James Davis Reimer

• Ph.D.
• Professor at University of the Ryukyus

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...

Seamounts are biodiversity hotspots that face increasing threats from anthropogenic activities. Seamounts host diverse sessile suspension-feeding organisms such as sponges and anthozoans, which are crucial for seamount ecosystems as they construct three-dimensional habitats utilized by numerous other animals. Therefore, accurate identification of s...

Three genera of the family Onchidiidae, Peronia, Wallaconchis, and Onchidella, are known to inhabit intertidal coral reef environments in the Ryukyu Islands; however, there have been only limited studies on their diversity. This study conducted surveys around 11 islands and 40 intertidal areas of the Ryukyus, elucidating species diversity utilizing...

Potential range expansion of scleractinian corals in high-latitude reefs is critically dependent on the coral host-symbiont relationship that determines coral growth and survival. Although increases in coral cover have been observed at higher latitudes, the identities of habitat-building reef corals and their symbionts are underreported. Here, we e...

Here, we provide the first in situ observations of foraging habitats of Chaetodon daedalma, which is endemic to the subtropical north‐west Pacific. Overall, 62.4% of bites were from the substratum, 30.7% from scleractinian corals, 3.3% from crustose coralline algae, 2.1% from macroalgae, and 1.2% from hydroids. The range in the percentage of bites...

Previous studies investigating marine fish diversity in Cambodia’s coastal ecosystems focused on visual methods, concentrating on reporting ecologically and economically important indicator taxa. This study, however, presents the first comprehensive assessment of marine fish biodiversity along the coast of two regions in Cambodia using environmenta...

Ocean acidification (OA), driven by rising atmospheric CO2, presents a serious threat to marine biodiversity, especially within coral reef ecosystems. Natural analogue sites, such as the high-pCO2 seep at Iōtorishima Island in Japan, offer insights into future conditions. This study investigated the holobiont communities of Symbiodiniaceae and bact...

The symbiosis between clownfishes (or anemonefishes) and their host sea anemones ranks among the most recognizable animal interactions on the planet. Found on coral reef habitats across the Indian and Pacific Oceans, 28 recognized species of clownfishes adaptively radiated from a common ancestor to live obligately with only 10 nominal species of ho...

Symbiotic marine invertebrates can be small, hidden or difficult to find, hampering the understanding of their distribution and ecological roles. Haplosyllis anthogorgicola is a polychaete inhabiting the gorgonian Anthogorgia bocki, where it lives in high densities within the host’s coenenchyme and occupies burrows formed by host tissue near coral...

In shallow water zooxanthellate coral communities, large aggregations of benthic groups other than scleractinians have been occasionally noted, and sometimes linked with various disturbances. Here we report on a large aggregation of a corallimorpharian, Rhodactis sp., at a site off Himeshima Island, Kochi, Japan from surveys in July 2023 and August...

Many colonial anthozoans are ecosystem engineers and contribute to creating intricate benthic communities that often harbor high levels of marine biodiversity. Here, we report on an extraordinarily large antipatharian colony observed on the West Mariana Ridge in the Northwest Pacific. Based on colony form, morphological analyses, and DNA barcoding...

the complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length and include 14 protein-coding genes (PCGs), two ribosomal RNA genes and one tRNA. to date, seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses an...

We report here on a large Heliopora reef at depths of 2 to 10 m off the east coast of Okinawajima Island, Japan. The reef was approximately 4610 m 2 in area, and was made of up "Heliopora sp. group sp. 2" sensu Taninaka et al. (2021). This reef is almost twice as large as a previously reported Heliopora reef in Oura Bay, also on the east coast of O...

Shallow water coral reefs in many parts of the world are experiencing phase shifts due to various disturbances, resulting in increases in the abundance of algal assemblages and non-scleractinian taxa, including soft corals (Octocorallia). However, the effects of these changes on reef-associated macrofauna are still not fully understood. In this stu...

Outbreaks of the cyanobacteriosponge Terpios hoshinota are one of the many issues contributing to coral reef decline in the Indo-Pacific. This species occasionally undergoes local outbreaks, becoming an aggressive space competitor and overgrowing and killing zooxanthellate corals. Large outbreaks have been observed in Taiwan and the Ryukyu Islands...

The KM24-03 (Leg 2) deep-sea research cruise (April 27-May 12, 2024) marked the first research expedition of the "Deep-Sea Archaic Refugia in Karst (D-ARK)" project (https://www.jamstec.go.jp/dark/e/) led by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). One of the objectives was to document the diversity of marine invertebrate...

Zoantharia is an order among the Hexacorallia (Anthozoa: Cnidaria), and includes at least 300 species. Previously reported genomes from scleractinian corals and actiniarian sea anemones have illuminated part of the hexacorallian diversification. However, little is known about zoantharian genomes and the early evolution of hexacorals. To explore gen...

Extensive global habitat degradation and the climate crisis are tipping the biosphere toward a “sixth” mass extinction and marine communities will not be spared from this catastrophic loss of biodiversity. The resilience of marine communities following large-scale disturbances or extinction events is mediated by the life-history traits of species a...

The zoantharian genus Umimayanthus consists largely of species that live in obligate symbioses with sponges. Although zoantharians have often been overlooked in field collecting campaigns and in research, sponges are usually well-collected, and many natural history museums harbor numerous sponge specimens. Thus, these sponge collections may also in...

Three genera of the family Onchidiidae, Peronia , Wallaconchis and Onchidella , are known to inhabit intertidal coral reef environments in the Ryukyu Islands, however, there have been only limited studies on their diversity. This study conducted surveys around 11 islands and 40 intertidal areas of the Ryukyus, elucidating species diversity utilizin...

A new species of the genus Nesometra Virgili, Poliseno, Fujita, Pratama, Fernández-Silva, and Reimer, 2023 is described based on the specimens collected from the Amami Islands and Ogasawara Islands, Japan and Cunningham Island, Australia. Nesometra integra n. sp. is distinguished from its single congener, N. sesokonis (Obuchi, Kogo, and Fujita, 200...

Corals are early-branching animals highly reliant on diverse symbionts for growth and reproduction. Most coral groups, including stony corals and hydrocorals, exhibit deep genetic divergence between the Atlantic (ATO) and Indo-Pacific (IPO) oceans, hampering their direct comparison. Although sibling zoanthid species (Hexacorallia: Zoantharia) devia...

Background Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in l...

The complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length, and include 14 protein coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses an...

The Fourth Global Coral Bleaching Event was officially confirmed by the National Oceanic and Atmospheric Administration (NOAA) and International Coral Reef Initiative (ICRI) on April 15, 2024, with press releases and a coordinated call to arms to address the impacts of climate change (https://icriforum.org/4gbe/). As the International Coral Reef So...

The recent rise in ocean temperatures, accompanied by other environmental changes, has notably increased the occurrence and spread of diseases in Octocorallia, many species of which are integral to shallow tropical and subtropical coral reef ecosystems. This study focuses on the understanding of these diseases, which has been largely limited to sym...

Global warming causes functional shifts and reorganisation in marine communities through range shifts to high-latitude reefs and cnidarian bleaching mortality in the tropics. Such changes threaten the integrity and structure of marine communities, especially as foundational and associated species are reduced or lost. However, comparatively little i...

The integrated approach of molecular phylogenetic and morphological analyses has revolutionized the systematics and our understanding of the evolutionary relationships of marine taxa. One such group is the hexacorallian order Zoantharia Rafinesque, 1815. The monotypic genus Thoracactis Gravier, 1918 has been little investigated since its placement...

Anthozoans are ecosystem engineers and contribute to creating intricate benthic communities that often harbor high levels of marine biodiversity. Here, we report on an extraordinarily large antipatharian colony observed on the Ritto Seamount in the Northwest Pacific. Based on colony form and DNA barcoding results, we identified the colony as Leiopa...

We report the first documentation of in situ release of reproductive materials by female colonies of a soft coral, in this case Sclerophytum cf. heterospiculatum, from the subtropical island of Okinawa, Japan. Spawn release was observed on the nights of September 2 and 3, 2023 (two and three nights after the full moon). This observation widens our...

The association between two hydrozoans, Stylaster sp. and Millepora spp., has been described as a case of pseudo-auto-epizoism, and has only been reported from the Caribbean region of the Atlantic Ocean. Here, we report on the occurrence of this association in the Pacific Ocean on coral reefs around Iriomote-jima Island, Japan, suggesting the assoc...

The Ogasawara Islands are a highly isolated oceanic archipelago in the Pacific Ocean that possess unique faunal and floral biodiversity with a high level of endemism. As historically more focus has been put on the terrestrial realm in examining diversification and evolutionary processes on oceanic islands, publicly accessible and spatially resolved...

The mutualism between clownfishes (or anemonefishes) and their giant host sea anemones are among the most immediately recognizable animal interactions on the planet and have attracted a great deal of popular and scientific attention. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes-...

This study evaluated the distribution and abundance of marine litter on 30 beaches around Okinawa Island, Japan. Beach quality indices and multivariate statistical analyses were used to assess the quality of the beaches and their pollution patterns. A total of 11,626 items weighing 513.49 kg with an average density of 0.13 ± 0.10 items/m2 were coll...

Aims Transformation of species and functional composition on subtropical reefs are ongoing due to poleward range shifts of some tropical species, with largely unknown consequences to ecosystem functioning. Trait‐based approaches are powerful tools to quantify such changes. Here, we evaluated changes in the trait composition of coral‐associated fish...

The recent rise in ocean temperatures, accompanied by other environmental changes, has notably increased the occurrence and spread of diseases in Octocorallia, of which many species are integral to shallow tropical and subtropical coral reef ecosystems. This study focuses on the understanding of these diseases, which has been largely limited to sym...

This study focuses on the analyses of the gastral cavity contents of two species of Ceriantharia, namely Isarachnanthus nocturnus Hartog, 1977, collected in São Sebastião, Brazil, and Pachycerianthus magnus Nakamoto, 1919, collected from two points along the coast of Okinawa Island, Japan. Both morphological (light microscopy) and metagenomic (whol...

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...

The symbiosis between giant sea anemones, photosynthetic algae of the family Symbiodiniaceae, and anemonefish is an iconic example of a mutualistic “menage à 3” ¹ . Patterns of associations among 28 species of anemonefish and 10 species of giant sea anemone hosts are complex: Some anemonefish species are highly specialized to inhabit only one speci...

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...

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 funct...

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...