Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea

Abstract

Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions This multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region.

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“…Dongsha Atoll is the largest coral reef atoll in the northern South China Sea and serves as an important fish stock contributor and plays a role in sustaining connectivity for coral reef species in the region (Liu et al, 2021;Yu et al, 2022). However, this unique ecosystem is extremely vulnerable due to the impacts of climate change, and illegal and unregulated fishing (Liu et al, 2021). Recurring disturbances (e.g., typhoon damage, coral bleaching) combined with specific environmental conditions (e.g., shallow waters, low wave action, high nutrient load) can trigger G. divaricata to proliferate inside the Dongsha lagoon, resulting in persistent overgrowths that can last for several years (Nieder et al, 2019).…”

The Ira Moana Project: A Genetic Observatory for Aotearoa’s Marine Biodiversity

“…GEOME is an open-access database that persistently links genetic data stored in INSDC repositories to spatio-temporal and ecological metadata and provides tools to facilitate data upload as well as spatial querying and download of genetic data and associated metadata (using the geomedb R package). GEOME has enabled the programmatic re-creation of population genetic datasets and calculation of genetic diversity measures based on DNA sequences (Liggins and Arranz, 2018;Crandall et al, 2019a,b;Liu et al, 2021) and differs from other similar efforts to collate population genetic data (e.g., "MacroPopGen, " Lawrence et al, 2019) in that it is a dynamic resource that can be easily and continually updated through user contributions.…”