Distribution and abundance of larval lake whitefish (Coregonus clupeaformis) in Stokes Bay, Lake Huron

Ryan, Kath; Crawford, Stephen S.

doi:10.1016/j.jglr.2014.05.008

Cited by 17 publications

(16 citation statements)

References 38 publications

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“…Ichthyoplankton were sampled at Stokes Bay, Lake Huron from 21 April to 08 July 2011, as part of an investigation focusing on the role of habitat in determining the distribution/abundance of lake whitefish (Ryan and Crawford, 2014). Sampling began as the ice retreated and the bay was accessible and safe to navigate by boat.…”

Section: Methodsmentioning

confidence: 99%

Increased taxonomic resolution of Laurentian Great Lakes ichthyoplankton through DNA barcoding: A case study comparison against visual identification of larval fishes from Stokes Bay, Lake Huron

Overdyk

Holm

Crawford

et al. 2016

Journal of Great Lakes Research

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Section: Methodsmentioning

confidence: 99%

Increased taxonomic resolution of Laurentian Great Lakes ichthyoplankton through DNA barcoding: A case study comparison against visual identification of larval fishes from Stokes Bay, Lake Huron

Overdyk

Holm

Crawford

et al. 2016

Journal of Great Lakes Research

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“…An interesting case study on which to focus is that of Lake whitefish (Coregonus clupeaformis). Lake whitefish are a commercially, culturally, ecologically and economically important group of salmonid fishes found throughout the Laurentian Great Lakes in Canada and the United States, particularly to the Saugeen Ojibway First Nation (SON) of Bruce Peninsula in Ontario, Canada, as well as non-indigenous fisheries (Ryan & Crawford, 2014). The colonization of refugia during Pleistocene glaciation is thought to have resulted in high levels of cryptic species diversity in North American freshwater fishes (Hubert et al, 2008;April et al, 2011;April et al, 2013a;April et al, 2013b).…”

Section: Lake Whitefish (Coregonus Clupeaformis)mentioning

confidence: 99%

HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves

Phillips

French

Hanner

et al. 2020

PeerJ Computer Science

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Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5–10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.

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Section: Application Of Hacsim To Real Speciesmentioning

confidence: 99%

Peer Review #2 of "HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves (v0.1)"

Suravajhala¹

2020

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Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5-10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.

show abstract

Distribution and abundance of larval lake whitefish (Coregonus clupeaformis) in Stokes Bay, Lake Huron

Abstract: DISTRIBUTION AND ABUNDANCE OF LARVAL LAKE WHITEFISH (COREGONUS CLUPEAFORMIS) IN STOKES BAY, LAKE HURON

Cited by 17 publications

References 38 publications

Increased taxonomic resolution of Laurentian Great Lakes ichthyoplankton through DNA barcoding: A case study comparison against visual identification of larval fishes from Stokes Bay, Lake Huron

Increased taxonomic resolution of Laurentian Great Lakes ichthyoplankton through DNA barcoding: A case study comparison against visual identification of larval fishes from Stokes Bay, Lake Huron

HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves

Peer Review #2 of "HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves (v0.1)"

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