Improved confidence intervals for the linkage disequilibrium method for estimating effective population size

Jones, Andrew; Ovenden, Jennifer R.; Wang, You‐Gan

doi:10.1038/hdy.2016.19

Cited by 97 publications

(99 citation statements)

References 24 publications

(45 reference statements)

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“…Effective population size ( N e ) was calculated using the method based on the linkage disequilibrium (LD; Hill, ; Waples, ; Waples & Do, ) as implemented in NeEstimator v.2.1 (Do et al, ). Minimum allele frequency of 0.02 and non‐parametric jackknifed confidence intervals were used for all analyses of N e (Jones, Ovenden, & Wang, ). The estimates of N e obtained for SNP data are known to suffer from a downward bias and were thus corrected using the equation 1a from Waples, Larson, and Waples () (haploid chromosome number = 40; Leitwein et al, ).…”

Section: Methodsmentioning

confidence: 99%

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

Lemopoulos

Prokkola

Uusi‐Heikkilä

et al. 2019

Ecology and Evolution

143

139

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The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction‐site‐associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout ( Salmo trutta ) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST , was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half‐ and full‐siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual‐level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual‐level genotype information, such as quantifying relatedness and individual‐level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

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Section: Methodsmentioning

confidence: 99%

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

Lemopoulos

Prokkola

Uusi‐Heikkilä

et al. 2019

Ecology and Evolution

143

139

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“…Genomic estimates of N e Although this paper considered only demographic data, genetically based estimates of effective size have skyrocketed in recent years (Palstra and Fraser, 2012), and this trend is only likely to increase with the ability to use next-generation DNA sequencing techniques to generate thousands of markers for nonmodel species (for example, see Hollenbeck et al, 2016;Jones et al, 2016). To provide context for interpreting these estimates, most of these new studies will have to consider the N e /N ratio, and hence results presented here will be relevant.…”

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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“…Singleton alleles were filtered from this and all other cohort samples with P crit = .02. The beta version of LDNe implements a corrected version of a new jackknife approach over individuals (Jones, Ovenden, & Wang, ) while producing identical point estimates as previous versions. Other single‐sample estimators of

{\overset{true^}{N}}_{b}

are available (Tallmon et al., ; Wang, ) but were biased low when applied to simulated brook trout data (A. Whiteley, unpublished results).…”

Section: Methodsmentioning

confidence: 99%

Keeping things local: Subpopulation N_b and N_e in a stream network with partial barriers to fish migration

Whiteley

Coombs

O’Donnell

et al. 2017

Evolutionary Applications

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For organisms with overlapping generations that occur in metapopulations, uncertainty remains regarding the spatiotemporal scale of inference of estimates of the effective number of breeders (Ntrue^b) and whether these estimates can be used to predict generational N e. We conducted a series of tests of the spatiotemporal scale of inference of estimates of N b in nine consecutive cohorts within a long‐term study of brook trout (Salvelinus fontinalis). We also tested a recently developed approach to estimate generational N e from Ntrue^b and compared this to an alternative approach for estimating Ntrue^e that also accounts for age structure. Multiple lines of evidence were consistent with Ntrue^b corresponding to the local (subpopulation) spatial scale and the cohort‐specific temporal scale. We found that at least four consecutive cohort‐specific estimates of Ntrue^b were necessary to obtain reliable estimates of harmonic mean Ntrue^b for a subpopulation. Generational Ntrue^e derived from cohort‐specific Ntrue^b was within 7%–50% of an alternative approach to obtain Ntrue^e, suggesting some population specificity for concordance between approaches. Our results regarding the spatiotemporal scale of inference for N b should apply broadly to many taxa that exhibit overlapping generations and metapopulation structure and point to promising avenues for using cohort‐specific Ntrue^b for local‐scale genetic monitoring.

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Improved confidence intervals for the linkage disequilibrium method for estimating effective population size

Cited by 97 publications

References 24 publications

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

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

Keeping things local: Subpopulation N_b and N_e in a stream network with partial barriers to fish migration

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Improved confidence intervals for the linkage disequilibrium method for estimating effective population size

Cited by 97 publications

References 24 publications

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

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

Keeping things local: Subpopulation Nb and Ne in a stream network with partial barriers to fish migration

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Keeping things local: Subpopulation N_b and N_e in a stream network with partial barriers to fish migration