Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens)

Abstract The important parameter of effective population size is rarely estimable directly from demographic data. Indirect estimates of effective population size may be made from genetic data such as temporal variation of allelic frequencies or linkage disequilibrium in cohorts. We suggest here that an indirect estimate of the effective number of breeders might be based on the excess of heterozygosity expected in a cohort of progeny produced by a limited number of males and females. In computer simulations, heterozygote excesses for 30 unlinked loci having various numbers of alleles and allele-frequency profiles were obtained for cohorts produced by samples of breeders drawn from an age-structured population and having known variance in reproductive success and effective number. The 95% confidence limits around the estimate contained the true effective population size in 70 of 72 trials and the Spearman rank correlation of estimated and actual values was 0.991. An estimate based on heterozygote excess might have certain advantages over the previous estimates, requiring only single-locus and single-cohort data, but the sampling error among individuals and the effect of departures from random union of gametes still need-to be explored.

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Evaluation of genetic effects on wild salmon populations from stock enhancement

ICES Journal of Marine Science ◽

10.1093/icesjms/fsaa235 ◽

2020 ◽

Author(s):

Ingerid J Hagen ◽

Ola Ugedal ◽

Arne J Jensen ◽

Håvard Lo ◽

Espen Holthe ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Salmo Salar ◽

Conservation Value ◽

Effective Number ◽

Effective Population ◽

Wild Salmon ◽

Effective Number Of Breeders ◽

Additional Strain ◽

Conservation Concern

Abstract Many salmonid populations are of conservation concern, and the release of hatchery-produced juveniles is a frequently used measure to alleviate declines and increase harvest opportunities. While such releases may be of conservation value for some populations, stocking may also decrease the effective population size and subsequently impose additional strain on already threatened populations. In this study, we assessed how the cohort-wise effective number of breeders in five populations of Atlantic salmon (Salmo salar) were affected by supplementation. Altogether, 19 cohorts were studied (2–7 cohorts per population) by estimating the proportion hatchery-released individuals and the effective number of wild and captive breeders in each cohort of the respective populations. We show that the effect of releasing captive-bred individuals varies both between populations and between years within the same population. A Ryman–Laikre effect—where the effective number of breeders has decreased as a consequence of supplementation—was observed for 11 cohorts. We discuss how supplementation can be adapted to optimize the effective population size, demonstrate that evaluation of supplementation can be reliably achieved, and show that supplementation programmes that lead to high proportions of hatchery-origin fish on spawning grounds are more likely to induce a Ryman–Laikre effect.

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Interrelations between effective population size and other pedigree tools for the management of conserved populations

Genetics Research ◽

10.1017/s0016672399004449 ◽

2000 ◽

Vol 75 (3) ◽

pp. 331-343 ◽

Cited By ~ 240

Author(s):

ARMANDO CABALLERO ◽

MIGUEL A. TORO

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Population Size ◽

Effective Population Size ◽

Genetic Parameters ◽

Effective Number ◽

Effective Population ◽

Clear Cut ◽

Captive Populations ◽

Practical Recommendations

Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.

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Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions

PLoS ONE ◽

10.1371/journal.pone.0258714 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0258714

Author(s):

Kristina Lehocká ◽

Simon A. Black ◽

Adrian Harland ◽

Ondrej Kadlečík ◽

Radovan Kasarda ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

North Africa ◽

Reference Population ◽

Captive Population ◽

Effective Number ◽

Pedigree Data ◽

Effective Population ◽

Loss Of Diversity

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

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Increased accuracy of artificial selection by using the realized relationship matrix

Genetics Research ◽

10.1017/s0016672308009981 ◽

2009 ◽

Vol 91 (1) ◽

pp. 47-60 ◽

Cited By ~ 374

Author(s):

B. J. HAYES ◽

P. M. VISSCHER ◽

M. E. GODDARD

Keyword(s):

Population Size ◽

Effective Population Size ◽

Family Relationships ◽

Random Mating ◽

Family Relationship ◽

Relationship Matrix ◽

Effective Number ◽

Effective Population ◽

Breeding Values ◽

Selection Methodology

SummaryDense marker genotypes allow the construction of the realized relationship matrix between individuals, with elements the realized proportion of the genome that is identical by descent (IBD) between pairs of individuals. In this paper, we demonstrate that by replacing the average relationship matrix derived from pedigree with the realized relationship matrix in best linear unbiased prediction (BLUP) of breeding values, the accuracy of the breeding values can be substantially increased, especially for individuals with no phenotype of their own. We further demonstrate that this method of predicting breeding values is exactly equivalent to the genomic selection methodology where the effects of quantitative trait loci (QTLs) contributing to variation in the trait are assumed to be normally distributed. The accuracy of breeding values predicted using the realized relationship matrix in the BLUP equations can be deterministically predicted for known family relationships, for example half sibs. The deterministic method uses the effective number of independently segregating loci controlling the phenotype that depends on the type of family relationship and the length of the genome. The accuracy of predicted breeding values depends on this number of effective loci, the family relationship and the number of phenotypic records. The deterministic prediction demonstrates that the accuracy of breeding values can approach unity if enough relatives are genotyped and phenotyped. For example, when 1000 full sibs per family were genotyped and phenotyped, and the heritability of the trait was 0·5, the reliability of predicted genomic breeding values (GEBVs) for individuals in the same full sib family without phenotypes was 0·82. These results were verified by simulation. A deterministic prediction was also derived for random mating populations, where the effective population size is the key parameter determining the effective number of independently segregating loci. If the effective population size is large, a very large number of individuals must be genotyped and phenotyped in order to accurately predict breeding values for unphenotyped individuals from the same population. If the heritability of the trait is 0·3, and Ne=1000, approximately 5750 individuals with genotypes and phenotypes are required in order to predict GEBVs of un-phenotyped individuals in the same population with an accuracy of 0·7.

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Relatedness and status number in seed orchard crops

Canadian Journal of Forest Research ◽

10.1139/x97-217 ◽

1998 ◽

Vol 28 (2) ◽

pp. 276-283 ◽

Cited By ~ 56

Author(s):

D Lindgren ◽

T J Mullin

Keyword(s):

Gender Differences ◽

Reproductive Success ◽

Population Size ◽

Effective Population Size ◽

Seed Orchard ◽

Reference Population ◽

Sexual Cycle ◽

Effective Number ◽

Effective Population ◽

Status Number

Status number is a measure of effective population size that is based on current relatedness only. Formulae are developed for group coancestry (=average coancestry) and status number for seed orchard crops. The formulae consider (1) differences in reproductive success among orchard genotypes, (2) relatedness between pairs of orchard genotypes, (3) inbreeding of orchard genotypes, (4) influence of pollen contamination (considering its relatedness both to itself and to the genotypes in the orchard), and (5) gender differences and sexual asymmetries of orchard genotypes. Properties of status number and other measures of effective number are discussed. They may refer to rate or state, to the reference population or the development of an idealized population, and to different moments in the sexual cycle.

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Genetic structure of a small closed population of the New Zealand white rabbit through pedigree analyses

World Rabbit Science ◽

10.4995/wrs.2018.7426 ◽

2018 ◽

Vol 26 (2) ◽

pp. 101

Author(s):

M. Sakthivel ◽

D. Balasubramanyam ◽

P. Kumarasamy ◽

A. Raja ◽

R. Anilkumar ◽

...

Keyword(s):

New Zealand ◽

Genetic Structure ◽

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Research Station ◽

Percentage Increase ◽

Effective Number ◽

Effective Population ◽

Mean Values

The genetic structure of a small population of New Zealand White rabbits maintained at the Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India, was evaluated through pedigree analyses. Data on pedigree information (n=2503) for 18 yr (1995-2012) were used for the study. Pedigree analysis and the estimates of population genetic parameters based on the gene origin probabilities were performed. The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.49 yr, 13.23 and 17.59%, respectively. The proportion of population inbred was 100%. The estimated mean values of average relatedness and individual increase in inbreeding were 22.73 and 3.00%, respectively. The percentage increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations and complete generations, respectively. The number of ancestors contributing the majority of 50% genes (fa50) to the gene pool of reference population was only 4, which might have led to reduction in genetic variability and increased the amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (fe) and the effective number of ancestors (fa), as expressed by the fe/fa ratio was 1.1, which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29% pedigree was complete, reflecting the well maintained pedigree records. The maximum known generations were 15, with an average of 7.9, and the average equivalent generations traced were 5.6, indicating a fairly good depth in pedigree. The realized effective population size was 14.93, which is very critical, and with the increasing trend of inbreeding the situation has been assessed as likely to become worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10%, which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred, with a very high inbreeding coefficient, and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.

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Assessing genetic diversity of various Canadian sheep breeds through pedigree analyses

Canadian Journal of Animal Science ◽

10.1139/cjas-2017-0187 ◽

2018 ◽

Vol 98 (4) ◽

pp. 741-749

Author(s):

Katarzyna Stachowicz ◽

Luiz F. Brito ◽

Hinayah R. Oliveira ◽

Stephen P. Miller ◽

Flávio S. Schenkel

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Production Efficiency ◽

Selection Response ◽

Effective Number ◽

Effective Population ◽

Genetic Progress ◽

Sheep Breeds ◽

Depth Analysis

The loss of genetic variability in a population will drastically affect the success of a breeding program by reducing selection response and fitness and, consequently, affecting reproduction, resilience, and production efficiency. The objective of this study was to perform an in-depth analysis of the pedigree of the Canadian sheep breeds to assess the levels of inbreeding, effective population size, and other metrics of genetic diversity, which included the five most important sheep breeds in Canada: Dorset, Polypay (PO), Rideau-Arcott, Romanov (RV), and Suffolk, using a large dataset (1 336 926 animals). As measures of genetic diversity, effective population size, inbreeding coefficient, effective number of founders, effective number of founder genomes, effective number of nonfounders, and effective number of ancestors were estimated. The completeness and depth of the Canadian sheep pedigree datasets were reasonably high, with <20% parental information missing. More attention should be given to PO breed, which was found to have the smallest effective population size (55), and RV breed, which had the highest average level of inbreeding (4.8%). Techniques such as optimum contribution selection and minimum coancestry mating could be used to minimize the inbreeding of future generations, while maintaining genetic progress at a desirable level.

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