Identification of Scleractinian Coral Recruits Using Fluorescent Censusing and DNA Barcoding Techniques

Abstract

The identification of coral recruits has been problematic due to a lack of definitive morphological characters being available for higher taxonomic resolution. In this study, we tested whether fluorescent detection of coral recruits used in combinations of different DNA-barcoding markers (cytochrome oxidase I gene [COI], open reading frame [ORF], and nuclear Pax-C intron [PaxC]) could be useful for increasing the resolution of coral spat identification in ecological studies. One hundred and fifty settlement plates were emplaced at nine sites on the fringing reefs of Kenting National Park in southern Taiwan between April 2011 and September 2012. A total of 248 living coral spats and juveniles (with basal areas ranging from 0.21 to 134.57 mm2) were detected on the plates with the aid of fluorescent light and collected for molecular analyses. Using the COI DNA barcoding technique, 90.3% (224/248) of coral spats were successfully identified into six genera, including Acropora, Isopora, Montipora, Pocillopora, Porites, and Pavona. PaxC further separated I. cuneata and I. palifera of Isopora from Acropora, and ORF successfully identified the species of Pocillopora (except P. meandrina and P. eydouxi). Moreover, other cnidarian species such as actinarians, zoanthids, and Millepora species were visually found using fluorescence and identified by COI DNA barcoding. This combination of existing approaches greatly improved the taxonomic resolution of early coral life stages, which to date has been mainly limited to the family level based on skeletal identification. Overall, this study suggests important improvements for the identification of coral recruits in ecological studies.

Molecular assessment ofPocillopora verrucosa(Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan

“…Of the 101 colonies sampled, 85 (84%) clustered with P. verrucosa (clade 2, Fig. 2 ), and match published mtORF references of this species ( Schmidt-Roach et al, 2012 ; Pinzón et al, 2013 ; Hsu et al, 2014 ; Marti-Puig et al, 2014 ; Gélin et al, 2017b ). A total of 15 (15%) clustered with the complex of species P. meandrina and P. eydouxi (clade 3, Fig.…”

“…They represent the dominant P. verrucosa haplotypes found in this study as they count for 93% of the genotyped P. verrucosa colonies. They were also previously found in coral recruits in the shallow waters of Kenting, southern Taiwan ( Hsu et al, 2014 ). In our study haplotype H8 was not found at 15 m. However, we suspect that this haplotype could be present at this depth given that it was collected at all other depths.…”

From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach

“…To this end, combinations of different genes, including mitochondrial and nuclear loci, have been proposed and used for different groups of anthozoans (Huang et al 2011) and the 28S rDNA for flatworms (Litvaitis and Rohde 1999, Litvaitis and Newman 2001). In anthozoans, species-level resolution is still limited due to frequent hybridisation (Quattrini et al 2019), resulting in low interspecific divergence (Shearer and Coffroth 2008, Dohna and Kochzius 2015), though these markers are possibly useful at the genus level (Hsu et al 2014). Other mitochondrial markers such as cytochrome b (Ward et al 2005, Sevilla et al 2007), 12S rRNA (Miya et al 2015) and D-loop control region (Lee et al 1995) have been suggested for use on barcoding fish species.…”

Living on the edge: Assessing the diversity of South African Pocillopora on the margins of the Southwestern Indian Ocean

“…eydouxi ; according to the descriptions of previous South African checklists [17,18]. The three SSHs were then correlated to current accepted morpho-genetic species designations from contemporary literature [5,7,8,10,11,26,27,29,30,66] and a collated study including all ORF haplotypes [4]; SSH09a related to P . eydouxi/meandrina , SSH13a related to P .…”