scholarly journals Measuring drift by mean deviation: unequal breeding sex ratio revisited

2021 ◽  
Author(s):  
Ben Qin
Keyword(s):  
Sex Ratio ◽  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Direct Measurement ◽  
Genetic Drift ◽  
Mean Deviation ◽  
Frequency Change ◽  
Effective Population ◽  
Rare Alleles

When it comes to estimating the magnitude of genetic drift, there is hardly any indexes other than the effective population size. Starting from the binomial sampling distribution, this research proposed using mean deviation of allele frequency change as a direct measurement of drift, then tested it in a classical example concerning unequal breeding sex ratio. This study found that: (1) mean deviation offers a new dimension in measuring the magnitude of drift; (2) the measurement displays a half-half pattern; (3) allele frequency determines the efficacy of hitchhiking effect of rare alleles, and in what way that half-half pattern should be divided.

scholarly journals A generalized approach for estimating effective population size from temporal changes in allele frequency.

Genetics ◽  
1989 ◽  
Vol 121 (2) ◽  
pp. 379-391 ◽  
Author(s):  
R S Waples
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Initial Conditions ◽  
Low Frequency ◽  
Frequency Change ◽  
Effective Population ◽  
Sampling Plans ◽  
Juvenile Mortality ◽  
Temporal Method

Abstract The temporal method for estimating effective population size (Ne) from the standardized variance in allele frequency change (F) is presented in a generalized form. Whereas previous treatments of this method have adopted rather limiting assumptions, the present analysis shows that the temporal method is generally applicable to a wide variety of organisms. Use of a revised model of gene sampling permits a more generalized interpretation of Ne than that used by some other authors studying this method. It is shown that two sampling plans (individuals for genetic analysis taken before or after reproduction) whose differences have been stressed by previous authors can be treated in a uniform way. Computer simulations using a wide variety of initial conditions show that different formulas for computing F have much less effect on Ne than do sample size (S), number of generations between samples (t), or the number of loci studied (L). Simulation results also indicate that (1) bias of F is small unless alleles with very low frequency are used; (2) precision is typically increased by about the same amount with a doubling of S, t, or L; (3) confidence intervals for Ne computed using a chi 2 approximation are accurate and unbiased under most conditions; (4) the temporal method is best suited for use with organisms having high juvenile mortality and, perhaps, a limited effective population size.

scholarly journals Temporal allele frequency change and estimation of effective size in populations with overlapping generations.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 1077-1090 ◽  
Author(s):  
P E Jorde ◽  
N Ryman
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Overlapping Generations ◽  
Temporal Frequency ◽  
Effective Size ◽  
Frequency Change ◽  
Effective Population ◽  
Frequency Shifts ◽  
Frequency Changes

Abstract In this paper we study the process of allele frequency change in finite populations with overlapping generations with the purpose of evaluating the possibility of estimating the effective size from observations of temporal frequency shifts of selectively neutral alleles. Focusing on allele frequency changes between successive cohorts (individuals born in particular years), we show that such changes are not determined by the effective population size alone, as they are when generations are discrete. Rather, in populations with overlapping generations, the amount of temporal allele frequency change is dependent on the age-specific survival and birth rates. Taking this phenomenon into account, we present an estimator for effective size that can be applied to populations with overlapping generations.

Analysis of genetic diversity in four Canadian swine breeds using pedigree data

2010 ◽  
Vol 90 (3) ◽  
pp. 331-340 ◽  
Author(s):  
M G Melka ◽  
F. Schenkel
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Relative Proportion ◽  
Random Genetic Drift ◽  
Pedigree Data ◽  
Effective Population ◽  
Animal Genetic Resources ◽  
Loss Of Genetic Diversity

Conservation of animal genetic resources entails judicious assessment of genetic diversity as a first step. The objective of this study was to analyze the trend of within-breed genetic diversity and identify major causes of loss of genetic diversity in four swine breeds based on pedigree data. Pedigree files from Duroc (DC), Hampshire (HP), Lacombe (LC) and Landrace (LR) containing 480 191, 114 871, 51 397 and 1 080 144 records, respectively, were analyzed. Pedigree completeness, quality and depth were determined. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness indexes of the four breeds were 90.4, 52.7, 89.6 and 96.1%, respectively. The estimated percentage of genetic diversity lost within each breed over the last three decades was approximately 3, 22, 12 and 2%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in DC, HP, LC and LR was 74.5, 63.6, 72.9 and 60.0%, respectively. The estimated current effective population size for DC, HP, LC and LR was 72, 14, 36 and 125, respectively. Therefore, HP and LC have been found to have lost considerable genetic diversity, demanding priority for conservation. Key words: Genetic drift, effective population size

scholarly journals Effective size of nonrandom mating populations.

Genetics ◽  
1992 ◽  
Vol 130 (4) ◽  
pp. 909-916 ◽  
Author(s):  
A Caballero ◽  
W G Hill
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Family Size ◽  
Genetic Drift ◽  
Effective Size ◽  
Effective Population ◽  
Gene Frequencies ◽  
Nonrandom Mating ◽  
Sib Mating ◽  
Census Number

Abstract Nonrandom mating whereby parents are related is expected to cause a reduction in effective population size because their gene frequencies are correlated and this will increase the genetic drift. The published equation for the variance effective size, Ne, which includes the possibility of nonrandom mating, does not take into account such a correlation, however. Further, previous equations to predict effective sizes in populations with partial sib mating are shown to be different, but also incorrect. In this paper, a corrected form of these equations is derived and checked by stochastic simulation. For the case of stable census number, N, and equal progeny distributions for each sex, the equation is [formula: see text], where Sk2 is the variance of family size and alpha is the departure from Hardy-Weinberg proportions. For a Poisson distribution of family size (Sk2 = 2), it reduces to Ne = N/(1 + alpha), as when inbreeding is due to selfing. When nonrandom mating occurs because there is a specified system of partial inbreeding every generation, alpha can be substituted by Wright's FIS statistic, to give the effective size as a function of the proportion of inbred mates.

scholarly journals A NEW METHOD FOR ESTIMATING THE EFFECTIVE POPULATION SIZE FROM ALLELE FREQUENCY CHANGES

Genetics ◽  
1983 ◽  
Vol 104 (3) ◽  
pp. 531-548
Author(s):  
Edward Pollak
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
New Method ◽  
Standard Errors ◽  
Effective Population ◽  
Census Size ◽  
Population Sizes ◽  
Frequency Changes ◽  
Approximate Expressions

ABSTRACT A new procedure is proposed for estimating the effective population size, given that information is available on changes in frequencies of the alleles at one or more independently segregating loci and the population is observed at two or more separate times. Approximate expressions are obtained for the variances of the new statistic, as well as others, also based on allele frequency changes, that have been discussed in the literature. This analysis indicates that the new statistic will generally have a smaller variance than the others. Estimates of effective population sizes and of the standard errors of the estimates are computed for data on two fly populations that have been discussed in earlier papers. In both cases, there is evidence that the effective population size is very much smaller than the minimum census size of the population.

A DIRECT ASSESSMENT OF THE ROLE OF GENETIC DRIFT IN DETERMINING ALLELE FREQUENCY VARIATION IN POPULATIONS OF EUPHYDRYAS EDITHA

Genetics ◽  
1985 ◽  
Vol 110 (3) ◽  
pp. 495-511
Author(s):  
Laurence D Mueller ◽  
Bruce A Wilcox ◽  
Paul R Ehrlich ◽  
David G Heckel ◽  
Dennis D Murphy
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Allele Frequencies ◽  
Frequency Variation ◽  
Effective Population ◽  
Variable Environment ◽  
Euphydryas Editha ◽  
Two Populations

ABSTRACT Estimates of allele frequencies at six polymorphic loci were collected over eight generations in two populations of Euphydryas editha. We have estimated, in addition, the effective population size for each generation for both populations with results from mark-recapture and other field data. The variation in allele frequencies generated by random genetic drift was then studied using computer simulations and our direct estimates of effective population size. Substantial differences between observed values and computer-generated expected values assuming drift alone were found for three loci (Got, Hk, Pgi) in one population. These observations are consistent with natural selection in a variable environment.

scholarly journals Evaluation of the Romosinuano cattle population structure in Mexico using pedigree analysis

2020 ◽  
Vol 33 (1) ◽  
pp. 44-59
Author(s):  
Rafael Núñez-Domínguez ◽  
Ricardo E Martínez-Rocha ◽  
Jorge A Hidalgo-Moreno ◽  
Rodolfo Ramírez-Valverde ◽  
José G García-Muñiz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Pedigree Analysis ◽  
Effective Population ◽  
Genetic Management ◽  
Generation Interval

Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.Keywords: effective population size; gene flow; genetic diversity; genetic drift; generation interval; inbreeding; pedigree; population structure; probability of gene origin; Romosinuano cattle. Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.Palabras clave: consanguinidad; deriva genética; diversidad genética; estructura poblacional; flujo de genes; ganado Romosinuano; intervalo generacional; pedigrí; probabilidad de origen del gen; tamaño efectivo de población. Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram rebanhos núcleo ou isolados. Para RP3, F e AR alcançaram 2,08 e 5,12% na UP, e 2,55 e 5,94% na SP. Para RP3, Nec foi 57 na UP e 45 na SP. Mais de 66% das perdas em diversidade genética foram ocasionadas pela deriva genética, exceto para RP3 no UP (44%). Conclusões: Depois que a associação da raça Romosinuano foi estabelecida no México, tem ocorrido uma redução da diversidade genética, principalmente devido a perdas aleatórias de genes.Palavras-chave: consanguinidade; deriva genética; diversidade genética, estrutura populacional; fluxo de genes; intervalo entre gerações; pedigree; probabilidade de origem do gene; Romosinuano; tamanho efetivo da população.

scholarly journals Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

Genetics ◽  
2016 ◽  
Vol 204 (2) ◽  
pp. 723-735 ◽  
Author(s):  
A. Jonas ◽  
T. Taus ◽  
C. Kosiol ◽  
C. Schlotterer ◽  
A. Futschik
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Experimental Evolution ◽  
Effective Population ◽  
Frequency Changes
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