Nb_HetEx: A Program to Estimate the Effective Number of Breeders

Zhdanova, O. L.; Pudovkin, Alexander I.

doi:10.1093/jhered/esn061

Cited by 74 publications

(68 citation statements)

References 9 publications

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“…NEESTIMATOR v2.01 (Do et al, 2014) was used to apply the heterozygosity method (Zhdanova and Pudovkin, 2008), the linkage disequilibrium method (Waples and Do, 2008), the coancestry method (Nomura, 2008), as well as three temporal methods (Nei and Tajima, 1981;Pollack, 1983, Jorde andRyman, 2007). The sibship method (Wang, 2009) was calculated using COLONY (Jones and Wang, 2010).…”

Section: Discussionmentioning

confidence: 99%

Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus)

et al. 2016

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The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.

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Section: Discussionmentioning

confidence: 99%

Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus)

et al. 2016

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“…The accuracy of the estimator was evaluated by Pudovkin et al (1996) using simulations and was applied to a few empirical data sets (Luikart and Cornuet, 1999). The method is simple and is implemented in several computer programs (for example, Zhdanova and Pudovkin, 2008;Jones and Wang, 2010;Do et al, 2014). However, the method has a low precision and accuracy, frequently providing infinitely large estimates of N e for small populations.…”

Section: Heterozygosity Excessmentioning

confidence: 99%

Prediction and estimation of effective population size

2016

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Effective population size (N e ) is a key parameter in population genetics. It has important applications in evolutionary biology, conservation genetics and plant and animal breeding, because it measures the rates of genetic drift and inbreeding and affects the efficacy of systematic evolutionary forces, such as mutation, selection and migration. We review the developments in predictive equations and estimation methodologies of effective size. In the prediction part, we focus on the equations for populations with different modes of reproduction, for populations under selection for unlinked or linked loci and for the specific applications to conservation genetics. In the estimation part, we focus on methods developed for estimating the current or recent effective size from molecular marker or sequence data. We discuss some underdeveloped areas in predicting and estimating N e for future research.Heredity ( INTRODUCTIONThe concept of effective population size, introduced by Sewall Wright (1931, 1933), is central to plant and animal breeding (Falconer and Mackay, 1996), conservation genetics (Frankham et al., 2010;Allendorf et al., 2013) and molecular variation and evolution (Charlesworth and Charlesworth, 2010), as it quantifies the magnitude of genetic drift and inbreeding in real-world populations. A substantial number of extensions to the basic theory and predictions were made since the seminal work of Wright, with main early developments by James Crow and Motoo Kimura (Kimura and Crow, 1963a;Crow and Kimura, 1970) and later by a list of contributors. Several review papers (Crow and Denniston, 1988;Caballero, 1994;Wang and Caballero, 1999;Nomura, 2005a) and population genetic books (Fisher, 1965;Wright, 1969;Ewens, 1979;Nagylaki, 1992) have summarised the existing theory in predicting the effective size of a population at different spatial and timescales under various inheritance modes and demographies. Comparatively, methodological developments (reviewed by Schwartz et al., 1999;Beaumont, 2003a;Wang, 2005;Palstra and Ruzzante, 2008;Luikart et al., 2010;Gilbert and Whitlock, 2015) in estimating the effective size of natural populations from genetic data lag behind but are accelerating in the past decade, thanks to the rapid developments of molecular biology.The classical developments of effective population size theory are based on the rate of change in gene frequency variance (genetic drift) or the rate of inbreeding. The effective population size is defined in reference to the Wright-Fisher idealised population, that is, a hypothetical population with very simplifying characteristics where genetic drift is the only factor in operation, and the dynamics of allelic and genotypic frequencies across generations merely depend on the population census (N) size. The effective size of a real population is then defined as the size of an idealised population, which would give rise to the rate of inbreeding and the rate of change in variance of gene frequencies actually observed in the population under consideration,

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“…2014): one based on heterozygous excess (Pudovkin et al. 1996; Zhdanova & Pudovkin 2008) and a second based on molecular co‐ancestry (Nomura 2008). …”

Section: Methodsmentioning

confidence: 99%

Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

Diefenbach

Hansen

Bohling

et al. 2015

Ecology and Evolution

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In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post‐reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present‐day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (N e) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent‐offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re‐establishing felid populations.

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Nb_HetEx: A Program to Estimate the Effective Number of Breeders

Cited by 74 publications

References 9 publications

Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus)

Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus)

Prediction and estimation of effective population size

Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

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