Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

Hare, Matthew P.; Nunney, Leonard; Schwartz, Michael K.; Ruzzante, Daniel E.; Burford, Martha O.; Waples, Robin S.; Ruegg, Kristen; Palstra, Friso

doi:10.1111/j.1523-1739.2010.01637.x

Cited by 287 publications

(346 citation statements)

References 91 publications

(121 reference statements)

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“…Effective population size estimates are strongly influenced by the mutation rate, with underestimation of rates resulting in large overestimates in population size (Luikart et al, 2010). In general, N ef is most difficult to estimate in large populations with moderate gene flow and this difficulty can lead to extremely large confidence intervals as are seen in our estimates (Hare et al, 2011). In this context, we suggest that our estimates of N ef should be considered as indicative of a large population with no bottleneck.…”

Section: Discussionmentioning

confidence: 79%

Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean

et al. 2015

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Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h = 0.933-0.987, π = 0.763-0.996% and R s = 4.22-4.37, H e = 0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat.

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Section: Discussionmentioning

confidence: 79%

Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean

et al. 2015

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“…A conservation strategy of high relevance in fisheries is supportive breeding (Hare et al, 2011), where a population is typically divided into a captive and a wild group and the offspring of the captive group are released into the wild habitat to mix with the offspring from the wild group. Because the captive group (permanent or transitional) is bred to produce a lot of offspring that are released into the wild group at each generation, the variance in family size is greatly elevated artificially and thus the N e of the entire population is reduced.…”

Section: Effective Population Size In Conservation Practicesmentioning

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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“…Those criteria are not met with the great scallop and as a consequence using and interpreting most Ne estimates should be carried out with caution. Moreover, the possibility of substantial immigration in the population could further bias estimates, as gene flow could have different impacts on different estimators (see Gilbert and Whitlock (2015), for a comprehensive analysis; for more details on the differences between estimation methods, see Barker (2011), Hare et al (2011), Phillipsen et al (2011 and Holleley et al (2014)). …”

Section: Effective Population Sizesmentioning

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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Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

Cited by 287 publications

References 91 publications

Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean

Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean

Prediction and estimation of effective population size

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

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