Estimation of Parameters of Inbreeding and Genetic Drift in Populations With Overlapping Generations

Wang, Jinliang; Brekke, Patricia; Huchard, Élise; Knapp, Leslie A.; Cowlishaw, Guy

doi:10.1111/j.1558-5646.2010.00953.x

Cited by 52 publications

(87 citation statements)

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“…We do not exclude possible downward bias due to the presence of samples from different cohorts. Wang et al (2010) stated that for iteroparous species, there is a higher probability of familial relationships with similar levels of relatedness to half-siblings (e.g. grandparent-offspring relationships).…”

Section: Discussionmentioning

confidence: 98%

Assessment of census (N) and effective population size (N e ) reveals consistency of N e single-sample estimators and a high N e /N ratio in an urban and isolated population of fire salamanders

Álvarez

Lourenço

Oró

et al. 2015

Conservation Genet Resour

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Amphibians are the most threatened vertebrates on Earth, and one of the main factors involved in their decline is the loss and fragmentation of their natural habitats. Contemporary urban development is a major cause of habitat fragmentation, and populations trapped within urban environments offer a unique opportunity to study effects of fragmentation. Here, we compared, for the first time in fire salamanders (Salamandra salamandra), estimates of census (N) and effective population size (N e ) in a small urban population in the city of Oviedo (Spain). We performed a 4 year capture-mark-recapture study and used three single-sample N e estimators based on 58 individuals genotyped for 15 polymorphic microsatellite loci. Our study showed a small (N ¼ 113 salamanders; 95 % CI 100-142) but dense population (mean 0.45 individuals per m 2 ), while single-sample estimators provided congruent N e estimates. A high N e /N population size ratio (range 0.50-0.84) obtained in this small and isolated population suggests the existence of mechanisms of genetic compensation (low reproductive variance and multiple paternity) in fire salamanders.

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Section: Discussionmentioning

confidence: 98%

Assessment of census (N) and effective population size (N e ) reveals consistency of N e single-sample estimators and a high N e /N ratio in an urban and isolated population of fire salamanders

Álvarez

Lourenço

Oró

et al. 2015

Conservation Genet Resour

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“…Researchers interested in applying the two-sample (temporal) method to agestructured species can find useful guidance in Waples (1990), Jorde and Ryman (1996) and Waples and Yokota (2007). The single-sample sibship method can be applied to species with overlapping generations using an approach suggested by Wang et al (2010). Robinson and Moyer (2013) and have evaluated performance of the single-sample method based on linkage disequilibrium with iteroparous species.…”

Section: Discussionmentioning

confidence: 99%

Life-history traits and effective population size in species with overlapping generations revisited: the importance of adult mortality

Waples

2016

Heredity

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The relationship between life-history traits and the key eco-evolutionary parameters effective population size (N e ) and N e /N is revisited for iteroparous species with overlapping generations, with a focus on the annual rate of adult mortality (d). Analytical methods based on populations with arbitrarily long adult lifespans are used to evaluate the influence of d on N e , N e /N and the factors that determine these parameters: adult abundance (N), generation length (T), age at maturity (α), the ratio of variance to mean reproductive success in one season by individuals of the same age (ϕ) and lifetime variance in reproductive success of individuals in a cohort (V k• ). Although the resulting estimators of N, T and V k• are upwardly biased for species with short adult lifespans, the estimate of N e /N is largely unbiased because biases in T are compensated for by biases in V k• and N. For the first time, the contrasting effects of T and V k• on N e and N e /N are jointly considered with respect to d and ϕ. A simple function of d and α based on the assumption of constant vital rates is shown to be a robust predictor (R 2 = 0.78) of N e /N in an empirical data set of life tables for 63 animal and plant species with diverse life histories. Results presented here should provide important context for interpreting the surge of genetically based estimates of N e that has been fueled by the genomics revolution.

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“…However, in the absence of an estimate of N e , N b provides some information about the risks of inbreeding and loss of genetic variation in conservation populations (for example, Whiteley et al, 2015). For the case of overlapping generations, Wang et al (2010) proposed a parentage assignment method to estimate the N e and generation interval from the sex, age and multilocus genotype information of a single sample of individuals taken at random from a population. Essentially, the method estimates the life table by parentage assignments, and both N e and generation interval are then calculated from the life table.…”

Section: Relatedness and Relationshipmentioning

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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Estimation of Parameters of Inbreeding and Genetic Drift in Populations With Overlapping Generations

Cited by 52 publications

References 50 publications

Assessment of census (N) and effective population size (N e ) reveals consistency of N e single-sample estimators and a high N e /N ratio in an urban and isolated population of fire salamanders

Assessment of census (N) and effective population size (N e ) reveals consistency of N e single-sample estimators and a high N e /N ratio in an urban and isolated population of fire salamanders

Life-history traits and effective population size in species with overlapping generations revisited: the importance of adult mortality

Prediction and estimation of effective population size

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