A simulation study of sample size for DNA barcoding

Ecology and Evolution

Arong Luo¹  Haiqiang Lan¹  Cheng Ling⁴  Aibing Zhang²  Lei Shi⁵  Simon Y. W. Ho³ 

[1] Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China;College of Life Sciences, Capital Normal University, Beijing, China;School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia;Department of Computer Science and Technology, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China;School of Statistics and Mathematics, Yunnan University of Finance and Economics, Kunming, China

关键词: Coalescence;    haplotype;    maximum pairwise distance;    mismatch distribution;    nucleotide diversity;   

DOI  :  10.1002/ece3.1846

来源: Wiley

【 摘 要 】

Abstract

For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a simulation approach to examine the effects of sample size on four estimators of genetic polymorphism related to DNA barcoding: mismatch distribution, nucleotide diversity, the number of haplotypes, and maximum pairwise distance. Our results showed that mismatch distributions derived from subsamples of ≥20 individuals usually bore a close resemblance to that of the full dataset. Estimates of nucleotide diversity from subsamples of ≥20 individuals tended to be bell-shaped around that of the full dataset, whereas estimates from smaller subsamples were not. As expected, greater sampling generally led to an increase in the number of haplotypes. We also found that subsamples of ≥20 individuals allowed a good estimate of the maximum pairwise distance of the full dataset, while smaller ones were associated with a high probability of underestimation. Overall, our study confirms the expectation that larger samples are beneficial for the efficacy of DNA barcoding and suggests that a minimum sample size of 20 individuals is needed in practice for each population.

【 授权许可】

CC BY   
© 2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.