James Davis Reimer

University of the Ryukyus · Department of Chemistry, Biology, and Marine Science

Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. the characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine...

Identifying how past environmental conditions shaped the evolution of corals and their skeletal traits provides a framework for predicting their persistence and that of their non-calcifying relatives under impending global warming and ocean acidification. Here we show that ocean geochemistry, particularly aragonite–calcite seas, drives patterns of...

Hexactinellid sponges are important members of deep-sea benthic ecosystems because they provide available hard substrate habitats for filter-feeding invertebrates. However, symbioses between hexactinellid sponges and their symbionts are poorly known. Zoantharians associated with hexactinellid sponges have been reported widely from deep-sea marine e...

Whilst natural analogues for future ocean conditions such as CO2 seeps and enclosed lagoons in coral reef regions have received much recent research attention, most efforts in such locations have focused on the effects of prolonged high CO2 levels on scleractinian corals and fishes. Here, we demonstrate that the three species of zooxanthellate zoan...

Nanipora Miyazaki & Reimer, 2015 is a recently described monotypic octocoral genus belonging to the family Helioporidae (class Octocorallia). Nanipora kamurai Miyazaki & Reimer, 2015 was formally described from shallow coral reefs around Zamami Island, within Kerama-shoto National Park, in Okinawa Prefecture, southern Japan. To date, Nanipora has b...

Ceriantharia is an anthozoan clade with a relatively small number of species (~55 extant species) and a relevant evolutionary profile. Because of its alternative phylogenetic affinities, it would be related to ancestral traits and early trends on molecular divergence on main cnidarian clades. To establish a genomic database and related knowledge on...

Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element d...

Context Global and local stressors can drive phase shifts from zooxanthellate scleractinian coral communities to macroalgae-dominated ecosystems. However, our understanding of altered ecosystem functioning, productivity and stability remains limited as pre-shift data are typically lacking for degraded coral-reef sites. Aims Here, we assessed functi...

The persistent exposure of coral assemblages to more variable abiotic regimes is assumed to augment their resilience to future climatic variability. Yet, while the determinants of coral population resilience across species remain unknown, we are unable to predict the winners and losers across reef ecosystems exposed to increasingly variable conditi...

Diseases are a growing global threat to scleractinian corals. This study used a relatively inexpensive commercial drone flown simultaneously along with reef walking/snorkeling to confirm the presence of cyanobacterial Black Band Disease (BBD) on a reef in subtropical Okinawa, Japan. At the surveyed reef, the scleractinian corals included encrusting...

High-latitude areas have been hypothesized as potential refugia in the future for those corals which can range-shift across the latitudes (from tropical to high or low latitudes). However, whether high latitude will be the future hope for corals either through succession (proliferation of regionally or locally endemic species) or emergence (range-s...

Sexual reproduction data are important to understand how organisms can replenish their populations and proliferate on coral reefs. Despite the importance of such data, the reproductive characteristics of most soft coral species are still unknown. Here, we examined the reproductive strategies of a species from the often-dominant genus Sclerophytum i...

Nanipora Miyazaki and Reimer, 2015 is a recently described monotypic octocoral genus belonging to the family Helioporidae (class Octocorallia). Nanipora kamurai Miyazaki & Reimer, 2015 was formally described from shallow coral reefs around Zamami Island, within Kerama-shoto National Park, in Okinawa, southern Japan. To date, Nanipora has been repor...

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with c...

The recent introduction of ChatGPT by OpenAI has broadly introduced artificially intelligent (AI) tools as writing aids to the general public. We examined the limits of available detection tools in identifying writing that was fully aided by AI. Short essays (fewer than 400 words) were written by humans in two languages (English, Malay) or were pro...

Dorometra Clark, 1917 Clark, A. H. (1917). A revision of the crinoid family Antedonidae, with the diagnoses of nine new genera. Journal of the Washington Academy of Sciences, 7, 127–131. [Google Scholar] (Comatulida: Antedonidae) is an Indo-Pacific genus of small-sized cryptic feather stars currently comprising nine species. The monophyly of this c...

Temperate reefs are at the forefront of warming-induced community alterations resulting from poleward range shifts. This tropicalisation is exemplified and amplified by tropical species’ invasions of temperate herbivory functions. However, whether other temperate ecosystem functions are similarly invaded by tropical species, and by what drivers, re...

This study summarises the status of microplastic research in marine and freshwater specimens in natural museum collections around the world. Abundances, distributions, and types of microplastics in the archived collections are discussed. Museum collections can fill knowledge gaps on evolution of microplastic pollution before and during the Plastice...

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to...

We present the complete genome sequence of Dorometra sesokonis. Genome sequencing was performed on genetic material from a single wild-collected individual. The sequence reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank.

We present the complete genome sequences of 13 species of the zoantharian suborder Brachycnemina (Haddon, and Shackleton, 1891; Poliseno et al., 2020). Genome sequencing was performed on genetic material from single wild-collected individuals. For each species the sequence reads were assembled using a de novo method followed by a finishing step. Th...

We present the complete genome sequences of 7 species of the zoantharian genus Epizoanthus . Illumina sequencing was performed on genetic material from single wild-collected individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank.

Associations between different taxa constitute critical data to recognize ecological symbioses. Acoela flatworms of the genus Waminoa are an overlooked but often present group in coral reef ecosystems. More than 97% of the reports on Waminoa individuals until now have found them on scleractinian coral species, and the relationships between Waminoa...

Symbioses play important roles in forming the structural and distributional patterns of marine diversity. Understanding how interspecies interactions through symbioses contribute to biodiversity is an essential topic. Host switching has been considered as one of the main drivers of diversification in symbiotic systems. However, its process and patt...

Three species of nannosquillid mantis shrimps, including two new species, Acanthosquilla ryukyuensis n. sp. and Acanthosquilla shoheii n. sp., are described based on specimens collected from the Ryukyu Islands, Japan. The two new species resemble A. derijardi Manning, 1970, but can be distinguished from A. derijardi by the following features: 1) ro...

Family Xanthidae comprises 15 subfamilies and over 600 accepted species; they are represented well in the foreshore marine environments. Members of family Xanthidae are multi-colored crabs, usually inhabiting rocky coasts, coral reefs, and mud flats, all of which are well represented along the Egyptian coast of the Red Sea. Here, we utilized cytoch...

Photograph records of four holothurian individuals upon which colonial ascidians were associated epizoically are reported from the waters around Akajima Island, Kerama Islands, Okinawa, Japan. Although holothurians are known to be hosts of many organisms, these new observations add a new perspective to understanding the ecological role of holothuri...

The term Marine Animal Forest (MAF) was first described by Alfred Russel Wallace in his book “The Malay Archipelago” in 1869. The term was much later re-introduced and various descriptions of MAFs were presented in great detail as part of a book series. The international research and conservation communities have advocated for the future protection...

Anemonefish are iconic examples of marine fishes living in mutualistic symbiosis with sea anemones. In a given sea anemone, the anemonefishes have a stereotyped social organization with a dominant female, a semi-dominant male, and several juveniles. A strict size-based hierarchy governs the social interactions within these colonies, with each indiv...

Sea cucumbers are important ecological engineers in marine ecosystems. However, the fishery demand of some species, especially large-epifaunal and commercially used (LEC) sea cucumbers, has risen drastically, resulting in serious depletion of local populations for many species. Despite this problem, basic ecological data on sea cucumbers, such as p...

Colour patterns in fish are often used as an important medium for communication. Anemonefish, characterized by specific patterns of white bars, inhabit host anemones and defend the area around an anemone as their territory. The host anemone is used not only by the anemonefish, but also by other fish species that use anemones as temporary shelters....

Octocorals possess sclerites, small elements comprised of calcium carbonate (CaCO 3 ) that are important diagnostic characters in octocoral taxonomy. Among octocorals, sea pens comprise a unique order (Pennatulacea) that live in a wide range of depths. Habitat depth is considered to be important in the diversification of octocoral species, but a la...

Understanding species-specific resource requirements is paramount in managing and protecting biodiversity in a world where environmental quality is in decline. Dietary data can inform predator–prey relationships and how changes in prey availability impact different species. However, for many coral reef fishes, prey and predatory events can be diffi...

We report the presence of the coral-killing sponge species Chalinula nematifera (de Laubenfels, 1954) in southern Japan via photographic records and specimens. The species appears to be a substrate generalist on scleractinians and occasionally octocorals, and is found across a wide variety of depths (0 to 24 m), as has been recently reported for th...

Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long‐term population performance, here we illustrate that short‐term (i.e. transient) demographic characteristics, including measures of...

Among family Zoanthidae (Anthozoa: Hexacorallia: Zoantharia), Zoanthus and Isaurus are widespread benthos on coral reefs, but the reproductive biology of both genera is generally unknown. Accordingly, sexual reproduction of two Zoanthidae species in Japan, Zoanthus kuroshio in Okinawa, and Isaurus tuberculatus in Okinawa and Kochi, was investigated...

Savalia savaglia is an Atlantic-Mediterranean zoantharian species with a patchy geographic and bathymetric distribution. Due to its longevity, S. savaglia may form large-sized colonies which play a crucial role in the ecosystem as habitat formers. Despite its ecological importance, little is known about the population structure and intraspecific ge...

Species of the genus Peronia Fleming, 1822, are air-breathing onchidiid sea slugs that inhabit intertidal reef flats of temperate to tropical zones. In the Ryukyu Islands of southern subtropical Japan, Peronia species are a traditional food source for local people. To date, there have been three species recorded around Okinawajima Island; P. verruc...

Within microeukaryotes, genetic and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians...

Scleractinian corals provide habitats for a broad variety of cryptofauna, which in turn may contribute to the overall functioning of coral symbiomes. Among these invertebrates, hydrozoans belonging to the genus Zanclea represent an increasingly known and ecologically important group of coral symbionts. In this study, we analysed 321 Zanclea colonie...

The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian...

There have been few detailed studies on the associations between cnidarians and gastropod mollusks. Several hypotheses have been suggested to explain the origins of these symbioses. However, respective benefits for gastropod mollusks and cnidarians have generally not been well examined, as there are many understudied cnidarian taxa associated with...

Tropicalization is rapidly restructuring subtropical marine communities. A key driver for tropicalization is changes in herbivory pressure that are linked with degrading ecosystem stability. Consequently, subtropical algal beds are being displaced by climate-mediated colonisation of coral communities. This process is thought to be aided by the elev...

Ocean warming is increasing the incidence, scale, and severity of global-scale coral bleaching and mortality, culminating in the third global coral bleaching event that occurred during record marine heatwaves of 2014-2017. While local effects of these events have been widely reported, the global implications remain unknown. Analysis of 15,066 reef...

Urbanized coral reefs experience anthropogenic disturbances caused by coastal development, pollution, and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habit...

The coral reefs of the Coral Triangle and nearby marine regions are the most biodiverse marine ecosystems in the world, providing ecosystem services to hundreds of millions of people. However, like coral reefs in other regions, these ecosystems are in decline due to a myriad of anthropogenically-induced stressors. To mitigate this decline, active c...

The taxonomy of species of Bivesicula Yamaguti, 1934 is analysed for samples from holocentrid, muraenid and serranid fishes from Japan, Ningaloo Reef (Western Australia), the Great Barrier Reef (Queensland), New Caledonia and French Polynesia. Analysis of three genetic markers ( cox 1 mtDNA, ITS2 and 28S rDNA) identifies three strongly supported cl...

Marine community datasets are key to the effective management and conservation of marine ecosystems, including coral reefs, which are increasingly threatened by a myriad of stressors. Although community information exists for many comparatively well-studied taxa, other common groups remain to be examined for even such basic information. In this stu...

Species identities of Goniobranchus nudibranchs with white bodies and various marginal bands have long been problematic. In this study, specimens of these Goniobranchus nudibranchs from the Philippines, Peninsular Malaysia, Japan, Papua New Guinea, and Madagascar were analyzed and molecular data were obtained in order to re-examine the relationship...

The Indo-Pacific zooxanthellate scleractinian coral genus Montipora is the host of many coral diseases. Among these are cyanobacterial Black Band Disease (BBD) and Skeletal Growth Anomalies (GAs), but in general data on both diseases are lacking from many regions of the Indo-Pacific, including from Okinawa, southern Japan. In this study, we collect...

During recent ecological surveys of Haemida Reef on Iriomotejima Island in the

The recently erected macrocnemic family Hydrozoanthidae comprises relatively few species recorded from tropical and subtropical regions. In the Atlantic Ocean, this family has been reported only from three locations: the Caribbean Sea, the Argentine continental shelf and the Cape Verde Islands. Based on a study of colonies collected during scuba di...

Shoreline armouring has progressively affected the coastal landscapes of countries all over the world, and armouring construction will increase in coming years as a consequence of climate change. Armouring has the potential to affect coastal environments and induce changes in the abundance and diversity of marine communities, and its effects might...

Substrate surface area and fractal complexity have been reported to influence the abundance and diversity of mobile cryptic animal communities. Surfaces with higher fractal dimensions not only offer additional space for colonization, but bias space availability toward smaller size ranges, increasing the number of available niches. Conversely, small...

The current exposure of species assemblages to high environmental variability may grant them resilience to future increases in climatic variability. In globally threatened coral reef ecosystems, management seeks to protect resilient reefs within variable environments. Yet, our lack of understanding for the determinants of coral population performan...

Terpios hoshinota is an aggressive, space‐competing sponge that kills various stony corals. Outbreaks of this species have led to intense damage to coral reefs in many locations. Here, the first large‐scale 16S rRNA gene survey across three oceans revealed that bacteria related to the taxa Prochloron, Endozoicomonas, SAR116, Ruegeria, and unclassif...

Hexactinellid sponges are important members of deep-sea benthic ecosystems because they provide available hard substrate habitats for filter-feeding invertebrates. However, symbioses between hexactinellid sponges and their symbionts are poorly known. Zoantharians associated with hexactinellid sponges have been reported widely from deep-sea marine e...

Recently, sea cucumbers (Echinodermata: Holothuroidea) have been over-exploited in many areas of the world, including in the Ryukyu Islands, southern Japan, due to increases in their economic importance. Nevertheless, management and protection of sea cucumbers are insufficient worldwide. The black sea cucumber Holothuria (Halodeima) atra Jaeger, 18...

Ankistromeces Nolan & Cribb, 2004 and Phthinomita Nolan & Cribb, 2006 are sister genera of threadlike blood flukes (Trematoda: Aporocotylidae) infecting teleost fishes of the tropical Indo-west Pacific. Here, we report new collections of these genera from Australia, Indonesia, and Japan. A new species of Ankistromeces, Ankistromeces kawamurai n. sp...

Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 million years ago, vetigastropods were the...

The mutualistic relationships between anemonefish (Amphiprion; Pomacentridae) and host sea anemones are well known, but host anemones are also used as shelter by damselfish (Pomacentridae), wrasses (Labridae) and cardinalfish (Apogonidae). The threespot dascyllus Dascyllus trimaculatus (Pomacentridae) is known to live on or near host anemones in th...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.