Inbreeding rate and effective population size: A comparison of estimates from pedigree analysis and a demographic model

1995 ◽  
Vol 71 (3) ◽  
pp. 299-304 ◽  
Author(s):  
Bradley F. Blackwell ◽  
P.D. Doerr ◽  
J. Michael Reed ◽  
Jeffrey R. Walters
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Pedigree Analysis ◽  
Demographic Model ◽  
Effective Population ◽  
Inbreeding Rate

scholarly journals Mobile elements reveal small population size in the ancient ancestors of Homo sapiens

2010 ◽  
Vol 107 (5) ◽  
pp. 2147-2152 ◽  
Author(s):  
Chad D. Huff ◽  
Jinchuan Xing ◽  
Alan R. Rogers ◽  
David Witherspoon ◽  
Lynn B. Jorde
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequences ◽  
Mobile Element ◽  
Small Population ◽  
Mobile Elements ◽  
Population History ◽  
Recent Common Ancestor ◽  
Demographic Model ◽  
Effective Population

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10−30), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

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.

Pedigree analysis of the Afrikaner cattle breed

2015 ◽  
Vol 57 ◽  
pp. 51-56 ◽  
Author(s):  
L. Pienaar ◽  
F.W.C. Neser ◽  
J.P. Grobler ◽  
M.M. Scholtz ◽  
M.D. MacNeil
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Cattle Breed ◽  
Pedigree Analysis ◽  
Rate Of Change ◽  
Full Potential ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Sanga Cattle

SummaryThe reduction of genetic variability in beef cattle has been extensively researched on a global scale. However, the genetic variability and inbreeding of indigenous cattle breeds of Southern Africa, referred to as Sanga cattle, has been less well characterized. Breeds of Sanga cattle include Afrikaner, Drakensberger and Nguni breeds. In recent years, the number of Afrikaner cattle and herds has decreased. Our objective was to determine the mean level of inbreeding (F), effective population size (Ne) and generation intervals of Afrikaner cattle using their recorded pedigree. A total of 244 718 records extending from 1940 until 2011 were analysed. The average inbreeding coefficient was 1.83 percent and the effective population size was 167.54. The average generation interval was calculated as 6.6 ± 3.9 years. Pedigree analysis on the Afrikaner cattle population yielded levels of inbreeding that appear to be both acceptable and manageable. By implication, the largeNeresults in a low rate of change inF. Current results study can be utilized by farmers and the breeders’ society to conserve the Afrikaner and utilize the breed to its full potential in the era of climate change.

scholarly journals Management of genetic diversity using gene dropping method based on pedigree information

2013 ◽  
Vol 56 (1) ◽  
pp. 518-526
Author(s):  
M. Khaldari ◽  
A. N. Javaremi ◽  
A. Pakdel ◽  
H. M. Yeganeh ◽  
P. Berg
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Low Frequency ◽  
Pedigree Analysis ◽  
Simulation Software ◽  
Pedigree Information ◽  
Genetic Contribution ◽  
Effective Population ◽  
Management Plans

Abstract. Preservation of genetic diversity in populations is an important task to ensure a possible longterm response to selection in animal breeding. The purpose of this study was to consider how pedigree analysis and gene dropping method could be used for management plans in order to maintain genetic variation in a population under selection of Japanese quail. Therefore, the distributions of alleles frequencies originated from founders were estimated on an actual pedigree using gene dropping simulation software. Then, genetic contribution of founders to the current population, components such as the F-statistics and effective population size were estimated. The results show that from 156 founders there are only 64 of them (22 males and 42 females) in the last generation. The average genetic contribution of a founder male and female contributing to the last generation were 1.87 and 1.40 %, respectively. A total of 87 and 95 % of the genome in the last generation were constituted by 34 and 42 founders, respectively. The effective population size decreased as inbreeding increases. The allele frequency averaged over replicates agreed with the genetic contribution. Some useful information regarding the management of genetic diversity such as the probability of allele extinction, the probability of alleles surviving at a critically low frequency and risk of future allele extinction were derived by using these distributions. Results show that pedigree analysis and gene dropping are valuable tools in optimizing decisions to preserve genetic variability.

Flock Composition, Effective Population Size and Inbreeding Rate of Kokok balenggek Chicken Breed under In-Situ Conservation

2015 ◽  
Vol 14 (2) ◽  
pp. 117-119 ◽  
Author(s):  
Rusfidra . ◽  
Mendro Gusrizal ◽  
Yuda Gusrin ◽  
Muhammad H. Abbas ◽  
Husmaini . ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
In Situ Conservation ◽  
Effective Population ◽  
Chicken Breed ◽  
Inbreeding Rate

scholarly journals Analysis of Genetic Diversity in the Czech Spotted Dog

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1416
Author(s):  
Karolína Machová ◽  
Anita Kranjčevičová ◽  
Luboš Vostrý ◽  
Emil Krupa
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Inbreeding Coefficient ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Founding Population ◽  
The Mean

Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed—the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity—which was calculated based on the reference population and pedigree completeness—were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence.

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