Likelihood-Based Estimation of the Effective Population Size Using Temporal Changes in Allele Frequencies: A Genealogical Approach

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 741-751 ◽  
Author(s):  
Pierre Berthier ◽  
Mark A Beaumont ◽  
Jean-Marie Cornuet ◽  
Gordon Luikart
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Classical Method ◽  
Extinction Risk ◽  
Effective Population ◽  
Upper Limit ◽  
Credible Intervals ◽  
Using Data ◽  
Statistic Approach

AbstractA new genetic estimator of the effective population size (Ne) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based Ne estimator () by using data from simulated populations with known Ne and real populations. The new likelihood-based estimator () showed narrower credible intervals and greater accuracy than () when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., Ne = 20 for five generations), as few as ~10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit <50 using the LB method. In contrast, ~20 loci are required for the same precision when using the classical F-statistic approach. The estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates Ne than does and thus is less likely to erroneously suggest that a population is large and has a low extinction risk.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

2019 ◽  
Vol 100 (4) ◽  
pp. 1169-1181 ◽  
Author(s):  
Russell S Pfau ◽  
Jim R Goetze ◽  
Robert E Martin ◽  
Kenneth G Matocha ◽  
Allan D Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Allelic Diversity ◽  
Effective Population ◽  
Kangaroo Rat ◽  
Time Periods ◽  
Mtdna Diversity ◽  
Using Data

Abstract The Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

scholarly journals Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus

2008 ◽  
Vol 4 (6) ◽  
pp. 755-757 ◽  
Author(s):  
James A Coyer ◽  
Galice Hoarau ◽  
Kjersti Sjøtun ◽  
Jeanine L Olsen
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allelic Richness ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Rocky Intertidal ◽  
Effective Population ◽  
Norwegian Population ◽  
Fucus Serratus ◽  
Southern Norway

The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size ( N e ). The unexpectedly low N e (73–386) and N e / N ratio (10 −3 –10 −4 ), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small N e proves to be a common feature of F. serratus , then being abundant may not be enough for the species to weather future environmental changes.

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.

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 Genetic loads at a polymorphic locus which is maintained by frequency-dependent selection

1970 ◽  
Vol 16 (2) ◽  
pp. 145-150 ◽  
Author(s):  
Motoo Kimura ◽  
Tomoko Ohta
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Gene Frequency ◽  
Polymorphic Locus ◽  
Small Populations ◽  
Effective Population ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Selective Neutrality

SUMMARYIf a polymorphic locus is maintained in finite populations by frequency-dependent selection with selective neutrality at equilibrium, it is generally accompanied by two genetic loads, i.e. the dysmetric and the drift loads. The former arises because the fitness of the population may not be at a maximum at the equilibrium gene frequency and the latter because genetic drift in small populations displaces the gene frequency from its equilibrium value.In some simple models of frequency-dependent selection considered, the drift load is independent of selection coefficients and is approximately equal to (n−1)/(2Ne), where n is the number of alleles and Ne is the effective population size.

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