Genetic and metagenetic analysis of zooplankton diversity

Biodiversity is an important measure of ecosystem status (Babcock and Pikitch, 2004), but accurate analysis of zooplankton biodiversity is complicated and can require numerous taxonomic experts for the many groups found in the pelagic assemblage. However, since most marine species have planktonic life stages, plankton sampling arguably provides the broadest array of multi-cellular species possible with a single sampling approach. Genetic and metagenetic approaches to estimating diversity can provide accurate assessments across a range of taxonomic levels, and ensure detection of new or unknown, cryptic, and rare species.

DNA barcoding has been successfully carried out for nearly every phylum and taxonomic group represented within the marine zooplankton assemblage, including protists (Morarda et al., 2009); cnidarians (Ortman, 2008, Ortman et al., 2010), calanoid copepods (Bucklin et al., 2003; Machida et al., 2006), euphausiids (Bucklin et al., 2007), ostracods (Angel et al., 2008), pteropod mollusks (Jennings et al., 2010a), chaetognaths (Jennings et al., 2010b), among other groups. These studies have demonstrated the usefulness of DNA barcodes for identification of known species, discovery of new species, and recognition of cryptic species within widespread or poorly known taxa. Other barcoding efforts have had a regional focus, with analysis of all identified specimens collected from a particular ocean region or during a survey cruise (e.g., Radulovici et al, 2009; Bucklin et al., 20010a, 2010b; Figure 6). Machida et al. (2009) pioneered the use of environmental barcoding (i.e., DNA sequencing of the COI barcode region from unsorted samples) for the metazoan zooplankton assemblage.

A similar approach can be used for different genes to examine diversity at various taxonomic levels. The nuclear small-subunit (18S) rRNA shows consistent patterns of divergence across invertebrate and vertebrate taxa, which typically discriminates genera, families, and higher taxonomic groups (Field et al., 1988; Winchell et al., 2002; Mallatt et al., 2004; Creer et al., 2010). Various 18S rRNA gene regions have been used that exhibit significant advantages for accurate classification of novel sequences and reliable amplification with consensus primers. These regions provide group-specific markers that complement the less reliable but more variable COI barcode region. This gene has recently been the basis of novel high throughput sequencing analysis of metazoan diversity (Creer et al., 2010; Fonseca et al., 2010; Lindeque et al., 2013).