen-Hsiung Li

Keyword(s):

Genetic Distance ◽

Mixed Model ◽

Present Model ◽

Natural Populations ◽

The Other ◽

Effective Number ◽

Infinite Allele Model ◽

Stepwise Mutation ◽

Allele Model ◽

Nei's Genetic Distance

ABSTRACT A model which is a mixture of the model of infinite alleles and the Ohta-Kimura model of stepwise mutation has been proposed for the study of eletcrophoretic variants in natural populations. Mutations which alter the mobility of a protein are divided into two classes: stepwise mutations and nonstepwise mutations. It is assumed that stepwise mutations follow the Ohta-Kimura model while nonstepwise mutations follow the infinite allele model. It is then shown that even if the proportion of nonstepwise mutations is only 5%, with the other 95% stepwise mutations, the effective number of alleles given by the present model is considerably larger than that given by the Ohta-Kimura model of stepwise mutation. The result has also been applied to study Nei's genetic distance.

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Ecological Genetics of the Wild Rabbit in Australia. II. Protein Variation in British, French and Australian Rabbits and the Geographical Distribution of the Variation in Australia

Australian Journal of Biological Sciences ◽

10.1071/bi9800371 ◽

1980 ◽

Vol 33 (3) ◽

pp. 371 ◽

Cited By ~ 31

Author(s):

BJ Richardson ◽

PM Rogers ◽

GM Hewitt

Keyword(s):

Genetic Distances ◽

Ecological Genetics ◽

Wild Rabbit ◽

Effective Population ◽

Average Heterozygosity ◽

Control Programs ◽

Phosphogluconate Dehydrogenase ◽

Protein Variation ◽

Population Sizes ◽

Mediterranean France

A survey for genetic variation was carried out using 21 proteins controlled by 26 loci in rabbits from Britain, Mediterranean France and Australia. Five enzymes, adenosine deaminase, phosphogluconate dehydrogenase, carboxylesterase, carbonate dehydratase and dihydrolipoamide reductase (NAD+) were found to be polymorphic. The average heterozygosity in wild rabbits was 6%. The genetic distances separating the various populations indicated that three different stocks were present in these populations. The rabbits from Britain and mainland Australia belonged to one group, those from France to a second group and the rabbits from southern Tasmania were a distinctive third group. Highly significant differences in gene frequency were found between the various local populations studied from mainland Australia. This variation showed no clear pattern and was attributed to genetic drift due to small effective population sizes. Bottlenecks in population size occur regularly in local rabbit populations in Australia through, for example, drought, myxomatosis outbreaks or rabbit control programs.

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Signatures of Population Expansion in Microsatellite Repeat Data

Genetics ◽

10.1093/genetics/148.4.1921 ◽

1998 ◽

Vol 148 (4) ◽

pp. 1921-1930 ◽

Cited By ~ 2

Author(s):

Marek Kimmel ◽

Ranajit Chakraborty ◽

J Patrick King ◽

Michael Bamshad ◽

W Scott Watkins ◽

...

Keyword(s):

Population Expansion ◽

Logistic Growth ◽

Racial Groups ◽

Equilibrium Conditions ◽

Allele Size ◽

Infinite Allele Model ◽

Moran Model ◽

Tetranucleotide Repeats ◽

Stepwise Mutation ◽

Allele Model

Abstract To examine the signature of population expansion on genetic variability at microsatellite loci, we consider a population that evolves according to the time-continuous Moran model, with growing population size and mutations that follow a general asymmetric stepwise mutation model. We present calculations of expected allele-size variance and homozygosity at a locus in such a model for several variants of growth, including stepwise, exponential, and logistic growth. These calculations in particular prove that population bottleneck followed by growth in size causes an imbalance between allele size variance and heterozygosity, characterized by the variance being transiently higher than expected under equilibrium conditions. This effect is, in a sense, analogous to that demonstrated before for the infinite allele model, where the number of alleles transiently increases after a stepwise growth of population. We analyze a set of data on tetranucleotide repeats that reveals the imbalance expected under the assumption of bottleneck followed by population growth in two out of three major racial groups. The imbalance is strongest in Asians, intermediate in Europeans, and absent in Africans. This finding is consistent with previous findings by others concerning the population expansion of modern humans, with the bottleneck event being most ancient in Africans, most recent in Asians, and intermediate in Europeans. Nevertheless, the imbalance index alone cannot reliably estimate the time of initiation of population expansion.

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