Three cryptic lineages of Seriatopora hystrix found in Ryukyu Archipelago indistinguishable by appearance

A joint research group including Doctoral Student Kenji Takata (at the time of the research) of the Graduate School of Agricultural and Life Sciences at the University of Tokyo, Undergraduate Student Yuji Narita (at the time of the research) of the Faculty of Agriculture at the University of Miyazaki, Professor Nina Yasuda of the Graduate School of Agricultural and Life Sciences at the University of Tokyo, Professor Saki Harii of the Tropical Biosphere Research Center at the University of the Ryukyus and others from the Japan Fisheries Research and Education Agency, the University of Tokyo, and Tohoku University, analyzed the genomes of 389 Seriatopora hystrix individuals across shallow to deep waters in the Ryukyu Archipelago. The study revealed the existence of three cryptic lineages that appear identical externally but exhibit distinct degrees of genetic similarity across both vertical depths and horizontal distances. While deep-water zones serve as refuges for some shallow-water corals, this effect varies by lineage. The findings highlight the importance of protecting habitats based not only on cryptic lineage differences and a simple shallow-versus-deep dichotomy, but also by factoring in intermediate depth zones. The study was published in Molecular Ecology.

Coral reefs are vital ecosystems supporting high marine biodiversity, but shallow-water coral communities are heavily impacted by factors like rising sea temperatures. Consequently, the "deep reef refuge hypothesis (DRRH)" has been proposed, suggesting that mesophotic coral ecosystems (depths of 30 to 150 meters), where temperature fluctuations are relatively minor, act as refuges and larval sources for shallow-water corals. However, the validity of the DRRH has been reported to vary by region and species. In the Ryukyu Archipelago, it was necessary to verify the degree of genetic connectivity between deep and shallow reefs while differentiating between cryptic lineages that cannot be distinguished by sight.

The research group collected 389 S. hystrix individuals from shallow, intermediate, and deep zones at multiple sites across Okinawa and the Yaeyama Islands in the Ryukyu Archipelago, performing genome-wide SNP analysis via MIG-seq.

First, after excluding clonal colonies generated through asexual reproduction, the analysis revealed that at least three cryptic lineages (α, β, and γ) exist within the S. hystrix species complex. These lineages do not distribute exclusively within specific depths. Rather, they coexist at the same locations and within the same depth bands. This indicates that even though the colonies look like the same species, the different lineages are highly likely to be distinct species, meaning each lineage must be managed as a separate conservation unit.

Analyzing the genetic distance between individual colonies within each lineage showed that genetic differentiation increased with greater horizontal distances between sites and greater differences in depth.

Notably, a depth difference of 30 m exhibited a level of genetic differentiation equivalent to a horizontal separation of approximately 16 to 32 km between shallow-water populations.

However, the magnitude of this genetic differentiation varied by lineage. Some lineages maintained a relatively strong genetic connection between shallow and deep waters, while others recruited almost exclusively close to their parent colonies, showing weak genetic exchange between deep and shallow zones.

Furthermore, the presence or absence of an intermediate habitat (at depths around 20 m) bridging the gap between shallow and deep zones was crucial for maintaining genetic connectivity between deep and shallow coral habitats.

In lineages where intermediate-depth populations were confirmed, these populations were shown to potentially function like a "hub" connecting the deep and shallow zones. Conversely, in lineages where no intermediate-depth populations were found, there was virtually no genetic exchange between shallow and deep waters.

This study demonstrates that whether deep coral reefs can serve as a refuge for shallow corals depends on the dispersal characteristics of each cryptic lineage, which cannot be identified or distinguished by appearance alone, combined with the topographical, ecological, and genetic continuity linking shallow, intermediate, and deep zones.

Moving forward, when evaluating the sustainability of coral communities under climate change, it will be essential to establish meticulous conservation strategies for each lineage that include intermediate-depth habitats connecting shallow and deep waters, rather than viewing deep reefs alone as the sole target for preservation.

Journal Information
Publication: Molecular Ecology
Title: Illuminating Deep Reef Refugia: Horizontal and Vertical Genomic Connectivity of Seriatopora hystrix in the Ryukyu Islands, Japan
DOI: 10.1111/mec.70362