Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish

Palstra, Friso; Ruzzante, Daniel E.

doi:10.1038/hdy.2011.31

Cited by 28 publications

(32 citation statements)

References 68 publications

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“…Recently, Palstra and Ruzzante (2011) found that the degree of connectivity in different salmon populations could be forecast from demographic and life history attributes. Species that are livebearers and mouth brooders, for example, are less likely to be constrained by larval dispersal because they tend to produce advanced offspring that are deposited into optimal habitats.…”

Section: Conceptual Frameworkmentioning

confidence: 99%

Moving beyond the current paradigm in marine population connectivity: are adults the missing link?

2013

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During the past century, the field of fisheries oceanography has dominated the study of population connectivity in marine environments. The influence of physical and biological processes and their relationship to transport and retention of early life history stages has been central in providing insight into population structuring and connectivity. However, the focus on dispersive early life history stages has meant that the role of adults has received less attention and is not fully understood or appreciated. We argue that adults play a vital role in population connectivity for a wide range of marine taxa and hypothesize that adult‐mediated population connectivity commonly results in a diverse array of population structuring. Two case‐studies on winter skate, Leucoraja ocellata, and winter flounder, Pseudopleuronectes americanus, are presented to illustrate the role adults play in marine connectivity at both broad and fine scales, respectively. Indeed, if adults are important for population connectivity, we argue that the role of larval processes is conditional on adult choice and only management and research pursuits that integrate the full life cycle of species will capture the full dynamics of metapopulation connectivity. Failure to include the roles of adults can lead to misinterpretation of the causes and consequences of changes in ecosystem structure and fisheries productivity.

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Section: Conceptual Frameworkmentioning

confidence: 99%

Moving beyond the current paradigm in marine population connectivity: are adults the missing link?

2013

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“…The resulting gene flow will contribute to the genetic constitution of the recipient population and affect the estimated N e. Difficulties in measuring N e also arise from the lack of adequately accounting for the spatial and metapopulation structure and clarity on how these affect N e . Depending on the variation in size and productivity of subpopulations and the patterns of migration and extinction/recolonization rates, the sum of N e 's of the subpopulations can either be greater or smaller than the effective size of the total (meta)population (N eT ) (Nunney 1999;Palstra and Ruzzante 2011). With high levels of dispersal, the concept of a (sub)population N e becomes increasingly meaningless since it is not acting as an independent unit (Nunney 2000).…”

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confidence: 99%

Short-Term Genetic Changes: Evaluating Effective Population Size Estimates in a Comprehensively Described Brown Trout (Salmo trutta) Population

et al. 2012

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The effective population size (N e ) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate N e are affected variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, and population substructure, as well as by the frequency patterns of genetic markers used and the sampling design. Here, we compare N e estimates obtained by different genetic methods and from demographic data and elucidate how the estimates are affected by various factors in an exhaustively sampled and comprehensively described natural brown trout (Salmo trutta) system. In general, the methods yielded rather congruent estimates, and we ascribe that to the adequate genotyping and exhaustive sampling. Effects of violating the assumptions of the different methods were nevertheless apparent. In accordance with theoretical studies, skewed allele frequencies would underestimate temporal allele frequency changes and thereby upwardly bias N e if not accounted for. Overlapping generations and iteroparity would also upwardly bias N e when applied to temporal samples taken over short time spans. Gene flow from a genetically not very dissimilar source population decreases temporal allele frequency changes and thereby acts to increase estimates of N e . Our study reiterates the importance of adequate sampling, quantification of life-history parameters and gene flow, and incorporating these data into the N e estimation.T HE effective population size (N e ) is an essential concept in evolutionary and conservation biology as it determines the strength of stochastic evolutionary processes relative to deterministic forces (Crow and Kimura 1970). In the absence of gene flow, the rate of loss of genetic diversity via genetic drift is greater in populations with small N e . The effective population size is, however, notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to characterize in natural systems. A number of different methods have been developed for estimating N e , and these are affected variously by different processes at the population level such as immigration, fluctuations in population size, population substructure, and life-history characteristics. When possible, it is therefore important to compare N e estimates obtained using different methods and elucidate how different processes affect the various methods for N e estimation (Fraser et al. 2007).Two main types of approaches have been used to estimate N e : genetic and demographic. Genetic methods attempt to infer the magnitude of the effective population size by characterizing the genetic consequences of limited population size, whereas demographic methods depend upon measurement of demographic parameters that have theoretically been shown to influence N e. The most common genetic approach is ...

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“…Palstra and Ruzzante (2011) urged further theoretical developments to avoid a downward bias in estimating linkage disequilibrium Ne in naturally occurring metapopulations. Our results have demonstrated that under certain circumstances even estimates for focal populations can be downwardly biased.…”

Section: Discussionmentioning

confidence: 99%

“…The samples would not represent a panmictic population, causing deviations from the expected linkage disequilibria and a bias in the linkage disequilibrium estimation of Ne . For example, a downward bias in Ne estimates was simulated by Palstra and Ruzzante (2011) when divergent populations were pooled.…”

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confidence: 99%

Linkage Disequilibrium Estimation of Effective Population Size with Immigrants from Divergent Populations: A Case Study on Spanish Mackerel (Scomberomorus commerson)

Macbeth

Broderick

Buckworth

et al. 2013

G3 Genes|Genomes|Genetics

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Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. However, pitfalls are predicted when the effective size is large because estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes of approximately 5000. This number was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow-barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest SD of Ne estimates occurred when low-frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or nonbreeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were greater than 24,000.

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Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish

Cited by 28 publications

References 68 publications

Moving beyond the current paradigm in marine population connectivity: are adults the missing link?

Moving beyond the current paradigm in marine population connectivity: are adults the missing link?

Short-Term Genetic Changes: Evaluating Effective Population Size Estimates in a Comprehensively Described Brown Trout (Salmo trutta) Population

Linkage Disequilibrium Estimation of Effective Population Size with Immigrants from Divergent Populations: A Case Study on Spanish Mackerel (Scomberomorus commerson)

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