Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture

Bravington, Mark V.; Grewe, Peter M.; Davies, Campbell R.

doi:10.1038/ncomms13162

Cited by 119 publications

(176 citation statements)

References 38 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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“…If such an explanation were supported, a large‐scale genetic sibship or parent‐offspring‐based tagging studies could allow managers to identify sea lamprey natal stream origins, which is the highest priority for the Great Lakes Sea Lamprey Control Program (SLCB Research Priorities, ). The feasibility and efficacy of genetic tagging studies to provide valuable management insights have been demonstrated across a broad range of species (Anderson & Garza, ; Bravington, Grewe, & Davies, ; De Barba et al, ). Importantly, genetic tagging studies can confidently identify full‐ and half‐sibling relationships without genotyping parents (Jones & Wang, ), especially when several hundred loci are genotyped (Santure et al, ) as demonstrated by simulated and empirical data shown here.…”

Section: Discussionmentioning

confidence: 99%

“…These preliminary results are based on only two tributaries but suggest an intriguing explanation that the genetic similarities of larvae TA B L E 4 Summary statistics from pedigree analyses for larval sea lamprey of different age classes collected from two streams management insights have been demonstrated across a broad range of species (Anderson & Garza, 2006;Bravington, Grewe, & Davies, 2016;De Barba et al, 2010). Importantly, genetic tagging studies can confidently identify full-and half-sibling relationships without genotyping parents (Jones & Wang, 2010), especially when several hundred loci are genotyped (Santure et al, 2010) as demonstrated by simulated and empirical data shown here.…”

Section: Effects Of Outlier Loci On Spatial Population Structurementioning

confidence: 97%

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

Sard

Smith

Homola

et al. 2020

Ecology and Evolution

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Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site‐associated DNA sequencing (RAD‐Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean FST 0.008; range 0.00–0.018) were concordant with previous microsatellite‐based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age‐1 and age‐2 families of full and half‐siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non‐native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.

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“…Bravington, Grewe, et al () took the viewpoint that offspring tag their parents, while here we have reversed the direction of tagging. This may appear arbitrary, but Skaug () pointed out that the direction of tagging (called the offspring–centric vs. parent–centric perspectives by him) can affect the complexity of the statistical derivations.…”

Section: Discussionmentioning

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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Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture

Cited by 119 publications

References 38 publications

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

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

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

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

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