Genome‐wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: Implications for coral restoration

Abstract

It is essential to consider genetic composition for both conventional coral restoration management and for initiating new interventions to counter the significant global decline in living corals. Population genetic structure at a fine spatial scale should be carefully evaluated before implementing strategies to achieve self‐sustaining ecosystems via coral restoration. This study investigated the population genetic structure of two acroporid species at Kume Island, Okinawa, Japan. There were 140 colonies of Acropora digitifera collected from seven study sites, and 81 colonies of Acropora tenuis from six sites. In total, 384 single nucleotide polymorphism (SNP) loci for A. digitifera and 470 SNPs for A. tenuis were obtained using a comparatively economical technique, Multiplexed ISSR Genotyping by sequencing. Observed heterozygosity was significantly lower than expected heterozygosity at all SNP sites in both acroporid species, suggesting deficient genetic diversity possibly caused by past massive coral bleaching. Even though both species are broadcast spawners, the population structure was different in the two species. No detectable structure was evident in A. digitifera, but two distinct clades were found in A. tenuis. The genetic homogeneity of A. digitifera at Kume Island suggests that this species could be used as a focal species for active restoration in terms of genetic differentiation at this island. By contrast, A. tenuis unexpectedly included two distinct clades with little or no admixture within a small study area, possibly representing two reproductively isolated cryptic species. Thus, when using A. tenuis, it would be prudent to avoid disturbing the genetic composition of wild populations until this question is answered.

Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef

“…Acropora tenuis is common on the GBR and throughout the Indo‐Pacific, and among the first corals to be characterized in population genomic investigations (e.g. present study; Cooke et al, 2020 ; Zayasu et al, 2021 ), complementing earlier studies based on microsatellites (Lukoschek et al, 2016 ; Riginos et al, 2019 ; Underwood, 2009 ). These new genomic studies all highlight cryptic divisions, largely undetected in studies with fewer loci.…”

Integration of population genetics with oceanographic models reveals strong connectivity among coral reefs across Seychelles

“…Broadcast-spawning corals generate enormous numbers of larvae, and only a small number of successful dispersal events are required to establish genetic connectivity between populations 13 . Quantifying the degree of connectivity within a coral metapopulation requires the use of population genetics 14 – 16 , but oceanographic models that simulate larval dispersal can provide a first-order approximation of whether or not genetic connectivity is likely 17 – 19 . Both methods have their limitations: genetic studies are expensive and require samples of a single species to be collected across the regional reef system, whereas most oceanographic models do not fully capture the range of physical and biological processes affecting larval dispersal, and rely on poorly constrained parameterisations for larval behaviour 20 .…”

Genomic Data Reveal Diverse Biological Characteristics of Scleractinian Corals and Promote Effective Coral Reef Conservation

“…Whole-genomic SNP analysis also revealed different population structures of two Acropora species at a small island in Okinawa Prefecture, Japan, despite the same reproductive mode. There was no detectable structure in A. digitifera , although two distinct genetic clades with little or no admixture were detected in A. tenuis , possibly representing the existence of two reproductively isolated cryptic species ( Zayasu et al 2021 ). Recent studies also show that genomic analyses could reveal the genetic basis of coral thermal tolerance and could facilitate accurate predictions of coral adaptation to future ocean warming (e.g.…”