Marine biodiversity and derived ecosystem services are critical to the healthy functioning of marine ecosystems, and to human economic and societal well-being. Thus, an understanding of marine biodiversity in different ecosystems is necessary for their conservation and management. Coral reefs in particular are noted for their high levels of biodiversity, and among the world’s coral reefs, the subtropical Ryukyu Islands (RYS; also known as the Nansei Islands) in Japan have been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of English language scientific literature in the Web of Science (WoS; 1995–2017) on six selected representative taxa spanning protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate a need to address ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), particularly sub-regions away from marine research stations. Second, we compared the numbers of English language scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAR), Great Barrier Reef (GBR), and the Red Sea (RES). As expected, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, research in the RYS on ‘marine protected areas’ and ‘herbivory’ was an order of magnitude lower than numbers in other regions. Additionally, while manuscript numbers on the RYS have increased from 1995 to 2016, the rate of increase (4.0 times) was seen to be lower than those in the CAR, RES, and GBR (4.6–8.4 times). Coral reefs in the RYS feature high levels of both endemism and anthropogenic threats, and subsequently they contain a concentration of some of the world’s most critically endangered marine species. To protect these threatened species and coral reef ecosystems, more data are needed to fill the research gaps identified in this study.

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Research on so-called "minor taxa" at mesophotic depths has lagged behind that of more commonly researched groups such as fish or hard corals. Exemplar taxa include species of the order Zoantharia, benthic colonial anemones that are cosmopolitan in distribution but understudied in many ecoregion and ecosystems. In this study, we examine the results of rare mesophotic to deep sea surveys (one rebreather, one remotely operated submersible (ROV) + net survey, two ROV surveys) from Japan and Israel. We examined the collected images and video data to provide a first estimate of Zoantharia diversity at mesophotic depths. Zoantharians were observed in all surveys, indicating their ubiquitous presence in mesophotic and deeper ecosystems. Additionally, specimens (n = 12) acquired via these surveys were phylogenetically analyzed with three DNA markers. Phylogenetic results showed the presence of undescribed species based on the uniqueness of acquired DNA sequences, including one specimen belonging to the family Abyssoanthidae, previously only reported from depths below 2000 m. Other specimens belong to groups that inhabit shallower and deeper depths (Antipathozoanthus, Epizoanthus, and Parazoanthidae). These results depart from surveys of mesophotic coral ecosystem fishes and crustaceans, which indicate affiliations almost exclusively with shallow genera and families. We hypothesize that mesophotic depths are an ecotone for zoantharian diversity, with links to both deeper and shallower ecosystem diversity. Future surveys in mesophotic depths should incorporate phylogenetic methods to better catalog so-called "minor taxa" (not only including Zoantharia) and enhance the scientific foundation for conserving the biodiversity of these threatened ecosystems.

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Species of the anthozoan order Zoantharia (=Zoanthidea) are common components of subtropical and tropical shallow water coral reefs. Despite a long history of research on their species diversity in the Caribbean, many regions within this sea remain underexamined. One such region is the Dutch Caribbean, including the islands of St. Eustatius, St. Maarten, Saba, Aruba, Bonaire, and Curaçao, as well as the Saba Bank, for which no definitive species list exists. Here, combining examinations of specimens housed in the Naturalis Biodiversity Center collection with new specimens and records from field expeditions, we provide a list of zoantharian species found within the Dutch Caribbean. Our results demonstrate the presence at least 16 described species, including the newly described Parazoanthus atlanticus, and the additional potential presence of up to four undescribed species. These records of new and undescribed species demonstrate that although the zoantharian research history of the Caribbean is long, further discoveries remain to be found. In light of biodiversity loss and increasing anthropogenic pressure on declining coral reefs, documenting the diversity of zoantharians and other coral reef species to provide baseline data takes on a new urgency.

Cnidarians are early‐diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re‐evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt‐genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt‐genomes of members of eight of nine zoantharian families. Although all examined mt‐genomes had the same gene order arrangement, there were variations among mt‐genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt‐DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt‐genome protein‐coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An “early” transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher‐level phylogeny and taxonomy of Zoantharia.