The endangered and poorly known Swamp Grass-babbler, Laticilla cinerascens (Passeriformes: Pellorneidae), confronts critical threats and vulnerability due to its specific habitat requirements and restricted populations in the northeastern region of the Indian Subcontinent. This study investigates the distribution of the species, habitat quality, geometry and shape complexity of connectivity among the protected areas (PAs), and responses to climate change in Northeast India under different climate change pathways by utilizing ensemble distribution models, and ecological metrics. From the total distribution extent (1,42,000 km2), approximately 9366 km2 (6.59 %) is identified as the suitable habitat for this threatened species. Historically centered around Dibru Saikhowa National Park (DSNP), the species faced a drastic decline due to anthropogenic activities and alteration in land use and lover cover. The study also reveals a significant decline in suitable habitat for L. cinerascens in future climate scenarios, with alarming reductions under SSP126 (>10 % in the timeframe 2041-2060 and > 30 % from 2061 to 2080), SSP245 (>90 % in both time periods), and SSP585 (>90 % in both timeframes) from the present scenario. At present, DSNP has the most suitable habitat within the distribution range but is projected to decline (>90 %) under more severe climate change scenarios, as observed in other PAs. Landscape fragmentation analysis indicates a shift in habitat geometry, highlighting the intricate impact of climate change. It predicts a substantial 343 % increase (in the SSP126) in small habitat patches in the future. Connectivity analysis among PAs shows a significant shift, with a decline exceeding 20 %. The analysis of shape complexity and connectivity geometry reveals a significant increase of over 220 % in the fragmentation of connectivity among PAs between 2061 and 2080 under the SSP585 climate change scenario compared to the present conditions. The study underscores the urgent need for conservation actions, emphasizing the complex interplay of climate change, habitat suitability, and fragmentation. Prioritizing PAs with suitable habitats and assessing their connectivity is crucial. Adaptive management strategies are essential to address ongoing environmental changes and safeguard biodiversity. Future research in critical areas is needed to establish long-term monitoring programs to lead/extend effective conservation strategies.
The hispid hare, Caprolagus hispidus, belonging to the family Leporidae is a small grassland mammal found in the southern foothills of the Himalayas, in India, Nepal, and Bhutan. Despite having an endangered status according to the IUCN Red List, it lacks studies on its distribution and is threatened by habitat loss and land cover changes. Thus, the present study attempted to assess the habitat suitability using the species distribution model approach for the first time and projected its future in response to climate change, habitat, and urbanization factors. The results revealed that out of the total geographical extent of 188,316 km2, only 11,374 km2 (6.03%) were identified as suitable habitat for this species. The results also revealed that habitat significantly declined across its range (>60%) under certain climate change scenarios. Moreover, in the present climate scenario protected areas such as Shuklaphanta National Park (0.837) in Nepal exhibited the highest mean extent of habitat whereas, in India, Dibru-Saikhowa National Park (0.631) is found to be the most suitable habitat. Notably, two protected areas in Uttarakhand, India, specifically Corbett National Park (0.530) and Sonanandi Wildlife Sanctuary (0.423), have also demonstrated suitable habitats for C. hispidus. Given that protected areas showing a future rise in habitat suitability might also be regarded as potential sites for species translocation, this study underscores the importance of implementing proactive conservation strategies to mitigate the adverse impacts of climate change on this species. It is essential to prioritize habitat restoration, focused protection measures, and further species-level ecological exploration to address these challenges effectively. Furthermore, fostering transboundary collaboration and coordinated conservation actions between nations is crucial to safeguarding the long-term survival of the species throughout its distribution range.
The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.
Bass , Genome, Mitochondrial , Animals , Phylogeny , Bass/genetics , Bayes Theorem , Base Composition , RNA, Transfer/genetics , RNA, Ribosomal/genetics , Serine/genetics
To assess the impact of sand mining on resource utilization by the red seabream (Pagrus major) and the trophic structure of fish assemblages two years after mining activities, we compared stable isotope ratios (δ13C and δ15N) and isotopic niches between aggregated mining and control sites in April and August 2022. Our results showed no spatial differences in the δ13C and δ15N values of red seabream between the sand mining and control sites, suggesting that the mining did not affect their dietary resources. Furthermore, the considerable overlap among fish consumers suggested that the fish food web in mining areas has trophic functions similar to those in natural habitats after mining activities. Overall, our study enhances our understanding of ecosystem conservation and the ecological-based management of coastal areas.
Perciformes , Sea Bream , Animals , Humans , Ecosystem , Environmental Biomarkers , Carbon Isotopes/analysis , Sand , Nitrogen Isotopes/analysis , Food Chain , Fishes , Human Activities , Republic of Korea
The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.
The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation.
Cichlids , Animals , Cichlids/genetics , Cameroon , Bayes Theorem , Codon, Terminator , Phylogeny , Polycomb-Group Proteins
Microbial community structures of harmful algal bloom (HAB) caused by Heterosigma akashiwo in Geoje were analyzed using the MiSeq platform. To analyze phytoplankton communities without cross-reactivity with predominant bacteria, a new phytoplankton-specific 23S universal primer set was designed by modifying two previously used ones. The new universal primer set turned out to be a useful tool for the analysis of the phytoplankton community; it showed a high specificity for phytoplankton without cross-reactivity to bacterial sequences as well as the wide taxon coverage presenting from prokaryotic cyanobacteria to eukaryotic algae. Next Generation Sequencing (NGS) data generated by two universal primer sets (16S and 23S) provided useful information about the H. akashiwo bloom. According to the 23S universal primer set, proportions of H. akashiwo increased by more than 200-fold as the bloom occurred and its numbers were high enough to detect in control sites. Its operational taxonomic units (OTUs) were detected in the bloom sites at low proportions suggesting that the 16S universal primer set may not be as effective for monitoring harmful algal blooming (HAB) as the 23S universal primer set. In addition, several abundant OTUs in Chlorophyta were not presented by the 16S universal primer set in this study. However, the 16S primer set was useful for detecting decreases in Foraminifera as HAB occurred suggesting that genomic analyses using two universal primer sets would provide more reliable data for understanding microbial community changes by various environmental or ecological events, including HAB. Genomic analyses using two universal primer sets was also useful for determining a correlation between microbial components as HAB occurred. Heterosigma akashiwo was positively correlated with other bloom species, including Karenia mikimotoi, Teleaulax amphioxeia, and bacteria in Verrucomicrobia.
Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species. A total of 19 species was identified from the stomach of D. mawsoni in this study, which included 14 fish species and five mollusks. More than 90% of contigs belonged to fish species, supporting the postulate that the major prey of D. mawsoni are fish. Two fish species, Macrourus whitsoni and Chionobathyscus dewitti, were the most important prey items (a finding similar to that of previous studies). We also obtained genotypes of prey items by NGS analysis, identifying an additional 17 representative haplotypes in this study. Comparison with three previous morphological studies and the NGS-based molecular identification in this study extended our knowledge regarding the prey of D. mawsoni, which previously was not possible. These results suggested that NGS-based diet studies are possible, if several current technical limitations, including the quality of the barcode database or the development of precise molecular quantification techniques to link them with morphological values, are overcome. To achieve this, additional studies should be conducted on various marine organisms.
We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404-411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology.
We determined the complete mitochondrial genome of Metapenaeopsis dalei (Rathbun, 1902), which is collected from East China Sea (124°E and 33.5°N). Total mitochondrial genome length of M. dalei was 15 939 bp, in which 13 proteins, two ribosomal RNAs, 22 transfer RNAs and a putative control region were encoded. The gene arrangement of M. dalei was well conserved with nine known Penaeidae mitochondrial genomes from COX1 to tRNATyr . The protein-coding genes started with ATN except for COX1 in which ACG is used. Four genes (COX2, COX3, ND3 and ND5) exhibited an incomplete stop codon. Nucleotide sequence identity of M. dalei mitochondrial genome to those of nine Penaeidae species ranged from 78% to 80%. Based on the COI region, M. dalei is most closely related to Penaeus notialis.
We characterized the complete mitochondrial genome of Squilloides leptosquilla (Brooks, 1886) collected from the southern waters of Korea, which is newly recorded into the Korean carcinological fauna. The total mitochondrial genome length of S. leptosquilla was 16,376 bp. This circular DNA encodes 13 proteins, two ribosomal RNAs, and 22 transfer RNAs, as well as a putative control region. Compared with other decapod crustacean mitochondrial genomes, the overall A + T content was relatively high (71.1%) as those among other stomatopod species. Nine and four protein-coding genes are encoded on the H-strand and on the L-strand, respectively. The short non-coding region (210 bp) between tRNA(Glu) and tRNA(Phe) may be the good candidate as the molecular marker to discriminate S. leptosequilla from other stomatopods.
Crustacea/genetics , Genome, Mitochondrial/genetics , Animals , Crustacea/classification , DNA Barcoding, Taxonomic , DNA, Mitochondrial/genetics , Genes, Mitochondrial/genetics , Phylogeny , RNA, Ribosomal/genetics , RNA, Transfer/genetics , Sequence Analysis, DNA
