An environmental DNA (eDNA) metabarcoding approach has been widely used for biodiversity monitoring of fishes, although it has rarely been applied to tropical and subtropical aquatic ecosystems, where species diversity is remarkably high. This study examined the extent to which species richness can be estimated in a small coral reef lagoon (1,500 × 900 m) near Okinawa Island, southern Japan, where the surrounding waters are likely to harbor more than 1,500 species of fish. During 2015–2017, a total of 16 capture‐based surveys were conducted to create a faunal list of fish species, followed by eDNA metabarcoding based on seawater samples taken from 11 sites in the lagoon on a day in May 2019. We also tested whether eDNA metabarcoding could detect differences between adjacent fish communities inhabiting the offshore reef edge and shore‐side seagrass beds within the lagoon. A total of 217 fish species were confirmed by the capture‐based samplings, while 291 fish species were detected by eDNA metabarcoding, identifying a total of 410 species distributed across 119 families and 193 genera. Of these 410 species, only 96 (24% of the total) were commonly identified by both methods, indicating that capture‐based surveys failed to collect a number of species detected by eDNA metabarcoding. Interestingly, two different approaches to estimate species richness based on eDNA data yielded values close to the 410 species, including one that suggested an additional three or more eDNA surveys from 11 sites (36 samples) would detect 90% of the 410 species. In addition, nonmetric multidimensional scaling for fish assemblages clearly distinguished between the fish communities of the offshore reef edge and those of the shore‐side seagrass beds. This study demonstrates that an eDNA metabarcoding approach is useful for estimating species richness and detection of habitat segregation even in ecosystems with remarkably high species diversity.
ACKNOWLEDGEMENTS 22 We thank K. Ueda and K. Sato for supporting this study. R. Nozu helped us perform the statistical 23 analysis. We also thank D. Barneche for kindly providing his compiled data with us for Figure 4.
Abstract
41An environmental DNA (eDNA) metabarcoding approach has been widely used for biodiversity 42 monitoring of fishes, although it has rarely been applied to tropical and subtropical aquatic 43 ecosystems, where species diversity is remarkably high. This study examined the extent to which 44 species richness can be estimated in a small coral reef lagoon (1500 × 900 m) near Okinawa Island, 45 southern Japan, where the surrounding waters are likely to harbor more than 1500 species of fish. 46 During 2015-2017, a total of 16 capture-based surveys were conducted to create a faunal list of fish 47 species, followed by eDNA metabarcoding based on seawater samples taken from 11 sites in the 48 lagoon on a day in May 2019. We also tested whether eDNA metabarcoding could detect 49 differences between adjacent fish communities inhabiting the offshore reef edge and shore-side 50 seagrass beds within the lagoon. A total of 217 fish species were confirmed by the capture-based 51 samplings, while 291 fish species were detected by eDNA metabarcoding, identifying a total of 410 52 species distributed across 119 families and 193 genera. Of these 410 species, only 96 (24% of the 53 total) were commonly identified by both methods, indicating that capture-based surveys failed to 54 collect a number of species detected by eDNA metabarcoding. Interestingly, two different 55 approaches to estimate species richness based on eDNA data yielded values close to the 410 56 species, including one that suggested an additional three or more eDNA surveys from 11 sites (36 57 samples) would detect 90% of the 410 species. In addition, non-metric multi-dimensional scaling 58 for fish assemblages clearly distinguished between the fish communities of the offshore reef edge 59 and those of the shore-side seagrass beds. 60 61 KEY WORDS 62
The Longman’s beaked whale (Indopacetus pacificus) is one of the rarest cetaceans worldwide. Since it was first described as its own species in 1926, they have been observed alive at sea on several occasions, and less than 20 strandings have been reported worldwide to date. Thus, basic information regarding this species, such as the maximum size of adult individuals or body length at birth, remains unknown. In this study, the external appearance and DNA analysis of a female Longman’s beaked whale stranded on Miyako Island, Okinawa, Japan, are reported. The external appearance of the specimen matched the features of the Longman’s beaked whale presented in previous studies. The mitochondrial DNA control-region sequences obtained from the specimen also matched the reference sequences of the species deposited in GenBank. Based on these features, the specimen was confirmed as a Longman’s beaked whale. The specimen was estimated to be neonate because of its body length (235 cm) and the clear several fetal folds observed on its body surface. To the best of our knowledge, this is the first report of a confirmed new born neonate of Longman’s beaked whale in the world.
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