Incomplete estimates of genetic diversity within species: Implications for DNA barcoding

Abstract

DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present levels of haplotype diversity, as well as patterning of standing genetic variation that exists within and between species. Typical sample sizes for molecular biodiversity assessment using DNA barcodes range from 5 to 10 individuals per species. However, required levels that are necessary to fully gauge haplotype variation at the species level are presumed to be strongly taxon-specific. Importantly, little attention has been paid to determining appropriate specimen sample sizes that are necessary to reveal the majority of intraspecific haplotype variation within any one species. In this paper, we present a brief outline of the current literature and methods on intraspecific sample size estimation for the assessment of COI DNA barcode haplotype sampling completeness. The importance of adequate sample sizes for studies of molecular biodiversity is stressed, with application to a variety of metazoan taxa, through reviewing foundational statistical and population genetic models, with specific application to ray-finned fishes (Chordata: Actinopterygii). Finally, promising avenues for further research in this area are highlighted.

Keywords: DNA barcoding; cytochrome c oxidase subunit I; sampling; species; statistics; sufficiency.

Figure 1

Longfin damselfish (Stegastes diencaeus) TCS (Templeton et al., 1992) haplotype network depicting an overall skewed distribution of observed haplotypes. Sizes of circles reflect the number of DNA sequences contained within each vertex. Tick marks indicate the number of mutational differences separating sampled haplotypes. DNA barcode sequence data used in the generation of the network were taken from supplemental material accompanying Phillips et al. (2015). The software PopArt (Leigh & Bryant, 2015) was used to create the haplotype network

Figure 2

Graphical depiction of Phillips et al.'s (2015) sampling model as described in detail within the main text. The x‐axis is meant to depict the number of specimens sampled, whereas the y‐axis is meant to convey the cumulative number of unique haplotypes uncovered for every additional individual that is randomly sampled. N and H refer to specimen and haplotype numbers that are observed for a given species. N* is the total sample size that is needed to capture all H* haplotypes that exist for a species