Microsatellite markers for multiple Pocillopora genetic lineages offer new insights about coral populations

Abstract

Population genetics of the coral genus Pocillopora have been more intensively studied than those of any other reef-building taxon. However, recent investigations have revealed that the current morphological classification is inadequate to represent genetic lineages. In this study, we isolated and characterized novel microsatellite loci from morphological Pocillopora meandrina (Type 1) and Pocillopora acuta (Type 5). Furthermore, we characterized previously reported microsatellite loci. A total of 27 loci (13 novel loci) proved useful for population genetic analyses at two sites in the Ryukyu Archipelago, in the northwestern Pacific. Clonal diversity differed in each genetic lineage. Genetic structure suggested by microsatellites corresponded to clusters in a phylogenetic tree constructed from a mitochondrial open reading frame (mtORF). In addition, we found an unknown mitochondrial haplotype of this mtORF. These microsatellite loci will be useful for studies of connectivity and genetic diversity of Pocillopora populations, and will also support coral reef conservation.

First evidence of asexual recruitment of Pocillopora acuta in Okinawa Island using genotypic identification

“…Clonality of P. acuta was documented in our previous population genetic analysis for corals in the Nansei Islands. A population at Ueno, Miyako Island showed clonality with only 10 different multilocus lineages, among 29 colonies ( Nakajima et al, 2017 ). Powerful waves during tropical storms may cause fragmentation of P. verrucosa colonies ( Aranceta-Garza et al, 2012 ), but only if fragment branches can survive long enough to reattach on the sea bottom can they give rise to viable new colonies.…”

“…It is impossible to identify these coral species as recruits by eye, due to the complex relationship between morphology and genetic species ( Schmidt-Roach et al, 2013 ; Schmidt-Roach et al, 2014a ; Schmidt-Roach et al, 2014b ; Nakajima et al, 2017 ). Genomic DNA from mature pocilloporid colonies and the 25 small colonies was extracted using a DNeasy Blood & Tissue Kit, following the standard protocol.…”

“…PCR products were cleaned with Exonuclease I (Takara) and Shrimp Alkaline Phosphatase (Takara). Sequencing was performed by Macrogen Japan, and sequences obtained were aligned with mtORF sequences reported in Nakajima et al (2017) and Flot et al (2011) to identify the genetic species of Pocillopora and Stylophora , respectively. We could not obtain the sequence of morphological P. verrucosa colonies collected from Zampa, because these colonies had died previously.…”

“…Nine microsatellite loci developed for Pocillopora by Nakajima et al (2017) were used to investigate the relationship between potential parental colonies and the small coral colonies discovered on the tank wall. These nine loci have perfect repeats (see Table 1 in Nakajima et al, 2017 ). Information about microsatellite loci is presented in Table 1 .…”

The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical data sets

“…STRUCTURE and the Δ K method have been widely applied to the detection of population genetic structure in marine organisms with planktonic dispersal and complex life histories (Palumbi, 2003). Corals are chief among them (Baums et al, 2012; Ledoux et al, 2015; Nakajima et al, 2017; Ruiz‐Ramos et al, 2015). Corals’ diverse life histories include asexual and sexual reproductive modes for some species (Baird et al, 2009).…”