Limitations of mitochondrial gene barcoding in Octocorallia

Abstract

The widespread assumption that COI and other mitochondrial genes will be ineffective DNA barcodes for anthozoan cnidarians has not been well tested for most anthozoans other than scleractinian corals. Here we examine the limitations of mitochondrial gene barcoding in the sub-class Octocorallia, a large, diverse, and ecologically important group of anthozoans. Pairwise genetic distance values (uncorrected p) were compared for three candidate barcoding regions: the Folmer region of COI; a fragment of the octocoral-specific mitochondrial protein-coding gene, msh1; and an extended barcode of msh1 plus COI with a short, adjacent intergenic region (igr1). Intraspecific variation was <0.5%, with most species exhibiting no variation in any of the three gene regions. Interspecific divergence was also low: 18.5% of congeneric morphospecies shared identical COI barcodes, and there was no discernible barcoding gap between intra- and interspecific p values. In a case study to assess regional octocoral biodiversity, COI and msh1 barcodes each identified 70% of morphospecies. In a second case study, a nucleotide character-based analysis correctly identified 70% of species in the temperate genus Alcyonium. Although interspecific genetic distances were 2× greater for msh1 than COI, each marker identified similar numbers of species in the two case studies, and the extended COI + igr1 + msh1 barcode more effectively discriminated sister taxa in Alcyonium. Although far from perfect for species identification, a COI + igr1 + msh1 barcode nonetheless represents a valuable addition to the depauperate set of characters available for octocoral taxonomy.

A second, cryptic species of the soft coral genus Incrustatus (Anthozoa: Octocorallia: Clavulariidae) from Tierra del Fuego, Argentina, revealed by DNA barcoding

“…These distances are greater than those found among individuals of the same species in any genus of octocorals examined to date (McFadden et al 2011) and suggest that these colonies belong to a new, cryptic species of Incrustatus. Although this new species appears to be indistinguishable from I. comauensis in the field, differences in the microscopic ornamentation of the coenenchymal sclerites support its status as a distinct species.…”

“…Although a genetic difference of 0.7 % at COI is at the upper end of the range of values normally observed among conspecific individuals in octocorals (McFadden et al 2011), the morphological differences that distinguish these two ecotypes are very slight (no vs. very few polyp sclerites). The two ecotypes also share identical DNA sequences at mtMutS, a locus that is typically more variable than COI in octocorals (McFadden et al 2011). Further study of ecological, reproductive, and biogeographical differences among the sub-tidal and intertidal forms of I. comauensis, might, however, support their status as separate species, as would evidence of genetic differentiation in sympatry.…”

“…Extraction of DNA from ethanol-preserved tissue samples, PCR amplification, and sequencing of the mtMutS (msh1) and COI genes followed the protocols published in McFadden et al (2011). In addition, we sequenced an approximately 810 nt fragment of the 28S nuclear ribosomal gene using primers 28S-Far (5 0 -CACGAGACCGATAGCGAA CAAGTA-3 0 ) and either 28S-Rar (5 0 -TCATTTCGACCC TAAGACCTC-3 0 ) or 28S-Rab (5 0 -TCGCTACGAGCTT CCACCAGTGTTT-3 0 ), and the same PCR protocol used for COI.…”

“…Although other mitochondrial gene regions, most notably the octocoral-specific mitochondrial mutS homolog (mtMutS, previously known as msh1), appear to be somewhat better barcodes for octocorals than the widely used cytochrome oxidase I (COI), both mitochondrial markers still only discriminate about 70-80 % of congeneric species (McFadden et al 2011). Despite their inability to separate some closely related species, however, the use of DNA barcodes in biodiversity surveys has already proven useful for detecting cryptic species in octocorals, taxa for which there is often a paucity of morphological characters available for taxonomy (McFadden et al 2006(McFadden et al , 2011.…”

Diversity, distribution and spatial structure of the cold-water coral fauna of the Azores (NE Atlantic)

“…Sarcodictyon charcoti, Titanideum obscurum, Thesea rigida) and may not cover the entire range of intraspecific morphological variability. The use of molecular tools may thus prove to be essential in assisting classical taxonomy in the discrimination between closely related species in these problematic groups (McFadden et al, 2011).…”