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

It is essential to consider genetic composition for both conventional
coral restoration management and for expanding new interventions to
counter the significant global decline in living corals. Population
genetic structure at fine spatial scale should be carefully evaluated
before implementing strategies to achieve self-sustaining ecosystems via
coral restoration. Here, we investigated the population genetic structure
of two acroporid species at Kume Island, Okinawa, Japan. 140 colonies of
Acropora digitifera from 7 study sites, and 81 colonies of Acropora tenuis
from 6 sites were collected. We obtained 384 SNP loci for A. digitifera
and 470 SNPs for A. tenuis using a comparatively economical technique,
Multiplexed ISSR Genotyping by sequencing (MIG-seq). 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, we found different population
structure 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 focal species for active restoration in terms of genetic
differentiation at this island. On the other hand, A. tenuis unexpectedly
included two distinct clades with no or little admixture within a small
spatial study area, possibly representing two reproductively isolated
cryptic species. Thus, when using A. tenuis, it would be prudent to avoid
disturbing genetic composition of wild populations until this question is
answered.

无论是传统珊瑚礁恢复管理，还是拓展新型干预手段以应对全球活珊瑚的显著衰退，遗传组成的考量都至关重要。在实施通过珊瑚恢复实现自我维持生态系统的策略前，需仔细评估精细空间尺度下的种群遗传结构。本文研究了日本冲绳久米岛两种鹿角珊瑚科（acroporid）物种的种群遗传结构。我们收集了来自7个研究点的140个指状鹿角珊瑚（Acropora digitifera）群体，以及6个研究点的81个柔枝鹿角珊瑚（Acropora tenuis）群体。采用相对经济的多重ISSR测序基因分型技术（Multiplexed ISSR Genotyping by sequencing，MIG-seq），我们获得了指状鹿角珊瑚的384个单核苷酸多态性（SNP）位点，以及柔枝鹿角珊瑚的470个SNP位点。两种鹿角珊瑚科物种在所有SNP位点的观测杂合度均显著低于期望杂合度，这表明其遗传多样性不足，可能由过去大规模珊瑚白化所致。尽管两种物种均为广布产卵者（broadcast spawners），但它们的种群结构存在差异：指状鹿角珊瑚未表现出可检测的种群结构，而柔枝鹿角珊瑚则存在两个明显分支。久米岛指状鹿角珊瑚的遗传均一性表明，就该岛的遗传分化而言，该物种可作为主动恢复的核心物种。另一方面，在狭小的空间研究区域内，柔枝鹿角珊瑚意外地包含两个几乎无基因交流的明显分支，这可能代表两个生殖隔离的隐存种。因此，在该问题得到解答前，使用柔枝鹿角珊瑚进行恢复时，需谨慎避免干扰野生种群的遗传组成。