Biology subjects

Reimer, J. D.

Publications and source records attributed to Reimer, J. D..

14 recordsLinked to original sources

bioRxiv2026

One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex

Defining what a species is remains one of the biggest questions in biology and directly challenges species delimitation in species complexes. The wide-spread Clarks' anemonefish Amphiprion clarkii has the widest range of all anemonefishes, from the Indian Ocean to the Central Pacific. However, the taxonomy of this species has been confused since its initial description due to its great variation in morphology and pigmentation even within the same locality. Here, we combined whole genome re-sequencing data from 166 individuals spanning most of the distribution of A. clarkii, including remote islands such as Ogasawara and Guam in the northwestern Pacific, and also including three individuals of the closely related A. tricinctus from the Marshall Islands. Our population genomic analyses reveal an unexpected level of divergence, with five deeply separated lineages corresponding to the Indian Ocean, Central Indo-Pacific, Melanesia, and the isolated population of Ogasawara. The fifth lineage comprises A. clarkii from Guam and A. tricinctus, revealing that A. tricinctus is phylogenetically nested within A. clarkii, challenging its current taxonomic status. The most divergent lineage, Melanesia, is genetically more distant from other A. clarkii lineages than several recognised species pairs within the Amphiprion genus, yet demographic modelling shows ongoing gene flow between all lineages. Together, our results highlight a hidden diversity and stress the necessity of an integrative taxonomic revision of the A. clarkii species complex.

evolutionary biology↗

bioRxiv2026

Atlantic and Indo-Pacific separation in Palythoa sibling species: phylogenomic analyses using ultraconserved elements

The delineation of closely related species remains a persistent challenge in Zoantharia, where morphological plasticity and limited genetic differentiation complicate taxonomy. In this study, we investigated the phylogenetic relationship between the widely distributed sibling taxa Palythoa tuberculosa (Indo-Pacific) and Palythoa caribaeorum (Atlantic) using ultraconserved elements (UCEs) recovered from genome skimming. A dataset comprising 116 loci (35,699 bp) across 37 specimens from Brazil, the Red Sea, Okinawa, and New Caledonia was analysed using both concatenated maximum-likelihood and coalescent-based approaches. Phylogenetic reconstructions did not recover monophyletic relationships corresponding to either species or geographic origin, instead revealing intermixed lineages across the Indo-Pacific and Atlantic regions. Concordance factor analyses indicated low gene concordance and moderate site concordance, suggesting pervasive gene tree discordance rather than a lack of phylogenetic signal. These patterns are consistent with previous studies based on mitochondrial, nuclear, and reduced-representation datasets, indicating that increased marker resolution does not resolve species boundaries within this complex. The observed lack of differentiation may reflect ongoing or recent connectivity among populations, potentially facilitated by long-distance dispersal promoted by anthropogenic rafting or historical range expansion, biological invasion, or biological processes such as incomplete lineage sorting. The results support the hypothesis that P. tuberculosa and P. caribaeorum represent a species complex or a case of incipient speciation rather than fully distinct evolutionary lineages. These findings indicate that genome-scale data alone may be insufficient to resolve very recent divergences, supporting the need for integrative approaches to resolve complicated species boundaries in zoantharians.

evolutionary biology↗

bioRxiv2026

Genomic insights into polyketide toxin synthesis and algal symbiosis using high-quality genome sequences of the early divergent hexacorallian genus Palythoa (Cnidaria, Zoantharia)

Palytoxin, first isolated from Palythoa toxica, is among the most potent marine toxins known. Despite decades of biochemical investigation, genetic bases underlying its potential biosynthesis in Palythoa remain unresolved. Here we present four high-quality genome assemblies of Palythoa species, including Palythoa cf. toxica, and integrate these with a chromosome-scale genome assembly of P. caribaeorum. Performing comparative genomic analyses, we screened for candidate genes potentially involved in palytoxin biosynthesis and examined patterns of genome evolution. Unexpectedly, we identified only two classes of ketosynthase (KS) domain-containing genes in Palythoa: fatty acid synthases (FAS) and bacterial-like polyketide synthases (PKSs). Contrasting other anthozoans, animal FAS-like PKS (AFPK) genes common to all Palythoa species were not detected. We found no evidence for lineage-specific expansion of PKS genes unique to Palythoa, suggesting that if palytoxin/palytoxin-like molecule biosynthesis is host-encoded, it may involve functional modification or co-opting pre-existing FAS and/or bacterial-like PKS pathways. Comparative analyses revealed expansions of gene families associated with transport and binding functions in Palythoa, potentially reflecting molecular adaptations linked to their sand-incorporating body structure. We identified TPT1 and CLEC4A as rapidly evolving genes in multiple Palythoa species, consistent with possible roles in growth regulation and host-microbe interactions. Additionally, comparison between azooxanthellate and zooxanthellate species revealed mutations within conserved protein domains of LePin, which has been implicated in cnidarian endosymbiosis, suggesting lineage-specific modifications associated with symbiotic state. This study establishes a foundation for zoantharian genomic research, provides insights into lineage-specific genomic signatures, and advances molecular and evolutionary biological knowledge of this ecologically important group.

genomics↗

bioRxiv2024

Shifts in Coral Reef Holobiont Communities in the High-CO2 Marine Environment of Iotorishima Island

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 I[o]torishima Island in Japan, offer insights into future conditions. This study investigated the holobiont communities of Symbiodiniaceae and bacteria in the zoantharian Palythoa tuberculosa at I[o]torishima and compared them to specimens from control sites in Okinawa and Hawaii. Using amplicon sequencing of the dinoflagellate internal transcribed spacer 2 (ITS2) region of ribosomal DNA and microbial 16S rRNA gene, we detected significant shifts in both Symbiodiniaceae and bacterial communities under high-pCO2 conditions at I[o]torishima. Specifically, P. tuberculosa at the seep site had reduced Symbiodiniaceae diversity, predominatly featuring Cladocopium C1 and C3 types. Additionally, its bacterial communities showed lower richness with distinct taxonomic profiles, including increased levels of Mollicutes and Vibrio spp. These results highlight the potentially adverse effects of OA on hexacoral holobionts and emphasize the need for detailed, high-resolution studies across various holobiont species and geographic locations. The shifts observed specifically in Symbiodiniaceae and bacterial communities at the I[o]torishima Seep suggest that holobionts may exhibit plasticity in response to environmental stress, which has implications for resilience and adaptation of zoantharians and other reef organisms amid climate change. This research provides crucial baseline data for predicting future coral reef compositions in an OA-affected world.

microbiology↗

bioRxiv2024

Nemo knows: clownfishes differentiate cryptic host species across fine and broad geographic scales and reveal a potential adaptive radiation in the clownfish-hosting sea anemones.

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 host sea anemones. Are the host sea anemones truly less diverse than clownfishes? Did the symbiosis with clownfishes trigger a reciprocal adaptive radiation in sea anemones, or minimally, a co-evolutionary response to the mutualism? To address these questions, we combined fine- and broad-scale biogeographic sampling with multiple independent genomic datasets for the bubble-tip sea anemone, Entacmaea quadricolor--the most common clownfish host anemone throughout the Indo-West Pacific. Fine-scale sampling and restriction site associated DNA sequencing (RADseq) throughout the Japanese Archipelago revealed three highly divergent cryptic species: two of which co-occur throughout the Ryukyu Islands and can be differentiated by the clownfish species they host. Remarkably, broader biogeographic sampling and bait-capture sequencing reveals that this pattern is not simply the result of local ecological processes unique to Japan, but part of a deeper evolutionary signal where some species of E. quadricolor serve as host to the generalist clownfish species Amphiprion clarkii and others serve as host to the specialist clownfish A. frenatus. In total, we delimit at least five cryptic species in E. quadricolor that have diversified within the last five million years. The rapid diversification of E. quadricolor combined with functional ecological and phenotypic differentiation supports the hypothesis that this may represent an adaptive radiation in response to mutualism with clownfishes. Our data indicate that clownfishes are not merely settling in locally available hosts but recruiting to specialized host lineages with which they have co-evolved. These findings have important implications for understanding how the clownfish-sea anemone symbiosis has evolved and will shape future research agendas on this iconic model system.

evolutionary biology↗

bioRxiv2024

Coral microbiomes from the Atlantic and Indo-Pacific oceans have the same alpha diversity but different composition

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) deviate from this pattern, their symbioses have so far only been studied on local scales. Here, we examined the microbiomes of Palythoa caribaeorum from the ATO and P. tuberculosa from the IPO. Our extensive geographical sampling and metabarcoding revealed that Palythoa microbiomes have similar alpha diversity in both oceans. The primary exceptions are the symbiodiniacean Cladocopium and Chlamydiae bacteria, which mirror the global diversity patterns of corals. Despite distinct overall microbial compositions between oceans, some regions shared remarkably similar communities, hinting at the importance of both symbiont phylogeny and function. Finally, we explore the shift from commensal/mutualistic microbes to opportunistic pathogens, crucial amid the ongoing environmental changes.

microbiology↗

bioRxiv2024

New mitochondrial gene order arrangements and evolutionary implications in the subclass Octocorallia

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 and evolutionary reconstructions of mitochondrial genome evolution within the whole subclass Octocorallia have been often overlooked. Here we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from seven to twelve, and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT- and GC-skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, and that the mitochondrial genome evolution in the subclass is discontinuous, with rearranged gene orders restricted only to some regions of the tree. We believe that different rearrangement events arose independently and most likely that new gene orders, instead of being derived from other rearranged orders, came from the ancestral and most common gene order. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa.

genomics↗

bioRxiv2024

Phylogenomics reveals coincident divergence between giant host sea anemones and the clownfish adaptive radiation.

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 [1-5]. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes-- a charismatic group of 28 described species in the genus Amphiprion [2]. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group [2]. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA [2, 3]. Far from being mere habitat space, the host sea anemones also receive substantial benefits from hosting clownfishes, making the mutualistic and co-dependent nature of the symbiosis well established [4, 5]. Yet the evolutionary consequences of mutualism with clownfishes have remained a mystery from the host perspective. Here we use bait-capture sequencing to fully resolve the evolutionary relationships among the 10 nominal species of clownfish-hosting sea anemones for the first time (Figure 1). Using time-calibrated divergence dating analyses we calculate divergence times of less than 25 MYA for each host species, with 9 of 10 host species having divergence times within the last 13 MYA (Figure 1). The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/576469v1_fig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@7053b4org.highwire.dtl.DTLVardef@876c65org.highwire.dtl.DTLVardef@dd6d9forg.highwire.dtl.DTLVardef@147fddd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Diversification of the clownfish-hosting sea anemones was coincident with the clownfish adaptive radiation. A) Time-calibrated maximum likelihood cladogram of Order Actiniaria based on 328 ultra-conserved element and exon loci (75% data occupancy matrix). The three clades containing the clownfish hosting sea anemones are highlighted reflecting the multiple evolutionary origins of symbiosis with clownfishes within superfamily Actinioidea. B-D) Detailed time-calibrated maximum likelihood cladograms of Entacmaea quadricolor, Clade Stichodactylina, and Clade Heteractina, respectively. In all panels, the orange line denotes the beginning of the clownfish adaptive radiation 13 MYA. Sea anemone superfamilies Actinostoloidea, Metridioidea, Actiniernoidea, and Edwardsioidea are collapsed for clarity. C_FIG

evolutionary biology↗

bioRxiv2023

Anemonefish are better taxonomists than humans.

The symbiosis between giant sea anemones, photosynthetic algae of the family Symbiodiniaceae, and anemonefish is an iconic example of a mutualistic "menage a 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 species of sea anemone (e.g., Amphiprion frenatus with Entacmaea quadricolor), whereas others are more generalist and can live in almost any host species (e.g., Amphiprion clarkii)1,2,3. Reasons for host preferences and the mechanisms involved are obscured, among other things, by the lack of resolution of giant sea anemone phylogeny. Recent molecular analyses have shown that giant sea anemones hosting anemonefish belong to three distinct clades: Entacmaea, Stichodactyla, and Heteractis4,5,6. Inside these clades, however, species delimitation has been impeded by morphological variability of the giant sea anemones and is poorly resolved with classical markers4,5. Here, we employed an extensive transcriptomic dataset from 55 sea anemones collected from southern Japan to build a robust phylogeny. With this dataset, we observed that the bubble-tip sea anemone E. quadricolor, currently considered to be a single species, can in fact be separated into at least four distinct cryptic lineages (A-D). Moreover, these lineages can be precisely distinguished by their association with anemonefish: A. frenatus is only found associated with lineage D, whereas A. clarkii lives in the other three lineages.

evolutionary biology↗

bioRxiv2021

Coral assemblages at higher latitudes favour short-term potential over long-term performance

The persistent exposure of coral communities 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 conditions. Using annual surveys of 3171 coral individuals across Australia and Japan (2017-2019), we explore spatial variation across the short- and long-term dynamics of competitive, stress-tolerant, and weedy assemblages to evaluate how thermal variability mediates the structural composition of coral communities. We illustrate how, by promoting short-term potential over long-term performance, coral assemblages can reduce their vulnerability to stochastic environments. However, compared to stress-tolerant, and weedy assemblages, competitive coral taxa display a reduced capacity for elevating their short-term potential. Accordingly, future climatic shifts threaten the structural complexity of coral assemblages in variable environments, emulating the degradation expected across global tropical reefs.

ecology↗

bioRxiv2021

Preliminary genetic assessment of three goatfish species in the Mediterranean Sea

We examined genetic diversity and connectivity of two indigenous Mediterranean goatfish species (Mullus barbatus and M. surmuletus), and a Lessepsian migrant species (Upeneus moluccensis), across the Nile Delta outflow using two mitochondrial DNA markers (COI and cyt b). Genetic diversity was high for the two Mediterranean species but relatively lower for the migrant species, suggesting founder effects after invasion from the Red Sea. Confirmation of this hypothesis, however, would require comparison with populations of origin in the Red Sea and the Indo-West Pacific. AMOVA and network analyses revealed no genetic partitioning for all species, indicating the Nile outflow does not currently, and may not have historically, posed a significant barrier to larval dispersal in these goatfish despite a present-day temperature and salinity gradient along the Mediterranean coastline of Egypt.

genetics↗

bioRxiv2021

Transient amplification enhances the persistence of tropicalising coral populations in marginal high latitude environments.

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 resistance, recovery, and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher-latitudes. Through the annual census of tropical and subtropical Acropora spp. colonies in Japan, between 2017-2019, we show how the transient amplification potential of a subtropical coral population supports its enhanced growth within unstable environmental conditions. The transient dynamics of both the tropical and subtropical populations were strongly influenced by their corresponding recruitment patterns. However, we demonstrate that variation in colony survival and fragmentation patterns between the two populations determines their relative capacities for transient amplification. This latitudinal variation in the transient dynamics of Acropora spp. populations emphasizes that coral populations can possess the demographic plasticity necessary for exploiting more variable, marginal conditions.

ecology↗

bioRxiv2021

The prevalence, predominance, and metabolic potentials of Candidatus Prochlorobium terpiosii in the coral-killing sponge, Terpios hoshinota

Terpios hoshinota is a ferocious, space-competing sponge that kills a variety of stony corals by overgrowth. Outbreaks of this species have led to intense coral reef damage and declines in living corals on the square kilometer scale in many geographical locations. Our large-scale 16S rRNA gene survey across three oceans revealed that the core microbiome of T. hoshinota included operational taxonomic units (OTUs) related to Prochloron, Endozoicomonas, Pseudospirillum, SAR116, Magnetospira, and Ruegeria. A Prochloron- related OTU was the most dominant cyanobacterium in T. hoshinota in the western Pacific Ocean, South China Sea, and Indian Ocean. The complete metagenome-assembled genome of the Prochloron-related cyanobacterium and our pigment analysis revealed that this bacterium had phycobiliproteins and phycobilins and lacked chlorophyll b, inconsistent with the iconic definition of Prochloron. Furthermore, the phylogenetic analyses based on 16S rRNA genes and 120 single-copy genes demonstrated that the bacterium was phylogenetically distinct to Prochloron, strongly suggesting that it should be a sister taxon to Prochloron; we therefore proposed this symbiotic cyanobacterium as a novel species under a new genus: Candidatus Paraprochloron terpiosii. With the recovery of the complete genome, we characterized the metabolic potentials of the novel cyanobacterium in carbon and nitrogen cycling and proposed a model for the interaction between Ca. Pp. terpiosi LD05 and T. hoshinota. In addition, comparative genomics analysis revealed that Ca. Paraprochloron and Prochloron showed distinct features in transporter systems and DNA replication. ImportanceThe finding that one species predominates cyanobacteria in T. hoshinota from different geographic locations indicates that this sponge and Ca. Pp. terpiosi LD05 share a tight relationship. This study builds the foundation for T. hoshinotas microbiome and paves a way for understanding the ecosystem, invasion mechanism, and causes of outbreak of this coral-killing sponge. Also, the first Prochloron-related complete genome enables us to study this bacterium with molecular approaches in the future and broadens our knowledge of the evolution of symbiotic cyanobacteria.

ecology↗

bioRxiv2019

Phylogenetic relationships among the clownfish-hosting sea anemones

The clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes. However, our evolutionary understanding of this symbiosis comes entirely from studies of clownfishes. A holistic understanding of a model mutualism requires systematic, biogeographic, and phylogenetic insight into both partners. Here, we conduct the largest phylogenetic analysis of sea anemones (Order Actiniaria) to date, with a focus on expanding the biogeographic and taxonomic sampling of the 10 nominal clownfish-hosting species. Using a combination of mtDNA and nuDNA loci we test 1) the monophyly of each clownfish-hosting family and genus, 2) the current anemone taxonomy that suggests symbioses with clownfishes evolved multiple times within Actiniaria, and 3) whether, like the clownfishes, there is evidence that host anemones have a Coral Triangle biogeographic origin. Our phylogenetic reconstruction demonstrates widespread poly-and para-phyly at the family and genus level, particularly within the family Stichodactylidae and genus Sticodactyla, and suggests that symbioses with clownfishes evolved minimally three times within sea anemones. We further recover evidence for a Tethyan biogeographic origin for some clades. Our data provide the first evidence that clownfish and some sea anemone hosts have different biogeographic origins, and that there may be cryptic species of host anemones. Finally, our findings reflect the need for a major taxonomic revision of the clownfish-hosting sea anemones.

evolutionary biology↗