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Synchronous multispecific coral spawning generally occurs annually and forms an integral part of the coral life cycle. Apart from spawning times and species participation, however, much else remains unknown. Here, we applied environmental DNA (eDNA) metabarcoding to study two tropical reef sites of contrasting coral cover before, during and after coral spawning. Using coral‐ITS2 and vertebrate‐12S markers, we evaluated eDNA as an alternative monitoring tool by assessing its capabilities in detecting spawning species and tracking relative abundances of coral and fish eDNA. Over 3 years, elevated eDNA coral signals during the event (proportional read increase of up to five‐fold) were observed, detecting a total of 38 coral and 133 fish species with all but one of the coral species visually observed to be spawning. This is also the first demonstration that eDNA metabarcoding can be used to infer the diurnal partitioning of night‐ and day‐time spawning, spawning in coral species overlooked by visual surveys, and the associated changes in fish trophic structures as an indicator of spawning events. Our study paves the way for applied quantitative eDNA metabarcoding approaches to better study ephemeral and important biological events. [ABSTRACT FROM AUTHOR]

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef‐associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high‐throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non‐metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger‐sized non‐coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems. [ABSTRACT FROM AUTHOR]

The oceans are harsh environments where insects are not expected to thrive, yet a few skaters of the genus Halobates Eschscholtz, 1822 (Hemiptera: Heteroptera: Gerridae) have completely adapted to life on the open seas. There are five oceanic Halobates species that have well-established and distinct distributions, but little is known about their population dynamics and intraspecific genetic variation. Moreover, existing knowledge on most species has been largely based on limited sample sizes. We examined the phylogeographic patterns and inferred past population dynamics of three Halobates species (H. micans Eschscholtz, 1822, H. sobrinus White, 1883 and H. splendens Witlaczil, 1886) based on an unprecedented large number of specimens (73–199 individuals each) collected from the Eastern Tropical Pacific (ETP) Ocean. These species have distinct biogeographies, with H. sobrinus occurring mostly along coastal Mexico, H. micans in the ETP north of the equator, and H. splendens largely south of the equator in the cold tongue of water derived from the Peru (Humboldt) current. We did not find evidence for sub-population structure within each species over distances as far as 6000–7000 km. Populations of all three species were found to deviate from neutrality, with evidence of past population growth. Genetic diversity and haplotype genealogies varied between species, implying distinct evolutionary trajectories. Coalescent analyses using Bayesian skyline plots suggested that H. splendens underwent a population expansion ~ 1 Ma, whereas H. sobrinus and H. micans experienced demographic growth ~ 120 Ka to 100 Ka, respectively. The period of population expansion of H. splendens roughly corresponds to the establishment of cool, productive waters in the cold tongue starting ~ 1 Ma and reaching modern temperatures ~ 800 Ka. Population expansions of both H. micans and H. sobrinus north of the equator occurred mostly during the last interglacial period, characterized by increased frequency and dominance of El Niño conditions, and a relatively southerly position of the Intertropical Convergence Zone of high rainfall. Intensification of El Niño conditions between ~ 75 and 125 Ka may have produced a warmer, low wind and nutrient-depleted habitat favoring population growth for both H. micans and H. sobrinus. Key insights drawn from the results of this study, alongside future resolution of evolutionary relationships among Halobates species, will complete our understanding of how these remarkable insects conquered the high seas where no other insect could. [ABSTRACT FROM AUTHOR]

Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended. [ABSTRACT FROM AUTHOR]