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Studying fundamental aspects of eukaryotic biology through genetic information can face numerous challenges, including contamination and intricate biotic interactions, which are particularly pronounced when working with uncultured eukaryotes. However, existing tools for predicting open reading frames (ORFs) from transcriptomes are limited in these scenarios. Here we introduce Transcript Identification and Selection (TIdeS), a framework designed to address these nontrivial challenges associated with current 'omics approaches. Using transcriptomes from 32 taxa, representing the breadth of eukaryotic diversity, TIdeS outperforms most conventional ORF-prediction methods (i.e. TransDecoder), identifying a greater proportion of complete and in-frame ORFs. Additionally, TIdeS accurately classifies ORFs using minimal input data, even in the presence of "heavy contamination". This built-in flexibility extends to previously unexplored biological interactions, offering a robust single-stop solution for precise ORF predictions and subsequent decontamination. Beyond applications in phylogenomic-based studies, TIdeS provides a robust means to explore biotic interactions in eukaryotes (e.g. host-symbiont, prey-predator) and for reproducible dataset curation from transcriptomes and genomes., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Background: Chiton species belonging to the genus Ischnochiton J. E. Gray, 1847 are commonly found in intertidal rocky shores worldwide, with the exception of the northern Atlantic and Arctic oceans. Ischnochiton species are characterised by imbricate girdle scales that are uniform in size, rounded, sculpted with striae or occasionally smooth. However, their species-level taxonomy is complicated due to the high variation in their shell microstructures. Despite more than a hundred species reported worldwide, taxonomic studies of this group remain relatively unexplored in Korean waters, with only a few species recorded to date., New Information: In this study, we compared the microstructural characteristics of tegmentum sculpture, girdle scales and radula amongst four Korean Ischnochiton species using high-resolution microscopic images and a scanning electron microscope (SEM). Along with mtDNA cox1 sequence comparison, a comprehensive analysis of their morphology revealed that I.hayamii Owada, 2018 was identified for the first time in Korean waters. This species is morphologically distinguished by its small body size of adults, smooth lateral areas on valves and small perinotum scales sculptured with weak longitudinal ribs. Phylogenetic analysis of the mtDNA cox1 sequence provides distinct resolution at the species level, but interrelationships amongst Ischnochiton species remain unresolved. Results from the morphological and molecular analyses presented in this study offer valuable taxonomic information for accurate species identification amongst closely-related Ischnochiton species., (Jina Park, Yukyung Kim, Eggy Triana Putri, Joong-Ki Park.)

Branchinotogluma Pettibone, 1985 is the most species-rich genus within the subfamily Lepidonotopodinae Pettibone, 1983, comprising 18 valid species from chemosynthesis-based ecosystems in the Pacific and Indian Oceans. Here, we report a new distributional record of Branchinotoglumabipapillata Zhou, Wang, Zhang & Wang, 2018, at the hydrothermal vent sites on the northern Central Indian Ridge (nCIR). This record represents the northernmost occurrence of B.bipapillata in the Indian Ocean. We conducted a comparative study of the nCIR population and other documented populations using distributional information, morphological traits, and genetic markers (two mitochondrial [ COI , 16S rRNA] and one nuclear [ 18S rRNA] genes). While most morphological characters of B.bipapillata were consistent with those found in the Southwest Indian Ridge (SWIR), variations were noted in the segment with the last branchiae. Molecular data revealed that all populations of B.bipapillata form a single clade, indicating a wide distribution from the SWIR to nCIR, covering ~4,000 km across various ridges in the Indian Ocean. This study presents extensive distribution of a vent species with well-connected populations throughout the Indian Ocean, distinguishing it from many other vent species affected by the dispersal barrier in the Indian Ocean., Competing Interests: The authors have declared that no competing interests exist., (Won-Kyung Lee, Se-Joo Kim.)

Habitat transitions in living organisms are key innovations often coupled with species diversification after their successful adaptation to new environment. The Cyrenidae is among the most well-known heterodont bivalve groups that have successfully invaded freshwater systems from brackish water environments and display diverse lineage-specific developmental modes. Phylogenetic and molecular clock-based divergence time analyses using 12 complete mitochondrial genome sequences suggest that Cyrenidae species independently colonized freshwater habitats during three distinct spatial and geological periods: one from the American continents approximately in the Early Jurassic and the two others from Australasian/East Asian continents in the Early/Middle Cretaceous and the Paleogene-Neogene boundary, respectively. This study provides significant insight into the temporal and spatial patterns of multiple freshwater invasions, aligning with ancient vicariance events inferred from different geological timelines of plate tectonics. Additionally, mitogenome phylogeny confirms the earlier hypothesis of the repeated parallel evolution of parental care system within this bivalve group., (© 2024. The Author(s).)

We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms., (© 2024. The Author(s), under exclusive licence to Springer Nature Japan KK.)

Mitochondria originated from an ancient endosymbiosis involving an alphaproteobacterium. 1 , This process has yielded varying gene compositions in modern mitogenomes, including the complete loss of this organellar genome in some extreme cases. 2 At the other end of the spectrum, jakobids harbor the most gene-rich mitogenomes, encoding 60-66 proteins. , Here, we introduce the mitogenome of Mantamonas sphyraenae, a protist from the deep-branching CRuMs supergroup. 3 Remarkably, it boasts the most gene-rich mitogenome outside of jakobids, by housing 91 genes, including 62 protein-coding ones. These include rare homologs of the four subunits of the bacterial-type cytochrome c maturation system I (CcmA, CcmB, CcmC, and CcmF) alongside a unique ribosomal protein S6. During the early evolution of mitochondria, gene transfer from the proto-mitochondrial endosymbiont to the nucleus became possible thanks to systems facilitating the transport of proteins synthesized in the host cytoplasm back to the mitochondrion. In addition to the universally found eukaryotic protein import systems, jakobid mitogenomes were reported to uniquely encode the SecY transmembrane protein of the Sec general secretory pathway, whose evolutionary origin was however unclear. The Mantamonas mitogenome not only encodes SecY but also SecA, SecE, and SecG, making it the sole eukaryote known to house a complete mitochondrial Sec translocation system. Furthermore, our phylogenetic and comparative genomic analyses provide compelling evidence for the alphaproteobacterial origin of this system, establishing its presence in LECA.4 This process has yielded varying gene compositions in modern mitogenomes, including the complete loss of this organellar genome in some extreme cases. 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 At the other end of the spectrum, jakobids harbor the most gene-rich mitogenomes, encoding 60-66 proteins. 8 Here, we introduce the mitogenome of Mantamonas sphyraenae, a protist from the deep-branching CRuMs supergroup. 15 , 16 Remarkably, it boasts the most gene-rich mitogenome outside of jakobids, by housing 91 genes, including 62 protein-coding ones. These include rare homologs of the four subunits of the bacterial-type cytochrome c maturation system I (CcmA, CcmB, CcmC, and CcmF) alongside a unique ribosomal protein S6. During the early evolution of mitochondria, gene transfer from the proto-mitochondrial endosymbiont to the nucleus became possible thanks to systems facilitating the transport of proteins synthesized in the host cytoplasm back to the mitochondrion. In addition to the universally found eukaryotic protein import systems, jakobid mitogenomes were reported to uniquely encode the SecY transmembrane protein of the Sec general secretory pathway, whose evolutionary origin was however unclear. The Mantamonas mitogenome not only encodes SecY but also SecA, SecE, and SecG, making it the sole eukaryote known to house a complete mitochondrial Sec translocation system. Furthermore, our phylogenetic and comparative genomic analyses provide compelling evidence for the alphaproteobacterial origin of this system, establishing its presence in LECA., Competing Interests: Declaration of interests L.E. is a member of the Current Biology advisory board., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Escherichia coli uses allantoin as the sole nitrogen source during anaerobic growth. In the final step of allantoin degradation, oxamic transcarbamylase (OXTCase) converts oxalurate to carbamoyl phosphate (CP) and oxamate. The activity of this enzyme was first measured in Streptococcus allantoicus in the 1960s, but no OXTCase enzyme or the encoding gene(s) have been found in any strain. This study discovered that allFGH ( fdrA , ylbE , and ylbF ) are the genes that encode the global orphan enzyme OXTCase. The three genes form an operon together with allK ( ybcF ), encoding catabolic carbamate kinase. The allFGHK operon is located directly downstream of the allECD operon that encodes enzymes for the preceding steps of OXTCase. The OXTCase kinetic parameters were analyzed using the purified protein composed of AllF-AllG-AllH (FdrA-YlbE-YlbF); for the substrate CP, K M were 1.3 mM and 15.4 U/mg OXTCase, respectively, and for the substrate oxamate, they were 36.9 mM and 27.0 U/mg OXTCase. In addition, the OXTCase encoded by the three genes is a novel transcarbamylase that shows no similarity with known enzymes of the transcarbamylase family such as aspartate transcarbamylase, ornithine transcarbamylase, and YgeW transcarbamylase. The present study elucidated the anaerobic allantoin degradation pathway of V max were 1.3 mM and 15.4 U/mg OXTCase, respectively, and for the substrate oxamate, they were 36.9 mM and 27.0 U/mg OXTCase. In addition, the OXTCase encoded by the three genes is a novel transcarbamylase that shows no similarity with known enzymes of the transcarbamylase family such as aspartate transcarbamylase, ornithine transcarbamylase, and YgeW transcarbamylase. The present study elucidated the anaerobic allantoin degradation pathway of E. coli . Therefore, we suggest that the genes fdrA , ylbE , and ylbF are renamed allF , respectively.IMPORTANCEThe anaerobic allantoin degradation pathway of allG , and allH , respectively.IMPORTANCEThe anaerobic allantoin degradation pathway of Escherichia coli includes a global orphan enzyme, oxamic transcarbamylase (OXTCase), which converts oxalurate to carbamoyl phosphate and oxamate. This study found that the allFGH ( fdrA ) genes encode OXTCase. The OXTCase activity and kinetics were successfully determined with purified recombinant AllF-AllG-AllH (FdrA-YlbE-YlbF). This OXTCase is a novel transcarbamylase that shows no similarity with known enzymes of the transcarbamylase family such as aspartate transcarbamylase (ATCase), ornithine transcarbamylase (OTCase), and YgeW transcarbamylase (YTCase). In addition, OXTCase activity requires three genes, whereas ATCase is encoded by two genes, and OTCase and YTCase are encoded by a single gene. The current study discovered OXTCase, the last unknown step in allantoin degradation, and this enzyme is a new member of the transcarbamylase group that was previously unknown.ylbE , and ylbF ) genes encode OXTCase. The OXTCase activity and kinetics were successfully determined with purified recombinant AllF-AllG-AllH (FdrA-YlbE-YlbF). This OXTCase is a novel transcarbamylase that shows no similarity with known enzymes of the transcarbamylase family such as aspartate transcarbamylase (ATCase), ornithine transcarbamylase (OTCase), and YgeW transcarbamylase (YTCase). In addition, OXTCase activity requires three genes, whereas ATCase is encoded by two genes, and OTCase and YTCase are encoded by a single gene. The current study discovered OXTCase, the last unknown step in allantoin degradation, and this enzyme is a new member of the transcarbamylase group that was previously unknown., Competing Interests: The authors declare no conflict of interest.

Constitutive mixoplankton-plastid-bearing microbial eukaryotes capable of both phototrophy and phagotrophy-are ubiquitous in marine ecosystems and facilitate carbon transfer to higher trophic levels within aquatic food webs, which supports enhanced sinking carbon flux. However, the regulation of the relative contribution of photosynthesis and prey consumption remains poorly characterized. We investigated the transcriptional dynamics behind this phenotypic plasticity in the prasinophyte green alga Pterosperma cristatum. Based on what is known of other mixoplankton species that cannot grow without photosynthesis (obligate phototrophs), we hypothesized that P. cristatum uses phagotrophy to circumvent the restrictions imposed on photosynthesis by nutrient depletion, to obtain nutrients from ingested prey, and to maintain photosynthetic carbon fixation. We observed an increase in feeding as a response to nutrient depletion, coinciding with an upregulation of expression for genes involved in essential steps of phagocytosis including prey recognition, adhesion and engulfment, transport and maturation of food vacuoles, and digestion. Unexpectedly, genes involved in the photosynthetic electron transfer chain, pigment biosynthesis, and carbon fixation were downregulated as feeding increased, implying an abatement of photosynthesis. Contrary to our original hypothesis, our results therefore suggest that depletion of inorganic nutrients triggered an alteration of trophic behavior from photosynthesis to phagotrophy in P. cristatum . While this behavior distinguishes P. cristatum from other groups of constitutive mixoplankton, its physiological response aligns with recent discoveries from natural microbial communities. These findings indicate that mixoplankton communities in nutrient-limited oceans can regulate photosynthesis against bacterivory based on nutrient availability., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

The cellular and molecular mechanisms governing sexual reproduction are conserved across eukaryotes. Nevertheless, hybridization can disrupt these mechanisms, leading to asexual reproduction, often accompanied by polyploidy. In this study, we investigate how ploidy level and ratio of parental genomes in hybrids affect their reproductive mode. We analyze the gametogenesis of sexual species and their diploid and triploid hybrids from the freshwater fish family Cobitidae, using newly developed cytogenetic markers. We find that diploid hybrid females possess oogonia and oocytes with original (diploid) and duplicated (tetraploid) ploidy. Diploid oocytes cannot progress beyond pachytene due to aberrant pairing. However, tetraploid oocytes, which emerge after premeiotic genome endoreplication, exhibit normal pairing and result in diploid gametes. Triploid hybrid females possess diploid, triploid, and haploid oogonia and oocytes. Triploid and haploid oocytes cannot progress beyond pachytene checkpoint due to aberrant chromosome pairing, while diploid oocytes have normal pairing in meiosis, resulting in haploid gametes. Diploid oocytes emerge after premeiotic elimination of a single-copied genome. Triploid hybrid males are sterile due to aberrant pairing and the failure of chromosomal segregation during meiotic divisions. Thus, changes in ploidy and genome dosage may lead to cyclical alteration of gametogenic pathways in hybrids., (© 2024. The Author(s).)

Rhizocephala is a group of endoparasitic barnacles, the morphological characteristics of which are degenerated, and which has recently undergone active molecular identification. Despite several recent studies of Korean rhizocephalans, a comprehensive analysis of rhizocephalan fauna has not yet been conducted. In this study, we analyzed morphological and molecular characteristics of 64 rhizocephalan samples from 15 decapod hosts sampled across the Korean coast. We found 16 Rhizocephala species of six genera from four Rhizocephala families, i.e. , Peltogasterellidae, Peltogastridae, Polyascidae, and Sacculinidae. Combining morphological examination and molecular analysis of mitochondrial cytochrome c oxidase I revealed three new species candidates, i.e. , Peltogasterella sp., Peltogaster sp., and Parasacculina sp. 1, and three rhizocephalans that have expanded their distribution range to the Korean coast, i.e. , Parasacculina oblonga , Sacculina angulata , and Sacculina gracilis , whose expanded their distribution range to Korean coast. A synthetic update of Korean Rhizocephala fauna including a species checklist and remarks regarding distribution and taxonomy is also presented.

DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2% to 50.7%. Concordance rates of orthologs and heterozygosity rates were between 82.4% and 91.7% and between 1.0% and 2.1%, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesised to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field., (© 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Ellobium chinense is an airbreathing, pulmonate gastropod species that inhabits saltmarshes in estuaries of the northwestern Pacific. Due to a rapid population decline and their unique ecological niche in estuarine ecosystems, this species has attracted special attention regarding their conservation and the genomic basis of adaptation to frequently changing environments. Here we report a draft genome assembly of E. chinense with a total size of 949.470 Mb and a scaffold N50 of 1.465 Mb. Comparative genomic analysis revealed that the GO terms enriched among four gastropod species are related to signal transduction involved in maintaining electrochemical gradients across the cell membrane. Population genomic analysis using the MSMC model for 14 re-sequenced individuals revealed a drastic decline in Korean and Japanese populations during the last glacial period, while the southern Chinese population retained a much larger effective population size (N e ). These contrasting demographic changes might be attributed to multiple environmental factors during the glacial-interglacial cycles. This study provides valuable genomic resources for understanding adaptation and historical demographic responses to climate change., (© 2024. The Author(s).)

The marine tetraflagellate Cymbomonas tetramitiformis has drawn attention as an early diverging green alga that uses a phago-mixotrophic mode of nutrition (i.e., the ability to derive nourishment from both photosynthesis and bacterial prey). The Cymbomonas nuclear genome was sequenced previously, but due to the exclusive use of short-read (Illumina) data, the assembly suffered from missing a large proportion of the genome's repeat regions. For this study, we generated Oxford Nanopore long-read and additional short-read Illumina data and performed a hybrid assembly that significantly improved the total assembly size and contiguity. Numerous endogenous viral elements were identified in the repeat regions of the new assembly. These include the complete genome of a giant Algavirales virus along with many genomes of integrated Polinton-like viruses (PLVs) from two groups: Gezel-like PLVs and a novel group of prasinophyte-specific PLVs. The integrated ∼400 kb genome of the giant Algavirales virus is the first account of the association of the uncultured viral family AG_03 with green algae. The complete PLV genomes from C. tetramitiformis ranged between 15 and 25 kb in length and showed a diverse gene content. In addition, heliorhodopsin gene-containing repeat elements of putative mirusvirus origin were identified. These results illustrate past (and possibly ongoing) multiple alga-virus interactions that accompanied the genome evolution of C. tetramitiformis., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Anaerobic bacteria often use antiporters DcuB (malate/succinate antiport) or DcuA (l-aspartate/succinate antiport) for the excretion of succinate during fumarate respiration. The rumen bacterium Actinobacillus succinogenes is able to produce large amounts of succinate by fumarate respiration, using the DcuB-type transporter DcuE for l-malate/succinate antiport. Asuc_0142 was annotated as a second DcuB-type transporter. Deletion of Asuc_0142 decreased the uptake rate for l-[ 14 C]aspartate into A. succinogenes cells. Properties of transport by heterologously expressed Asuc_0142 were investigated in an Escherichia coli mutant deficient of anaerobic C4DC transporters. Expression of Asuc_0142 resulted in high uptake activity for l-[ 14 C]fumarate or l-[ 14 C]aspartate, but the former showed a strong competitive inhibition by l-aspartate. In E. coli loaded with l-[ 14 C]aspartate, [ 14 C]succinate or [ 14 C]fumarate, extracellular C4DCs initiated excretion of the intracellular substrates, with a preference for l-aspartate ex /succinate in or l-aspartate ex /fumarate in antiport. These findings indicate that Asuc_0142 represents a DcuA-type transporter for l-aspartate uptake and l-aspartate ex /C4DC in antiport, differentiating it from the DcuB-type transporter DcuE for l-malate ex /succinate in antiport. Sequence analysis and predicted structural characteristics confirm structural similarity of Asuc_0142 to DcuA, and Asuc_0142 was thus re-named as DcuA As . The bovine rumen fluid contains l-aspartate (99.6 µM), whereas fumarate and l-malate are absent. Therefore, bovine rumen colonisers depend on l-aspartate as an exogenous substrate for fumarate respiration. A. succinogenes encodes HemG (protoporphyrinogen oxidase) and PyrD (dihydroorotate dehydrogenase) for haem and pyrimidine biosynthesis. The enzymes require fumarate as an electron acceptor, suggesting an essential role for l-aspartate, DcuA As , and fumarate respiration for A. succinogenes growing in the bovine rumen.

Mantamonads were long considered to represent an "orphan" lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the "CRuMs" supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup., (© 2023. Springer Nature Limited.)

Animal-vehicle collisions (AVC) threaten animals as well as human life and property. AVC with ungulates, called ungulate-vehicle collision (UVC), often seriously endangers human safety because of the considerable body size of ungulates. In the Republic of Korea, three ungulate species, Capreolus pygargus , Hydropotes inermis , and Sus scrofa , account for a large proportion of AVC. This study aimed to understand the characteristics of UVC by examining various parameters related to habitat, traffic, and seasonality using MaxEnt. The results showed that the peak UVC seasons coincided with the most active seasonal behaviors of the studied ungulates. For the modeling results, in C. pygargus , habitat variables are most important for models across seasons, and UVC events are most likely to occur in high mountain chains. In H. inermis , habitat and traffic variables are most important for models across seasons. Although the important habitat for the models were different across seasons for S. scrofa , the maximum speed was consistently critical for models across all seasons. Factors critical to UVC in the Republic of Korea were different for the three ungulate species and across seasons, indicating that seasonal behavior should be considered along with landscape and traffic characteristics to mitigate UVC.

Batillaridae is a common gastropod family that occurs abundantly in the shallow coastal zone of the intertidal mudflats of the northwest Pacific Ocean, Australasia, and North America. In this family, Batillaria attramentaria is known for its biological invasion and colonization in estuarine and intertidal zones. It can endure and adapt the harsh intertidal conditions such as frequent temperature alteration, salinity, and air exposure. Therefore, we sequenced and assembled this Korean batillariid genome to get insight into its intertidal adaptive features. Approximately 53 Gb of DNA sequences were generated, and 863 scaffolds were assembled into a draft genome of 0.715 Gb with 97.1% BUSCO completeness value. A total of 40,596 genes were predicted. We estimated that B. attramentaria and Conus consors diverged about 230 million years ago (MYA) based on the phylogenetic analysis of closely related gastropod species. This genome study sets the footstep for genomics studies among native and introduced Batillaria populations and the Batillaridae family members., (© 2023. The Author(s).)

Calcinus is the colorful hermit crab genus belonging to the family Diogenidae and is often found in coral reefs of the tropical Indo-West Pacific region, including southern Honshu, Japan, which is the northern limit of their occurrence. In the present study, we found C. vachoni for the first time in the intertidal zone of Jeju Island-the southernmost island of South Korea. We examined their morphology and provided a diagnosis of their morphological details with illustrations. In addition, the Korean Calcinus population was genetically characterized using mtDNA cox1 sequences and by placing them into three previously reported regional haplogroups. The phylogenetic tree from maximum likelihood analysis revealed that Korean C. vachoni is assigned to the C. vachoni haplogroups exclusively, one of the three well-supported mitochondrial haplogroups with distinct geographic ranges ( i.e ., C . vachoni , C . aff. vachoni Cooks, and C . aff. vachoni Mascarenes). This result provides new information on the species distribution of C.vachoni , extending their geographic range further north into the southern coast of Korea. In this study, we also first report the potential association of C. vachoni with their co-occurring colonial anemone species Palythoa aff. mutuki and dead coral head of Pocillopora species based on our on-site observation and a public coral collection database of Calcinus species. However, their ecological association with co-occurring coral species is putatively assumed for now and therefore has to be validated by compelling evidence from further field observation and experimental studies ( i.e ., whether the presence/absence of colonial anemones affects the behavior and survival of the hermit crabs)., Competing Interests: The authors declare that they have no competing interests., (© 2023 Jung and Park.)

In pair-living species, female and male pairs may maintain stable social bonds by adjusting spatial and social associations. Nevertheless, each sex invests differently to maintain the pair bond, and the investment can depend on the presence of paternal care or 'male services.' While most species live in pairs, the sex responsible for pair bond maintenance in gibbons is still controversial. We investigated pair bond maintenance and parental care in three pairs of wild Javan gibbons in Gunung Halimun-Salak National Park, Indonesia, for over 21 months. We found that Javan gibbon fathers groomed their offspring more than adult females, especially as offspring got older. While both parents increased playing time with offspring when offspring became older and more independent, fathers played with offspring 20 times more than mothers on average. Grooming within Javan gibbon pairs was male-biased, suggesting that pair bond maintenance was heavily the job of males. However, offspring age as a proxy for paternal care did not affect the pair bond maintenance. Our study highlights that adult male Javan gibbons may have an important role in pair bond maintenance and the care of juveniles.

When a population is partially protected from fluctuating selection, as when a seed bank is present, variance in fitness will be reduced and reproductive success of the population will be promoted. This study further investigates the effect of such a 'refuge' from fluctuating selection using a mathematical model that couples demographic and evolutionary dynamics. While alleles that cause smaller fluctuations in population density should be positively selected according to classical theoretic predictions, this study finds the opposite: alleles that increase the amplitude of population size fluctuation are positively selected if population density is weakly regulated. Under strong density regulation with a constant carrying capacity, long-term maintenance of polymorphism caused by the storage effect emerges. However, if the carrying capacity of the population is oscillating, mutant alleles whose fitness fluctuates in the same direction as population size are positively selected, eventually reaching fixation or intermediate frequencies that oscillate over time. This oscillatory polymorphism, which requires fitness fluctuations that can arise with simple trade-offs in life-history traits, is a novel form of balancing selection. These results highlight the importance of allowing joint demographic and population genetic changes in models, the failure of which prevents the discovery of novel eco-evolutionary dynamics.

A new species of the genus Pycnogonum was discovered in the mesophotic zone of Munseom Islet, Jejudo Island, Korea. Pycnogonum ( Nulloviger ) bifurcatum sp. nov. is the first case of sea spiders in Korean fauna not only included in the subgenus Nulloviger but also collected in the mesophotic zone of Munseom Islet. The new species is morphologically close to Pycnogonum ( Pycnogonum ) asiaticum and P. ( N. ) carinatum , sharing the granular integument, the dorsomedian tubercles on the trunk, and the post-ocular tubercle. The new species can be easily distinguished from the congeners by combination of the following characteristics: the prominent dorsomedian tubercles on the trunk, the lateral processes 1-3 touching each other, and the small auxiliary claws. A key is provided to distinguish 12 species of the subgenus Nulloviger morphologically, and molecular data of the new species are provided for species identification and further studies.

Natal dispersal is an important life-history trait in all animal taxa. In pair-living species, parent-offspring competition derived from the offspring's maturity can motivate the natal dispersal of offspring. However, not much has been known about the dispersal mechanisms of pair-living gibbons. To test food and mate competition as potential reasons for dispersal, we investigated the effect of the offspring age and sex on relationships between parents and offspring in wild Javan gibbon (Hylobates moloch) in Gunung Halimun-Salak National Park, Indonesia. We collected behavioral data for two years between 2016 and 2019. We found that aggression from parents toward offspring increased in both feeding and non-feeding context as the offspring got older. Offspring received more aggression from the parent of the same sex in the general context. While offspring decreased co-feeding and grooming time with parents as they got older, there was no change in the proximity and approach to parents. The results imply the presence of both intra-group food and mate competition which increase with the offspring's age. We highlight that increased competition between maturing offspring and parents changes their social relationships and peripheralizes offspring from the natal group which will eventually motivate offspring to disperse in Javan gibbons., (© 2023. The Author(s).)

Increased access to genome-wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable because genomic data are not available to most rare plant species. In the hope of bridging the gap between conservation science and practice, we outline how conservation practitioners can more efficiently employ population genetic information in plant conservation. We first review the current knowledge about neutral genetic variation (NGV) and adaptive genetic variation (AGV) in seed plants, regarding both within-population and among-population components. We then introduce the estimates of among-population genetic differentiation in quantitative traits ( Q ST ) and neutral markers ( F ST comparisons, particularly on how to capture most AGV and NGV on both in-situ and ex-situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials ( Q  = 18) to capture 99% of NGV and AGV, respectively, whereas four populations would be needed in case of herbaceous perennials ( ST - F ST comparisons, particularly on how to capture most AGV and NGV on both in-situ and ex-situ programs. Based on a review of published studies, we found that, on average, two and four populations would be needed for woody perennials ( n could be misleading, particularly in woody species. To maximize the preservation of the maximum levels of both AGV and NGV, we suggest using maximum n  = 14). On average, Q ST is about 3.6, 1.5, and 1.1 times greater than F ST in woody plants, annuals, and herbaceous perennials, respectively. Hence, conservation and management policies or suggestions based solely on inference on F ST could be misleading, particularly in woody species. To maximize the preservation of the maximum levels of both AGV and NGV, we suggest using maximum Q ST rather than average Q ST . We recommend conservation managers and practitioners consider this when formulating further conservation and restoration plans for plant species, particularly woody species., Competing Interests: All the authors state that there is no conflict of interest., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize 11 new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea, and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp., and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface, and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution., (© 2022 International Society of Protistologists.)

Escherichia coli can use allantoin as its sole nitrogen source under anaerobic conditions. The ureidoglycolate produced by double release of ammonia from allantoin can flow into either the glyoxylate shunt or further catabolic transcarbamoylation. Although the former pathway is well studied, the genes of the latter (catabolic) pathway are not known. In the catabolic pathway, ureidoglycolate is finally converted to carbamoyl phosphate (CP) and oxamate, and then CP is dephosphorylated to carbamate by a catabolic carbamate kinase (CK), whereby ATP is formed. We identified the ybcF gene in a gene cluster containing fdrA - ylbE - ylbF - ybcF that is located downstream of the allDCE -operon. Reverse transcription PCR of total mRNA confirmed that the genes fdrA , ylbE , ylbF , and ybcF are co-transcribed. Deletion of ybcF caused only a slight increase in metabolic flow into the glyoxylate pathway, probably because CP was used to de novo synthesize pyrimidine and arginine. The activity of the catabolic CK was analyzed using purified YbcF protein. The V max is 1.82 U/mg YbcF for CP and 1.94 U/mg YbcF for ADP, and the K gene of M value is 0.47 mM for CP and 0.43 mM for ADP. With these results, it was experimentally revealed that the ybcF gene of E. coli encodes catabolic CK, which completes anaerobic allantoin degradation through substrate-level phosphorylation. Therefore, we suggest renaming the ybcF gene as allK .

The mytilid mussel Bathymodiolus thermophilus lives in the deep-sea hydrothermal vent regions due to its relationship with chemosynthetic symbiotic bacteria. It is well established that symbionts reside in the gill bacteriocytes of the mussel and can utilize hydrogen sulfide, methane, and hydrogen from the surrounding environment. However, it is observed that some mussel symbionts either possess or lack genes for hydrogen metabolism within the single-ribotype population and host mussel species level. Here, we found a hydrogenase cluster consisting of additional H 2 -sensing hydrogenase subunits in a complete genome of B. thermophilus symbiont sampled from an individual mussel from the East Pacific Rise (EPR9N). Also, we found methylated regions sparsely distributed throughout the EPR9N genome, mainly in the transposase regions and densely present in the rRNA gene regions. CRISPR diversity analysis confirmed that this genome originated from a single symbiont strain. Furthermore, from the comparative analysis, we observed variation in genome size, gene content, and genome re-arrangements across individual hosts suggesting multiple symbiont strains can associate with B. thermophilus. The ability to acquire locally adaptive various symbiotic strains may serve as an effective mechanism for successfully colonizing different chemosynthetic environments across the global oceans by host mussels., (© 2022. The Author(s).)

Human visitors affect the behavior of captive animals, which is the so-called visitor effect. The number and behavior of visitors may influence stress-related behaviors in captive animals, such as self-scratching, yawning, and visitor-directed vigilance. A social group setting can be applied to alleviate such negative visitor effects and facilitate social behavior and interactions between individuals. In this study, we examined how the number and behavior of visitors are related to stress-related behaviors of a captive mixed-species gibbon pair comprising a yellow-cheek gibbon (Nomascus gabriellae) and a white-handed gibbon (Hylobates lar). The two gibbons were separated during the study period, and we examined whether the social isolation stimulated the visitor effect. The frequency of stress-related behaviors of the gibbons increased and the social playing between them decreased proportionally to visitor number. In the indoor enclosure, the gibbons increased their visitor-directed vigilance when visitors shouted or struck the glass partition. Our findings indicate that the number and behavior of visitors negatively affect captive gibbons and that a mixed-species social setting can help gibbons reduce visitor-induced stress. Future studies with larger sample sizes will improve the understanding of the visitor effect and the social setting in the captivity., (© 2022. The Author(s).)

Background: The Japanese mantis shrimp Oratosquilla oratoria has two genetic lineages in its Chinese and Japanese populations, which are considered cryptic species. However, the Korean O. oratoria populations have only been studied morphologically, and their genetic diversity pattern remains unknown., Objective: To examine the genetic diversity of the Korean O. oratoria populations to explore its cryptic diversity and underlying processes., Methods: We sequenced the mitochondrial cytochrome c oxidase I gene of 107 O. oratoria individuals from 8 sampling sites in South Korea. Their genetic diversity and haplotype data were compared to previously reported data from 16 Chinese and 6 Japanese populations., Results: The haplotype network, analysis of molecular variance, F ST values, and Bayesian skyline plot of the Korean O. oratoria populations confirmed that they were divided into two genetic lineages corresponding to the two previously identified cryptic species, which might be correlated to ocean currents and water temperature. In addition, the population genetic analysis indicated that both lineages had high genetic diversity. Although the Geoje region belongs to the southern group, it only contained lineage N, which could be related to the specific environmental characteristics of Geoje or the hybridization of the two lineages of O. oratoria., Conclusion: Korean O. oratoria populations have enough cryptic diversity to be described as cryptic species and are correlated with ocean currents and water temperatures. Lineage N dominance in Geoje might be related to environmental characteristics or hybridization., (© 2022. The Author(s) under exclusive licence to The Genetics Society of Korea.)

Siboglinid tubeworms thrive in hydrothermal vent and seep habitats via a symbiotic relationship with chemosynthetic bacteria. Difficulties in culturing tubeworms and their symbionts in a laboratory setting have hindered the study of host-microbe interactions. Therefore, released symbiont genomes are fragmented, thereby limiting the data available on the genome that affect subsequent analyses. Here, we present a complete genome of gammaproteobacterial endosymbiont from the tubeworm Lamellibrachia satsuma collected from a seep in Kagoshima Bay, assembled using a hybrid approach that combines sequences generated from the Illumina and Oxford Nano-pore platforms. The genome consists of a single circular chromosome with an assembly size of 4,323,754 bp and a GC content of 53.9% with 3,624 protein-coding genes. The genome is of high quality and contains no assembly gaps, while the completeness and contamination are 99.33% and 2.73%, respectively. Comparative genome analysis revealed a total of 1,724 gene clusters shared in the vent and seep tubeworm symbionts, while 294 genes were found exclusively in L. satsuma symbionts such as transposons, genes for defense mechanisms, and inorganic ion transportations. The addition of this complete endosymbiont genome assembly would be valuable for comparative studies particularly with tubeworm symbiont genomes as well as with other chemosynthetic microbial communities., (© 2022. Author(s).)

Species biodiversity organises along elevational trends and is generally expected to decrease with increasing elevation. This pattern is regulated by numerous factors, although principally overridden by temperature in ectotherms such as amphibians. Here, we collated elevation data ( n = 55,182) collected between 1909 and 2020. We then determined elevation distribution patterns and species communities for all amphibians in the Republic of Korea. Species were found to range from sea level up to 1,393 m a.s.l. The average elevational distribution was significantly different between species but also between anura and caudata. On average, anura were found at lower elevations with a peak in species richness and abundance matching with the lowlands. In opposition, the peak in species richness and abundance for caudata matched with low hilly landscapes. The altitudinal distributions of species were strongly skewed, with all 23 species found within the 0-199 m range, and steadily decreasing with only five species within the last elevational range (1,200-1,399 m). Finally, only a few species were found below 30 m, reflecting a likely risk of salinisation in this environment. Our results help understand the altitudinal distribution of amphibians in the Republic of Korea.

The preservation and restoration of habitats and ecological connectivity inside cities is crucial to ensure wildlife can find suitable areas to forage, rest and reproduce, as well as to disperse, thereby allowing metapopulation functioning. In this study, we used data collected by a citizen science program between 2016 and 2018 to determine which families of pollinators were the most frequently observed in Seoul and with which habitats pollinators had the highest affinities. Using species distribution modeling and landscape graph approaches, we located the main habitats and corridors to reinforce connectivity for six pollinator families. Finally, we identified habitats and corridors where conservation actions should be prioritized. In total, 178 species belonging to 128 genera and 60 families were observed. Hymenopterans were the most recorded, followed by dipterans and lepidopterans. The most suitable habitats for pollinators were constituted of public parks, university campuses, and Cultural Heritage sites. In a dense city like Seoul, most of the conservation corridors are located in built-up areas. Innovative urban planning and architecture are therefore required as well as the setting-up of ecological management practices to lead to a more sustainable urbanism for pollinators and wildlife in general.

Turtle leeches have not been recorded in Korea, although they occur in geographically adjacent countries including China and Japan. This study describes a turtle leech, Ozobranchus jantseanus (Clitellata: Ozobranchidae), found from Reeve's turtle (Mauremys reevesii) in Korea. Of the 143 Reeve's turtles collected from the freshwater reservoir in Jinju City, Gyeongsangnam-do, Korea, 95 unidentified leeches were found in 8 (5.6%) individuals. The leeches had 22 somites with 11 pairs of externally exposed branchiae, body-sized posterior suckers, and spines on the dorsal surface. We identified these leeches as Ozobranchus jantseanus Oka, 1912 (Clitellata: Ozobranchidae). This species of turtle leeches found in Korea may fill the gap in the biodiversity of East Asian annulus.

Global warming is the main cause for the rise of both global temperatures and sea-level, both major variables threatening biodiversity. Rising temperatures threaten to breach the thermal limits of organisms while rising sea-level threatens the osmotic balance of coastal animals through habitat salinization. However, variations in thermal tolerance under different salinity stresses have not yet been thoroughly studied. In this study, we assessed the critical thermal maxima (CTmax) of amphibian tadpoles in different salinity conditions. We collected tadpoles of Duttaphrynus melanostictus, Fejervarya limnocharis and Microhyla fissipes from coastal areas and housed them in freshwater, low, and high salinity treatments for 7 days of acclimation. The CTmax, survival rate, and development rate of tadpoles in high salinity treatments were significantly lower than that of the two other treatments. Our results indicate that physiological performances and heat tolerances of tadpoles are negatively affected by salinization. Maximum entropy models showed that CTmax and sea-level rise are predicted to negatively affect the distribution of the three focal species. The present results suggest that global warming can lead to negative dual-impacts on coastal animals because of reduced thermal tolerances at elevated salinity. The impacts of global warming on anurans in coastal areas and other habitats impacted by salinization may be more severe than predicted and it is likely to cause similar dual-impacts on other ectotherms., (© 2022. The Author(s).)

Background: Most amphibians use a repertoire of acoustic signals to propagate signals in social contexts. The description of these repertoires provides a key towards the understanding of the behaviour of individuals and the evolutionary functions of calls. Here, we assessed the variations in advertisement calls within and between two fossorial sympatric species, Uperodon systoma and Uperodon globulosus, that share their breeding season and breeding sites. For each species, we applied Beecher's index of total information capacity (H S ) for the individual vocal signature, determined the difference in call properties and demonstrated the segregation in the calling microhabitat niche between the two species., Results: Our results demonstrated that the advertisement calls of U. systoma are pulsatile with a call rate of 3.00 ± 0.97 calls per second while those of U. globulosus are not pulsatile with a lower call rate of 0.53 ± 0.22 calls per second. For both species, the variations in call properties among individuals was higher than that within individual, a pattern consistent with that of other fossorial anurans. The body condition and air temperature did not significantly impact the call properties of either species. The outcome of the Beecher's index (H S ) showed that the calls of U. systoma can be used to identify 14 different individuals and the calls of U. globulosus can be used to identify 26 different individuals. The statistical analyses on the advertisement call of the two species showed a significant difference in the temporal properties as the call duration, and fall time and rise time were significantly different between the two species. Lastly, we successfully demonstrated that there is a clear segregation in calling site microhabitat between the two species, where U. globulosus calls floating close to the bank of the waterbody while U. systoma calls floating further away from the bank., Conclusion: This study highlights the potential for pre-mating isolation, character displacement and assortative mating in two syntopic fossorial anurans, leading to association between acoustic, calling microhabitat niche and body index divergence as important behavioural and ecological traits., (© 2022. The Author(s).)

Background: The Chinese mitten crab (Eriocheir sinensis) and the Japanese mitten crab (E. japonica) of the family Varunidae, which are also critical fishery species in their native habitats, including China, Japan, and South Korea, exhibit a rare migration life history for the decapod life cycle. Eriocheir sinensis and E. japonica in South Korea may have originated from speciation or secondary contact in South Korea after speciation of these two species; however, the genetic relationship between these South Korean populations remains unclear, and need to be clarified., Objective: This study examined the population genetic properties of E. sinensis and E. japonica in South Korea to reveal the origin of their co-existence., Methods: Mitochondrial DNA cytochrome c oxidase I sequences of 120 E. sinensis and E. japonica from 6 sampling sites in South Korea were sequenced. Their genetic diversity and haplotype data were compared to previously reported data from the Chinese mainland, Taiwan, Japan, and Russia., Results: The haplotype network, analysis of molecular variance, F ST values, Mantel test, and Bayesian skyline plot results of South Korean E. sinensis and E. japonica demonstrated that E. sinensis and E. japonica were isolated from their central populations, Chinese and Japanese populations, by the distance due to the temperature, salinity, ocean current flow, or a geohistorical event. In addition, genetic analysis indicated that the South Korean populations of the two species were marginal populations, exhibiting low genetic diversity, significant negative neutrality values, and radial haplotype networks. The current results also suggest that the Geum River is an overlapping habitat for the natural populations of E. sinensis and E. japonica in South Korea. Further research is required to examine the geohistorical and evolutionary event between E. sinensis and E. japonica in South Korea., Conclusions: The co-existence of E. sinensis and E. japonica in South Korea may have originated from secondary contact after their speciation., (© 2022. The Author(s) under exclusive licence to The Genetics Society of Korea.)

The family Conidae, commonly known as cone snails, is one of the most intriguing gastropod groups owing to their diverse array of feeding behaviors (diets) and toxin peptides (conotoxins). Conuslischkeanus Weinkauff, 1875 is a worm-hunting species widely distributed from Africa to the Northwest Pacific. In this study, we report the mitochondrial genome sequence of C.lischkeanus and inferred its phylogenetic relationship with other Conus species. Its mitochondrial genome is a circular DNA molecule (16,120 bp in size) composed of 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. Phylogenetic analyses of concatenated nucleotide sequences of 13 PCGs and two ribosomal RNA genes showed that C.lischkeanus belongs to the subgenus Lividoconus group, which is grouped with species of the subgenus Virgiconus, and a member of the largest assemblage of worm-hunting (vermivorous) species at the most basal position in this group. Mitochondrial genome phylogeny supports the previous hypothesis that the ancestral diet of cone snails was worm-hunting, and that other dietary types (molluscivous or piscivorous) have secondarily evolved multiple times from different origins. This new, complete mitochondrial genome information provides valuable insights into the mitochondrial genome diversity and molecular phylogeny of Conus species., (Yucheol Lee, Joong-Ki Park.)

Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.

Ecological niche modeling is a tool used to determine current potential species' distribution or habitat suitability models which can then be used to project suitable areas in time. Projections of suitability into past climates can identify locations of climate refugia, or areas with high climatic stability likely to contain the highest levels of genetic diversity and stable populations when climatic conditions are less suitable in other parts of the range. Modeling habitat suitability for closely related species in recent past can also reveal potential periods and regions of contact and possible admixture. In the east palearctic, there are five Dryophytes (Hylid treefrog) clades belonging to two groups: Dryophytes japonicus group: Clades A and B; and Dryophytes immaculatus group: Dryophytes immaculatus , Dryophytes flaviventris , and Dryophytes suweonensis . We used maximum entropy modeling to determine the suitable ranges of these five clades during the present and projected to the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. We also calculated climatic stability for each clade to identify possible areas of climate refugia. Our models indicated suitable range expansion during the LGM for four clades with the exclusion of D. immaculatus . High climatic stability in our models corresponded to areas with the highest numbers of recorded occurrences in the present. The models produced here can additionally serve as baselines for models of suitability under climate change scenarios and indicate species ecological requirements., Competing Interests: The authors declare that they have no competing interests., (© 2022 Andersen et al.)

The phylogeography of the Kaloula genus in East Asia is still poorly understood. One of the difficulties is the absence of fossils to corroborate molecular dating estimates. Here, we examined the mitochondrial structure of Kaloula spp. in East Asia and focused on the impact of glaciations on the northernmost species: Kaloula borealis. We determined the phylogenetic relationships, molecular dating, and genetic connectivity assessments within the genus from 1211 bp of concatenated mitochondrial 12S and 16S. The relaxed clock analyses reveal the emergence of Kaloula spp. common ancestor in East and Southeast Asia between the Eocene and Oligocene, c. 38.47 Ma (24.69-53.65). The genetic diversification of lineages then increased on the East Asian Mainland during the Lower Miocene, c. 20.10 (8.73-30.65), most likely originating from the vicariance and radiation triggered by the orogeny of the Qinghai-Tibetan Plateau. Later, the dispersal towards the North East Asian Mainland during the Upper Miocene drove the population diversification of K. borealis c. 9.01 Ma (3.66-15.29). Finally, the central mainland population became isolated following orogenesis events and diverged into K. rugifera during the Pliocene, c. 3.06 Ma (0.02-10.90). The combination of population genetic and barrier analyses revealed a significant genetic isolation between populations of Kaloula spp. matching with the massive Qinling-Daba Mountain chain located in south-central China. Finally, we highlight a young divergence within the Eastern Mainland population of K. borealis, possibly attributed to refugia in south eastern China from which populations later expanded., (© 2021 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.)

Mutation is the primary determinant of genetic diversity in influenza viruses. The rate of mutation, measured in an absolute time-scale, is likely to be dependent on the rate of errors in copying RNA sequences per replication and the number of replications per unit time. Conditions for viral replication are probably different among host taxa, potentially generating the host specificity of the viral mutation rate, and possibly between highly and low pathogenic (HP and LP) viruses. This study investigated whether mutation rates per year in avian influenza A viruses depend on host taxa and pathogenicity. We inferred mutation rates from the rates of synonymous substitutions, which are assumed to be neutral and thus equal to mutation rates, at four segments that code internal viral proteins (PB2, PB1, PA, NP). On the phylogeny of all avian viral sequences for each segment, multiple distinct subtrees (clades) were identified that represent viral subpopulations, which are likely to have evolved within particular host taxa. Using simple regression analysis, we found that mutation rates were significantly higher in viruses infecting chickens than domestic ducks and in those infecting wild shorebirds than wild ducks. Host dependency of the substitution rate was also confirmed by Bayesian phylogenetic analysis. However, we did not find evidence that the mutation rate is higher in HP than in LP viruses. We discuss these results considering viral replication rate as the major determinant of mutation rate per unit time., (© The Author(s) 2022. Published by Oxford University Press.)

Taxa with vast distribution ranges often display unresolved phylogeographic structures and unclear taxonomic boundaries resulting in hidden diversity. This hypothesis-driven study reveals the evolutionary history of Bufonidae, covering the phylogeographic patterns found in Holarctic bufonids from the West Gondwana to the phylogenetic taxonomy of Asiatic true toads in the Eastern Palearctic. We used an integrative approach relying on fossilized birth-death calibrations, population dynamics, gene-flow, species distribution, and species delimitation modeling to resolve the biogeography of the clade and highlight cryptic lineages. We verified the near-simultaneous Miocene radiations within Western and Eastern Palearctic Bufo , c. 14.49-10.00 Mya, temporally matching with the maximum dust outflows in Central Asian deserts. Contrary to earlier studies, we demonstrated that the combined impacts of long dispersal and ice-age refugia equally contributed to the current genetic structure of Bufo in East Asia. Our findings reveal a climate-driven adaptation in septentrional Eastern Asian Bufo , explaining its range shifts toward northern latitudes. We resolve species boundaries within the Eastern Palearctic Bufo , and redefine the taxonomic and conservation units of the northeastern species: B. sachalinensis and its subspecies., Competing Interests: SO, SL, IM, HD, KM, DA, MJ, YK, DS, KY, MC, YC, YB, JH, YJ, AB No competing interests declared, (© 2022, Othman et al.)

Morphological and molecular analyses of Korean rhizocephalan barnacle species were performed to examine their host ranges and taxonomy. Morphological examination and molecular analysis of mtDNA cox1 , 16S, and nuclear 18S rRNA sequences revealed nine rhizocephalan species from three genera of the two families, Sacculinidae and Polyascidae. Phylogenetic analysis of molecular sequences revealed two new species candidates in the genus Parasacculina , and three Sacculina species ( S. pilosella , S. pinnotherae , and S. imberbis ) were transferred to the genus Parasacculina. Examination of host ranges revealed higher host specificity and lower infestation rates in Korean rhizocephalan species than rhizocephalans from other geographic regions. This is the first report of the taxonomy, species diversity, and host ranges of Korean parasitic rhizocephalan barnacles based on their morphological and molecular analyses. More information from extensive sampling of parasitic barnacles from a wide range of crustacean host species is necessary to fully understand their taxonomy, prevalence on decapod hosts, and phylogenetic relationships among major rhizocephalan taxa., Competing Interests: The authors declare there are no competing interests., (©2021 Jung et al.)

Wild-type Escherichia coli was adapted to syntrophic growth with Methanobacterium formicicum for glycerol fermentation over 44 weeks. Succinate production by E. coli started to increase in the early stages of syntrophic growth. Genetic analysis of the cultured E. coli population by pooled sequencing at eight time points suggests that (i) rapid evolution occurred through repeated emergence of mutators that introduced a large number of nucleotide variants and (ii) many mutators increased to high frequencies but remained polymorphic throughout the continuous cultivation. The evolved E. coli populations exhibited gains both in fitness and succinate production, but only for growth under glycerol fermentation with M. formicicum (the condition for this laboratory evolution) and not under other growth conditions. The mutant alleles of the 69 single nucleotide polymorphisms (SNPs) identified in the adapted E. coli populations were constructed individually in the ancestral wild-type E. coli. We analyzed the phenotypic changes caused by 84 variants, including 15 nonsense variants, and found that FdrA D296Y was the most significant variant leading to increased succinate production. Transcription of fdrA was induced under anaerobic allantoin degradation conditions, and FdrA was shown to play a crucial role in oxamate production. The FdrA D296Y variant increased glyoxylate conversion to malate by accelerating oxamate production, which promotes carbon flow through the C4 branch, leading to increased succinate production. IMPORTANCE Here, we demonstrate the ability of E. coli to perform glycerol fermentation in coculture with the methanogen M. formicicum to produce succinate. We found that the production of succinate by E. coli significantly increased during successive cocultivation. Genomic DNA sequencing, evaluation of relative fitness, and construction of SNPs were performed, from which FdrA D296Y was identified as the most significant variant to enable increased succinate production by E. coli. The function of FdrA is uncertain. In this study, experiments with gene expression assays and metabolic analysis showed for the first time that FdrA could be the "orphan enzyme" oxamate:carbamoyltransferase in anaerobic allantoin degradation. Furthermore, we demonstrate that the anaerobic allantoin degradation pathway is linked to succinate production via the glyoxylate pathway during glycerol fermentation.

Tropical rainforests are characterized by a high diversity of plant species. Each plant species presents with differential phenological patterns in fruit production. In some species, all individual trees produce fruit simultaneously within clustered periods; whereas in others, each individual tree fruits at irregular time intervals. By observing this pattern, some primate species use the presence of fruits in one tree as a cue to find fruit in other trees of the same synchronously fruiting tree species. Here, we investigated whether the highly frugivorous Javan gibbons (Hylobates moloch) in Gunung Halimun-Salak National Park in Indonesia have knowledge of synchronous characteristics of fruiting trees and whether they can further distinguish fruit species with different synchrony levels, that is, tree species with highly synchronous fruiting patterns versus tree species with less synchronous fruiting patterns. Across 12 months we collected biweekly phenological data on 250 trees from 10 fruit species and observed Javan gibbons' visits to those species. We found that a fruit discovery in the beginning of fruiting seasons triggered gibbons to visit trees of the same fruit species. However, gibbons' visit rates did not differ between highly synchronous and asynchronous species. Our results suggest that Javan gibbons have knowledge of synchronous characteristics of fruiting trees in general, but they do not differentiate highly synchronous versus asynchronous fruit species. We speculate that Javan gibbons, who live in relatively small ranges with very low tree density of preferred fruit species, are likely able to track and remember fruiting states of individual trees without needing to distinguish fruit species with different synchrony levels. Moreover, gibbons may make little benefit of distinguishing highly synchronous versus asynchronous fruit species, probably due to gibbons' heavy use of asynchronous figs. Our study provides an insight into how gibbon's foraging strategies may have been shaped in response to their ecological environment., (© 2021 Wiley Periodicals LLC.)

In metropolitan Seoul, populations of the cicada Hyalessa fuscata in hotter urban heat islands ("high UHIs") exhibit higher thermal tolerance than those in cooler UHIs ("low UHIs"). We hypothesized that heat stress may activate the expression of genes that facilitate greater thermal tolerance in high-UHI cicadas than in those from cooler areas. Differences in the transcriptomes of adult female cicadas from high-UHI, low-UHI, and suburban areas were analyzed at the unheated level, after acute heat stress, and after heat torpor. No noticeable differences in unheated gene expression patterns were observed. After 10 min of acute heat stress, however, low-UHI and suburban cicadas expressed more heat shock protein genes than high-UHI counterparts. More specifically, remarkable changes in the gene expression of cicadas across areas were observed after heat torpor stimulus, as represented by a large number of up- and downregulated genes in the heat torpor groups compared with the 10 min acute heat stress and control groups. High-UHI cicadas expressed the most differentially expressed genes, followed by the low-UHI and suburban cicadas. There was a notable increase in the expression of heat shock, metabolism, and detoxification genes; meanwhile, immune-related, signal transduction, and protein turnover genes were downregulated in high-UHI cicadas versus the other cicada groups. These results suggested that under heat stress, cicadas inhabiting high-UHIs could rapidly express genes related to heat shock, energy metabolism, and detoxification to protect cells from stress-induced damage and to increase their thermal tolerance toward heat stress. The downregulation of apoptosis mechanisms in high-UHI cicadas suggested that there was less cellular damage, which likely contributed to their high tolerance of heat stress.

Determining the range, status, ecology and behaviour of species from areas where surveys and samplings are uncommon or difficult to conduct is a challenge, such as in the Democratic People's Republic of Korea (DPR Korea). Here, we used genetic samples, field surveys, call recordings, photographic identification and a literature review to estimate the presence, range and status of amphibians in the DPR Korea. From our combined results and based on the IUCN Red List categories and criteria, we were able to estimate the national threat levels for most species. Our results demonstrated the presence of 18 native species and the suspected presence of Karsenia koreana and two Onychodactylus species. We reported the first record for Rana uenoi in the vicinity of Pyongyang using molecular tools and similarly confirmed the presence of Dryophytes japonicus at the same location. Based on distribution and modelling, we can expect the contact zone between species within the Rana and Onychodactylus genera to be located along the Changbai Massif, a mountain range that marks a shift in ecoregions and acts as a barrier to dispersion. The species richness was higher in the lowlands and at lower latitudes, with such areas populated by up to 11 species, while more northern regions were characterised by species richness of about half of that value. The combination of ecological models and known threats resulted in the recommendation of ten species as threatened at the national level following the IUCN Red List categories and criteria. This high number of threatened species was anticipated based on the high threat level to amphibians in bordering nations and globally. While the ecology of species in the DPR Korea is still understudied, we argue that species relying on agricultural wetlands such as rice paddies are not under imminent threat due to the enduring presence of extensive agricultural landscapes with low rates of chemical use and mechanisation. The maintenance of such landscapes is a clear benefit to amphibian species, in contrast to more industrialised agricultural landscapes in neighbouring nations. In comparison, the status of species dependent on forested habitats is unclear and threat levels are likely to be higher because of deforestation, as in neighbouring nations.

Snakebite envenomings remain a neglected disease across the globe causing severe injuries and death. An understanding of regional snakebite patterns is a necessary prerequisite for public health programs aimed at reducing snakebite risks. However, such regional knowledge is poorly documented or lacking in many countries where the risk of snakebite envenomings receive little medical attention, and the Republic of Korea is one of these countries. Here, we reviewed the literature on snakebites published between 1970 and 2020 as well as public healthcare data recorded between 2010 and 2019 to determine the patterns of snakebite envenomings in the Republic of Korea. Our results, based on literature data, show Gangwon province as a hotspot of snakebite occurrences and identify middle-aged males living in rural areas as the demographic group at highest risk of venomous snakebites. We also highlight major limitations for further understanding snakebite patterns in the country, most notably the lack of proper species identification for snakes and conflicting patterns of envenomings revealed by different sources of data. Our study provides baseline information on venomous snakebites occurring in the Republic of Korea, thereby filling a gap in the knowledge of snakebite trends in the country., (Copyright © 2021 Elsevier Ltd. All rights reserved.)