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

Phillips, Jarrett D ; French, Steven H ; Hanner, Robert H ; Gillis, Daniel J

PeerJ. Computer science, 2020-01, Vol.6, p.e243-e243, Article e243 [Periódico revisado por pares]

United States: PeerJ. Ltd

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Título:
HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves
Autor: Phillips, Jarrett D ; French, Steven H ; Hanner, Robert H ; Gillis, Daniel J
Assuntos: Accumulation ; Algorithm ; Algorithms ; Bar codes ; Biodiversity ; Bioinformatics ; Computational Biology ; Computer simulation ; Data Science ; Data systems ; Deoxyribonucleic acid ; DNA ; DNA barcoding ; Extrapolation ; Frequency distribution ; Gene sequencing ; Genetic diversity ; Haplotypes ; Iterative method ; Novels ; Optimization Theory and Computation ; Parameter estimation ; Robustness ; Sample size ; Sampling ; Sampling sufficiency ; Scientific Computing and Simulation ; Species
É parte de: PeerJ. Computer science, 2020-01, Vol.6, p.e243-e243, Article e243
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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Descrição: 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 ( aplotype ccumulation urve ulator) 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.
Editor: United States: PeerJ. Ltd
Idioma: Inglês

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

Phillips, Jarrett D ; French, Steven H ; Hanner, Robert H ; Gillis, Daniel J

United States: PeerJ. Ltd

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