Close-Kin Mark-Recapture

Bravington, Mark V.; Skaug, Hans J.; Anderson, Eric C.

doi:10.1214/16-sts552

Cited by 154 publications

(340 citation statements)

References 34 publications

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“…If however such large samples are collected, other population quantities can be estimated using the same data. Absolute abundance and demographic parameters (fecundity, mortality) can be estimated with the close‐kin mark–recapture (CKMR) method (Bravington, Grewe, & Davies, ; Bravington, Skaug, & Anderson, ). This method is based on the identification of pairs of close relatives (parents–offspring or half sibling pairs).…”

Section: Resultsmentioning

confidence: 99%

Estimating effective population size of large marine populations, is it feasible?

et al. 2018

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Sustainable exploitation of marine populations is a challenging task relying on information about their current and past abundance. Fisheries‐related data can be scarce and unreliable making them unsuitable for quantitative modelling. One fishery independent method that has attracted attention in this context consists in estimating the effective population size (Ne), a concept founded in population genetics. We reviewed recent empirical studies on Ne and carried out a simulation study to evaluate the feasibility of estimating Ne in large fish populations with the currently available methods. The detailed review of 26 studies found that published empirical Ne values were very similar despite differences in species and total population sizes (N). Genetic simulations for an age‐structured fish population were carried out for a range of population and samples sizes, and Ne was estimated using the Linkage Disequilibrium method. The results showed that already for medium‐sized populations (1 million individuals) and common sample sizes (50 individuals), negative estimates were likely to occur which for real applications is commonly interpreted as indicating very large (infinite) Ne. Moreover, on average, Ne estimates were negatively biased. The simulations further indicated that around 1% of the total number of individuals might have to be sampled to ensure sufficiently precise estimates of Ne. For large marine populations, this implies rather large samples (several thousands to millions of individuals). If however such large samples were to be collected, many more population parameters than only Ne could be estimated.

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Section: Resultsmentioning

confidence: 99%

Estimating effective population size of large marine populations, is it feasible?

et al. 2018

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“…In the nonspatial context, Bravington et al . () have outlined how these data can be used to estimate sex‐specific abundance and survival rates in a modified mark–recapture framework called close‐kin mark–recapture (CKMR). An extension of this framework into the spatial domain would utilize the migratory‐ and abundance‐related information in these data to separate the two, and obtain quantitative estimates of between river migration rates.…”

Section: Discussionmentioning

confidence: 99%

“…With more markers, direct methods can also reveal kinship beyond parent–offspring, potentially removing the need to sample adults (Bravington et al . ). The spatial distribution of cross‐cohort half‐sibling pairs for example, provides insight into their parents’ breeding movements.…”

Section: Introductionmentioning

confidence: 97%

Inferring contemporary and historical genetic connectivity from juveniles

et al. 2016

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Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river shark found only in tropical northern Australia and southern Papua New Guinea. Contemporary adult and juvenile shark movements, estimated with the spatial distribution of kin pairs across and within three river systems, was contrasted with historical long-term connectivity patterns, estimated from mitogenomes and genome-wide SNP data. We found strong support for river fidelity in juveniles with the within-cohort relationship analysis. Male breeding movements were highlighted with the cross-cohort relationship analysis, and female reproductive philopatry to the river systems was revealed by the mitogenomic analysis. We show that accounting for juvenile river fidelity and female philopatry is important in population structure analysis and that targeted sampling in nurseries and juvenile aggregations should be included in the genomic toolbox of threatened species management.

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“…We consider the situation where males (♂) and females (♀) have different age‐specific fecundities. Using the notion of “relative reproductive output” (Bravington, Skaug, et al, , eq. 3.1), we get the following estimator for 2015 census size,

\begin{matrix} {\overset{N}{true}}_{c (C K M R)} = & \frac{n_{J}}{H + 1} \sum_{a = 1 +}^{3 +} (\frac{F_{a}^{()(♂)}}{{\bar{F}}^{()(♂)}} + \frac{F_{a}^{()(♀)}}{{\bar{F}}^{()(♀)}}) \\ \times & (S_{a - 1} \times n_{a - 1, 2014} + n_{a, 2015} + n_{a + 1, 2016} + n_{a + 2, 2017}), \end{matrix}

…”

Section: Methodsmentioning

confidence: 99%

Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance

et al. 2019

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Knowing how many individuals there are in a population is a fundamental problem in the management and conservation of freshwater and marine fish. We compare abundance estimates (census size, Nc) in seven brook trout Salvelinus fontinalis populations using standard mark–recapture (MR) and the close‐kin mark–recapture (CKMR) method. Our purpose is to validate CKMR as a method for estimating population size. Close‐kin mark–recapture is based on the principle that an individual's genotype can be considered a “recapture” of the genotypes of each of its parents. Assuming offspring and parents are sampled independently, the number of parent–offspring pairs (POPs) genetically identified in these samples can be used to estimate abundance. We genotyped (33 microsatellites) and aged c. 2,400 brook trout individuals collected over 5 consecutive years (2014–2018). We provide an alternative interpretation of CKMR in terms of the Lincoln–Petersen estimator in which the parents are considered as tagging the offspring rather than the offspring “recapturing” the parents. Despite various sources of uncertainty, we find close agreement between standard MR abundance estimates obtained through double‐pass electrofishing and CKMR estimates, which require information on age‐specific fecundity, and population‐ and age‐specific survival rates. Population sizes (trueN^) are estimated to range between 300 and 6,000 adult individuals. Our study constitutes the first in situ validation of CKMR and establishes it as a useful method for estimating population size in aquatic systems where assumptions of random sampling and thorough mixing of individuals can be met.

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Close-Kin Mark-Recapture

Cited by 154 publications

References 34 publications

Estimating effective population size of large marine populations, is it feasible?

Estimating effective population size of large marine populations, is it feasible?

Inferring contemporary and historical genetic connectivity from juveniles

Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance

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