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Wong MK, Chen WJ. Exploring the phylogeny and depth evolution of cusk eels and their relatives (Ophidiiformes: Ophidioidei). Mol Phylogenet Evol 2024; 199:108164. [PMID: 39084413 DOI: 10.1016/j.ympev.2024.108164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 07/27/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
With 289 known species in 51 genera, the ophidiiform family Ophidiidae together with their relatives from the Carapidae (36 species in eight genera) of the same suborder Ophidioidei dominate the deep sea, but some occur also in shallow water habitats. Despite their high species diversity in the deep sea and wide bathymetric distributions, their phylogenetic relationships and evolution remain unexplored due in part to sampling difficulties. Thanks to the biodiversity exploratory program entitled "Tropical Deep-Sea Benthos" and joint efforts between Taiwan and French teams for sampling from different localities across the Indo-West Pacific over the last two decades, we are able to compile comprehensive datasets for investigations. In this study, 59 samples representing 36 of 59 known ophidioid genera are selected and used to construct a multi-gene dataset to infer the phylogenetic relationships of ophidioid fishes and their relatives. Our results reveal that the Ophidiidae forms a paraphyletic group with respect to the Carapidae. The four main clades of Ophidioidei resolved are the (1) clade comprising species from the subfamily Brotulinae; (2) clade that includes species in the genera Acanthonus and Xyelacyba; (3) clade grouping Hypopleuron caninum with species from the family Carapidae; and (4) clade containing the species in the subfamily Brotulotaenilinae, Neobythitinae (in part), and Ophidiinae. Accordingly, we suggest the following new revisions based on our results and proposed morphological diagnoses. The subfamily Brotulinae should be elevated to the family level. The genera Xyelacyba and probably Tauredophidium (unsampled in this study) should be included in the newly established family Acanthonidae with Acanthonus. The families Carapidae and Ophidiidae are re-defined. Our time-calibrated phylogenetic and ancestral depth reconstructions enable us to clarify the evolutionary history of ophidiiform fishes and infer past patterns of species distributions at different depths. While Ophidiiformes is inferred to have originated in shallow waters around 96.25 million years ago (Mya), the common ancestor to the Ophidioidei is inferred to have invaded the deep sea around 90.22 Mya, the dates coinciding with the global anoxic event of the OAE2. The observed bathymetric distribution patterns in Ophidioidei most likely point to the mesopelagic zone as the center of origin and diversification. This was followed by multiple events of depth transitions or range expansions towards either shallower waters or greater depth zones, which were likely triggered by past climate changes during the Paleogene-Neogene.
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Affiliation(s)
- Man-Kwan Wong
- Institute of Oceanography, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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Yang TY, Zhu ZY, Liu YP, Wang SG. The First Genome-Wide Survey of Shortbelly Eel (Dysomma anguillare Barnard, 1923) to Provide Genomic Characteristics, Microsatellite Markers and Complete Mitogenome Information. Biochem Genet 2024; 62:2296-2313. [PMID: 37906301 DOI: 10.1007/s10528-023-10543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Dysomma anguillare is a demersal eel widespread distributing in tropical waters of the Indo-West Pacific and Atlantic. As an important component of the coastal fishery and marine ecosystem, the lack of genomic information for this species severely restricts the progress of relevant researches. In this study, the abecedarian genome-wide characteristics and phylogenetic relationships analyses were carried out based on next-generation sequencing (NGS) platform. The revised genome size was approximately 1 310 Mb, with the largest scaffold length reaching 23 878 bp through K-mer (K = 17) method. The heterozygosity, repetitive rate and average GC content were about 0.94%, 51.93% and 42.23%, respectively. A total of 1 160 104 microsatellite motifs were identified from the de novo assembled genome of D. anguillare, in which dinucleotide repeats accounted for the largest proportion (592 234, 51.05%), the highest occurrence frequency (14.58%) as well as the largest relative abundance (379.27/Mb). The high-polymorphic and moderate-polymorphic loci composed around 73% of the total single sequence repeats (SSRs), showing a latent capacity for subsequent population genetic structure and genetic diversity appraisal researches. Another byproduct of whole-genome sequencing, the double-stranded and circular mitogenome (16 690 bp) was assembled to investigate the evolutionary relationships of D. anguillare. The phylogenic tree constructed with maximum likelihood (ML) method showed that D. anguillare was closely related to Synaphobranchidae species, and the molecular systematic results further supported classical taxonomy status of D. anguillare.
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Affiliation(s)
- Tian-Yan Yang
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China.
| | - Zi-Yan Zhu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Yu-Ping Liu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Si-Ge Wang
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
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Zhu Z, Liu Y, Zhang S, Wang S, Yang T. Genomic microsatellite characteristics analysis of Dysommaanguillare (Anguilliformes, Dysommidae), based on high-throughput sequencing technology. Biodivers Data J 2023; 11:e100068. [PMID: 38327339 PMCID: PMC10848815 DOI: 10.3897/bdj.11.e100068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/31/2023] [Indexed: 02/09/2024] Open
Abstract
Microsatellite loci were screened from the genomic data of Dysommaanguillare and their composition and distribution were analysed by bioinformatics for the first time. The results showed that 4,060,742 scaffolds with a total length of 1,562 Mb were obtained by high-throughput sequencing and 1,160,104 microsatellite loci were obtained by MISA screening, which were distributed on 770,294 scaffolds. The occurrence frequency and relative abundance were 28.57% and 743/Mb, respectively. Amongst the six complete microsatellite types, dinucleotide repeats accounted for the largest proportion (592,234, 51.05%), the highest occurrence frequency (14.58%) and the largest relative abundance (379.27/Mb). A total of 1488 microsatellite repeats were detected in the genome of D.anguillare, amongst which the hexanucleotide repeat motifs were the most abundant (608), followed by pentanucleotide repeat motifs (574), tetranucleotide repeat motifs (232), trinucleotide repeat motifs (59), dinucleotide repeat motifs (11) and mononucleotide repeat motifs (4). The abundance of microsatellites of the same repeat type decreased with the increase of copy numbers. Amongst the six types of nucleotide repeats, the preponderance of repeated motifs are A (191,390, 43.77%), CA (150,240, 25.37%), AAT (13,168, 14.05%), CACG (2,649, 8.14%), TAATG (119, 19.16%) and CCCTAA (190, 19.16%, 7.65%), respectively. The data of the number, distribution and abundance of different types of microsatellites in the genome of D.anguillare were obtained in this study, which would lay a foundation for the development of high-quality microsatellite markers of D.anguillare in the future.
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Affiliation(s)
- Ziyan Zhu
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Yuping Liu
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research InstituteGuangzhouChina
| | - Sige Wang
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
| | - Tianyan Yang
- Zhejiang Ocean University, Zhoushan, ChinaZhejiang Ocean UniversityZhoushanChina
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Espíndola VC, Johnson GD, De Pinna MCC. Facial and opercular muscles in the Anguilliformes (Elopomorpha: Teleostei): Comparative anatomy and phylogenetic implications for the basal position of Protanguilla. J Morphol 2023; 284:e21556. [PMID: 36630618 DOI: 10.1002/jmor.21556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023]
Abstract
The teleost order Anguilliformes, true eels, comprises more than 1000 described species in 20 families, commonly known as eels, congers, morays, and gulper eels. Comprehensive studies of Anguilliformes are limited, resulting in a lack of consensus for morphology-based phylogenetic hypotheses. A detailed morphological analysis of the cephalic and opercular myology offers a promising new source of characters to help elucidate the intrarelationships of Anguilliformes. Our study is the most extensive myological analysis for the group and includes 97 terminal taxa, with representatives from each of the 20 families of Anguilliformes plus outgroup clades. Results demonstrate that muscle characters inform phylogenetic relationships within Anguilliformes, and we propose two new synapomorphies for all extant members, including Protanguilla palau, the "living fossil"-adductor mandibulae originating on the parietal (vs. restricted to suspensorium) and segmentum mandibularis absent (vs. present). Exceptions for the first condition characterize highly modified saccopharyngoids, and for the second one, Notacanthidae. More importantly, we suggest three new synapomorphies for the remaining extant anguilliforms (except in highly modified saccopharyngoids)-adductor mandibulae originates on the frontals (vs. frontals naked), adductor mandibulae stegalis is separated from the rictalis (vs. ricto-stegalis fused into a single piece), and the levator operculi inserts on the lateral surface of the opercle (vs. medial surface of the opercle). Our phylogenetic optimization strongly corroborates the hypothesis that Protanguilla is the sister group of all other extant eels. A further goal of this paper is to clearly document the substantive conflicts between the available molecular data and the extensive and diverse morphological evidence.
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Affiliation(s)
- Vinicius C Espíndola
- Division of Fishes, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - G David Johnson
- Division of Fishes, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Mario C C De Pinna
- Museu de Zoologia, Setor de ictiologia, Universidade de São Paulo, São Paulo, SP, Brazil
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Yang T, Liu Y, Ning Z. Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals (Basel) 2023; 13:ani13030362. [PMID: 36766251 PMCID: PMC9913227 DOI: 10.3390/ani13030362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The family Ophichthidae has the largest number and the most various species (about 359 valid species) in the order Anguilliformes worldwide. Both morphological and molecular characteristics have been used to assess their taxonomic status. However, due to the ambiguous morphological features, molecular data such as mitochondrial DNA sequences have been implemented for the correct identification and classification of these fishes. In this study, the gene arrangement and structure characteristics of two Ophichthidae mitochondrial genomes were investigated for the first time. The total mitogenome lengths of O. evermanni and O. erabo were 17,759 bp and 17,856 bp, respectively. Comparing with the ancestral mitochondrial gene order, the irregular gene rearrangement happened between ND6 and tRNA-Pro (P) genes with another similar control region emerging between tRNA-Thr (T) and ND6 genes, which could be explained by the tandem duplication and random loss (TDRL) model appropriately. ML phylogenetic tree demonstrated that the family Ophichthidae was monophyletic origin, but genus Ophichthus might be polyphyletic because of the confused cluster relationships among different species.
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Two New Moray Eels of Genera Diaphenchelys and Gymnothorax (Anguilliformes: Muraenidae) from Taiwan and the Philippines. Zool Stud 2021; 60:e24. [PMID: 34853614 DOI: 10.6620/zs.2021.60-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/07/2021] [Indexed: 11/18/2022]
Abstract
Two new moray eels of the genera Diaphenchelys and Gymnothorax from Taiwan and the Philippines are described. Diaphenchelys laimospila sp. nov. is described based on two specimens that represent the third species and a new geographic record of the genus. It can be distinguished from the other two congeners by the number of cephalic sensory pores, vertebral formula, morphometric measurements, and the coloration pattern. Gymnothorax pseudokidako sp. nov. is a muraenid with a dark brown body covered by pale snowflake-like blotches. It differs from the most similar species Gymnothorax kidako (Temminck and Schlegel) by having a relatively short tail (50.5-53.0% vs. 52.9-56.4% of TL), more dentary teeth (17-26 vs. 16-20), fewer total vertebrae (134-139 vs. 137-143), and the absence of white margin on anal fin (vs. prominent white margin). These two new species were also confirmed by molecular analyses, the mitochondrial COI gene (593 bp) for D. laimospila, and the nuclear EGR3 gene (767 bp) for G. pseudokidako.
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Dornburg A, Near TJ. The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-122120-122554] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina 28223, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511, USA
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Takezaki N. Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data. Genome Biol Evol 2021; 13:6178791. [PMID: 33739405 PMCID: PMC8103497 DOI: 10.1093/gbe/evab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Regarding the phylogenetic relationship of the three primary groups of teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha (eels and relatives), Clupeocephala (the remaining teleost fish), early morphological studies hypothesized the first divergence of Osteoglossomorpha, whereas the recent prevailing view is the first divergence of Elopomorpha. Molecular studies supported all the possible relationships of the three primary groups. This study analyzed genome-scale data from four previous studies: 1) 412 genes from 12 species, 2) 772 genes from 15 species, 3) 1,062 genes from 30 species, and 4) 491 UCE loci from 27 species. The effects of the species, loci, and models used on the constructed tree topologies were investigated. In the analyses of the data sets (1)–(3), although the first divergence of Clupeocephala that left the other two groups in a sister relationship was supported by concatenated sequences and gene trees of all the species and genes, the first divergence of Elopomorpha among the three groups was supported using species and/or genes with low divergence of sequence and amino-acid frequencies. This result corresponded to that of the UCE data set (4), whose sequence divergence was low, which supported the first divergence of Elopomorpha with high statistical significance. The increase in accuracy of the phylogenetic construction by using species and genes with low sequence divergence was predicted by a phylogenetic informativeness approach and confirmed by computer simulation. These results supported that Elopomorpha was the first basal group of teleost fish to have diverged, consistent with the prevailing view of recent morphological studies.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
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9
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Zhang K, Zhu K, Liu Y, Zhang H, Gong L, Jiang L, Liu L, Lü Z, Liu B. Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes. Sci Rep 2021; 11:2411. [PMID: 33510193 PMCID: PMC7844273 DOI: 10.1038/s41598-021-81622-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023] Open
Abstract
The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.
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Affiliation(s)
- Kun Zhang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Kehua Zhu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Yifan Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Hua Zhang
- grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Li Gong
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Lihua Jiang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Liqin Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Zhenming Lü
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Bingjian Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
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Soares RX, da Costa GWWF, Cioffi MDB, Bertollo LAC, Motta-Neto CCD, Molina WF. Molecular cytogenetics insights in two pelagic big-game fishes in the Atlantic, the tarpon, Megalops atlanticus (Elopiformes: Megalopidae), and the sailfish, Istiophorus platypterus (Istiophoriformes: Istiophoridae). NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Some pelagic and usually large sized fishes are preferential targets for sport and commercial fishing. Despite their economic importance, cytogenetic data on their evolutionary processes and management are very deficient, especially due to logistical difficulties. Here, information for two of such charismatic species, the tarpon, Megalops atlanticus (Elopiformes: Megalopidae), and the sailfish, Istiophorus platypterus (Istiophoriformes: Istiophoridae), both with a wide Atlantic distribution, were provided. Cytogenetic data were obtained using conventional methods (Giemsa staining, Ag-NORs technique, and C-banding), base-specific fluorochrome staining and fluorescence in situ hybridization (FISH) with rDNA probes. Megalops atlanticus has 2n = 50 chromosomes, all acrocentric ones (NF = 50), while Istiophorus platypterus has 2n = 48 chromosomes, 2m + 2st + 44a (NF = 52). Megalops atlanticus populations from the South Atlantic and Caribbean share identical karyotypic patterns, likely associated with gene flow between them. In turn, I. platypterus presents karyotype similarities with phylogenetically close groups, such as Carangidae. The chromosomal characteristics of these species highlight their independent evolutionary paths. Additionally, the current data contribute to knowledge of new aspects of pelagic fish fauna and will support further comparative studies with congeneric species, clarifying evolutionary karyotype trends of these fish groups.
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de Sousa RPC, Silva-Oliveira GC, Furo IO, de Oliveira-Filho AB, de Brito CDB, Rabelo L, Guimarães-Costa A, de Oliveira EHC, Vallinoto M. The role of the chromosomal rearrangements in the evolution and speciation of Elopiformes fishes (Teleostei; Elopomorpha). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2020.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chen WJ, Borsa P. Diversity, phylogeny, and historical biogeography of large-eye seabreams (Teleostei: Lethrinidae). Mol Phylogenet Evol 2020; 151:106902. [PMID: 32619569 DOI: 10.1016/j.ympev.2020.106902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 06/19/2020] [Accepted: 06/26/2020] [Indexed: 12/01/2022]
Abstract
The large-eye seabreams or Monotaxinae is one of two subfamilies in the Lethrinidae, a family of perch-like coral reef fishes. Despite its widespread occurrence and its commercial interest in the tropical Indo-West Pacific (IWP), this subfamily has traditionally been considered a taxonomically difficult group. Based on 268 samples collected from all 15 known large-eye seabream species throughout their distribution ranges, we investigated the taxonomic diversity and phylogenetic relationships in the subfamily. From the results of multiple analyses on four gene markers, we confirmed the monophyly of all four genera in the subfamily (Gnathodentex, Gymnocranius, Monotaxis and Wattsia). We confirmed the occurrence of two species in the genus Monotaxis. We reported 15 delimited species within the most speciose genus Gymnocranius, four of which are potentially new species. The time-calibrated phylogenetic reconstruction enabled us to clarify the evolutionary history of the large-eye seabreams and to infer past patterns of species distribution. The most recent common ancestor to the Monotaxinae likely occurred in the central IWP ca. 32 million years ago. A burst of species diversification likely took place during the Mid- to Late Miocene, coinciding with tectonic change in the central IWP region. This gave rise to most extant lineages in Gymnocranius. The observed geographic distribution patterns in the subfamily most likely point to the central IWP as the area of origin and diversification. This was followed by multiple events of centrifugal range expansion towards either the Indian Ocean or the western Pacific Ocean, or both. Our results thus provide new support for S. Ekman's center-of-origin hypothesis.
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Affiliation(s)
- Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Philippe Borsa
- Institut de recherche pour le développement, IRD-UMR 250, 911 Avenue Agropolis, 34394 Montpellier cedex, France.
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Maugars G, Pasquier J, Atkinson C, Lafont AG, Campo A, Kamech N, Lefranc B, Leprince J, Dufour S, Rousseau K. Gonadotropin-inhibitory hormone in teleosts: New insights from a basal representative, the eel. Gen Comp Endocrinol 2020; 287:113350. [PMID: 31794732 DOI: 10.1016/j.ygcen.2019.113350] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022]
Abstract
Since its discovery in birds, gonadotropin-inhibitory hormone (GnIH) has triggered investigation in the other groups of vertebrates. In the present study, we have identified a single gnih gene in the European eel (Anguilla anguilla), a representative species of a basal group of teleosts (Elopomorphs). We have also retrieved a single gnih gene in Osteoglossomorphs, as well as in more recently emerged teleosts, Clupeocephala. Phylogeny and synteny analyses allowed us to infer that one of the two gnih paralogs emerged from the teleost-specific whole genome duplication (TWGD or 3R), would have been lost shortly after the 3R, before the emergence of the basal groups of teleosts. This led to the presence of a single gnih in extant teleosts as in other vertebrates. Two gnih paralogs were still found in some teleost species, such as in salmonids, but resulting from the additional whole genome duplication that specifically occurred in this lineage (4R). Eel gnih was mostly expressed in the diencephalon part of the brain, as analyzed by quantitative real-time PCR. Cloning of eel gnih cDNA confirmed that the sequence of the GnIH precursor encoded three putative mature GnIH peptides (aaGnIH-1, aaGnIH-2 and aaGnIH-3), which were synthesized and tested for their direct effects on eel pituitary cells in vitro. Eel GnIH peptides inhibited the expression of gonadotropin subunits (lhβ, fshβ, and common a-subunit) as well as of GnRH receptor (gnrh-r2), with no effect on tshβ and gh expression. The inhibitory effect of GnIH peptides on gonadotropic function in a basal teleost is in agreement with an ancestral inhibitory role of GnIH in the neuroendocrine control of reproduction in vertebrates.
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Affiliation(s)
- G Maugars
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France
| | - J Pasquier
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France
| | - C Atkinson
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France
| | - A-G Lafont
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France
| | - A Campo
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France
| | - N Kamech
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France
| | - B Lefranc
- Laboratory of Neuronal and Neuroendocrine Differentiation and Communication, INSERM U1239, Normandy University, Rouen, France
| | - J Leprince
- Laboratory of Neuronal and Neuroendocrine Differentiation and Communication, INSERM U1239, Normandy University, Rouen, France
| | - S Dufour
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France
| | - K Rousseau
- Muséum National d'Histoire Naturelle, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS, IRD, SU, UCN, UA, Paris, France.
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Identification and stable expression of vitellogenin receptor through vitellogenesis in the European eel. Animal 2020; 14:1213-1222. [PMID: 31971122 DOI: 10.1017/s1751731119003355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In teleosts, vitellogenin (Vtg) is a phospholipoglycoprotein synthesized by the liver, released into the blood circulation and incorporated into the oocytes via endocytosis mediated by the Vtg receptor (VTGR) to form the yolk granules. The VTGR is crucial for oocyte growth in egg-laying animals but is also present in non-oviparous vertebrates, such as human. The VTGR belongs to the low-density lipoprotein receptor superfamily (LDLR) and is also named very-low-density lipoprotein receptor (VLDLR). In this study, we identified and phylogenetically positioned the VTGR of a basal teleost, the European eel, Anguilla anguilla. We developed quantitative real-time PCR (qRT-PCR) and investigated the tissue distribution of vtgr transcripts. We compared by qRT-PCR the ovarian expression levels of vtgr in juvenile yellow eels and pre-pubertal silver eels. We also analyzed the regulation of ovarian vtgr expression throughout vitellogenesis in experimentally matured eels. The Vtg plasma level was measured by homologous ELISA experimental maturation. Our in silico search and phylogenetical analysis revealed a single vtgr in the European eel, orthologous to other vertebrate vtgr. The qRT-PCR studies revealed that vtgr is mainly expressed in the ovary and also detected in various other tissues such as brain, pituitary, gill, fat, heart, and testis, suggesting some extra-ovarian functions of VTGR. We showed that vtgr is expressed in ovaries of juvenile yellow eels with no higher expression in pre-pubertal silver eels nor in experimentally matured eels. This suggests that vtgr transcription already occurs during early pre-vitellogenesis of immature eels and is not further activated in vitellogenic oocytes. European eel Vtg plasma level increased throughout experimental maturation in agreement with previous studies. Taken together, these results suggest that vtgr transcript levels may not be a limiting step for the uptake of Vtg by the oocyte in the European eel.
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15
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Campbell MA, Chanet B, Chen J, Lee M, Chen W. Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. ZOOL SCR 2019. [DOI: 10.1111/zsc.12372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Bruno Chanet
- Département Origines et Évolution Muséum National d'Histoire Naturelle Paris France
| | - Jhen‐Nien Chen
- Institute of Oceanography National Taiwan University Taipei Taiwan
| | - Mao‐Ying Lee
- Institute of Oceanography National Taiwan University Taipei Taiwan
| | - Wei‐Jen Chen
- Institute of Oceanography National Taiwan University Taipei Taiwan
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16
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Johnson GD. Revisions of Anatomical Descriptions of the Pharyngeal Jaw Apparatus in Moray Eels of the Family Muraenidae (Teleostei: Anguilliformes). COPEIA 2019. [DOI: 10.1643/ci-19-211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- G. David Johnson
- Division of Fishes, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 MRC 159, Washington, D.C. 20013-7012;
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17
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Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes. Int J Biol Macromol 2019; 135:609-618. [PMID: 31132441 DOI: 10.1016/j.ijbiomac.2019.05.139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/30/2019] [Accepted: 05/21/2019] [Indexed: 11/20/2022]
Abstract
Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.
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da Silva JPCB, Datovo A, Johnson GD. Phylogenetic interrelationships of the eel families Derichthyidae and Colocongridae (Elopomorpha: Anguilliformes) based on the pectoral skeleton. J Morphol 2019; 280:934-947. [PMID: 31012502 DOI: 10.1002/jmor.20991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 11/09/2022]
Abstract
A cladistic analysis of the eel families Derichthyidae and Colocongridae is herein proposed for the first time on the basis of morphological data. We discovered dozens of new phylogenetic characters derived from a detailed analysis of the pectoral skeleton, an anatomical system neglected by most previous studies. Our maximum parsimony analysis indicates that Colocongridae sensu lato is paraphyletic, with its two constituent genera Coloconger and Congriscus appearing as successive sister groups of derichthyids. Monophyly of the family Derichthyidae, which has been questioned by some studies, is herein strongly supported by 10 unambiguous synapomorphies. We also stress the importance of the appendicular skeleton as a useful source of phylogenetic information for the resolution of systematic problems within Anguilliformes.
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Affiliation(s)
- João Paulo C B da Silva
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Aléssio Datovo
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
| | - G David Johnson
- Division of Fishes, Smithsonian Institution, National Museum of Natural History, Washington, D.C., USA
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19
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Miest JJ, Politis SN, Adamek M, Tomkiewicz J, Butts IAE. Molecular ontogeny of larval immunity in European eel at increasing temperatures. FISH & SHELLFISH IMMUNOLOGY 2019; 87:105-119. [PMID: 30590168 DOI: 10.1016/j.fsi.2018.12.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/12/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Temperature is a major factor that modulates the development and reactivity of the immune system. Only limited knowledge exists regarding the immune system of the catadromous European eel, Anguilla anguilla, especially during the oceanic early life history stages. Thus, a new molecular toolbox was developed, involving tissue specific characterisation of 3 housekeeping genes, 9 genes from the innate and 3 genes from the adaptive immune system of this species. The spatial pattern of immune genes reflected their function, e.g. complement component c3 was mainly produced in liver and il10 in the head kidney. Subsequently, the ontogeny of the immune system was studied in larvae reared from hatch to first-feeding at four temperatures, spanning their thermal tolerance range (16, 18, 20, and 22 °C). Expression of some genes (c3 and igm) declined post hatch, whilst expression of most other genes (mhc2, tlr2, il1β, irf3, irf7) increased with larval age. At the optimal temperature, 18 °C, this pattern of immune-gene expression revealed an immunocompromised phase between hatch (0 dph) and teeth-development (8 dph). The expression of two of the studied genes (mhc2, lysc) was temperature dependent, leading to increased mRNA levels at 22 °C. Additionally, at the lower end of the thermal spectrum (16 °C) immune competency appeared reduced, whilst close to the upper thermal limit (22 °C) larvae showed signs of thermal stress. Thus, protection against pathogens is probably impaired at temperatures close to the critical thermal maximum (CTmax), impacting survival and productivity in hatcheries and natural recruitment.
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Affiliation(s)
- Joanna J Miest
- Evolutionary Ecology of Marine Fish, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, Germany; School of Science, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK.
| | - Sebastian N Politis
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mikolaj Adamek
- Fish Disease Research Unit, Centre of Infectious Diseases, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Jonna Tomkiewicz
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ian A E Butts
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
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20
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Chen JN, Samadi S, Chen WJ. Rhodopsin gene evolution in early teleost fishes. PLoS One 2018; 13:e0206918. [PMID: 30395593 PMCID: PMC6218077 DOI: 10.1371/journal.pone.0206918] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 01/03/2023] Open
Abstract
Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.
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Affiliation(s)
- Jhen-Nien Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Sarah Samadi
- Institute de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle–CNRS, Sorbonne Université, EPHE, Paris, France
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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21
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Freeman MA, Kristmundsson Á. Studies of Myxidium giardi Cépède, 1906 infections in Icelandic eels identifies a genetically diverse clade of myxosporeans that represents the Paramyxidium n. g. (Myxosporea: Myxidiidae). Parasit Vectors 2018; 11:551. [PMID: 30348210 PMCID: PMC6198514 DOI: 10.1186/s13071-018-3087-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/30/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The myxosporean Myxidium giardi Cépède, 1906 was described infecting the kidney of the European eel, Anguilla anguilla (L.), having spindle-shaped myxospores and terminal sub-spherical polar capsules. Since then, numerous anguillid eels globally have been documented to have similar Myxidium infections. Many of these have been identified using the morphological features of myxospores or by the location of infection in the host, and some have been subsequently synonymised with M. giardi. Therefore, it is not clear whether M. giardi is a widely distributed parasite, infecting numerous species of eels, in multiple organs, or whether some infections represent other, morphologically similar but different species of myxosporeans. The aim of the present study was to assess the status of M. giardi infections in Icelandic eels, and related fish hosts in Malaysia and to use spore morphology and molecular techniques to evaluate the diversity of myxosporeans present. RESULTS The morphologies of the myxospores from Icelandic eels were very similar but the overall dimensions were significantly different from the various tissue locations. Myxospores from the kidney of the Malaysian tarpon, Megalops cyprinoides (Broussonet), were noticeably smaller. However, the SSU rDNA sequences from the different tissues locations in eels, were all very distinct, with percentage similarities ranging from 92.93% to as low as 89.8%, with the sequence from Malaysia being even more dissimilar. Molecular phylogenies consistently placed these sequences together in a clade that we refer to as the Paramyxidium clade that is strongly associated with the Myxidium clade (sensu stricto). We erect the genus Paramyxidium n. g. (Myxidiidae) to accommodate these histozoic taxa, and transfer Myxidium giardi as Paramyxidium giardi Cépède, 1906 n. comb. as the type-species. CONCLUSIONS There is not a single species of Myxidium (M. giardi) causing systemic infections in eels in Iceland. There are three species, confirmed with a robust phylogeny, one of which represents Paramyxidium giardi n. comb. Additional species probably exist that infect different tissues in the eel and the site of infection in the host fish is an important diagnostic feature for this group (Paramyxidium n. g. clade). Myxospore morphology is generally conserved in the Paramyxidium clade, although actual spore dimensions can vary between some species. Paramyxidium spp. are currently only known to infect fishes from the Elopomorpha.
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Affiliation(s)
- Mark A. Freeman
- Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Árni Kristmundsson
- Institute for Experimental Pathology, University of Iceland, Reykjavík, Iceland
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22
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Hilton EJ, Lavoué S. A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei). NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180031] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
ABSTRACT The bony-tongue fishes, Osteoglossomorpha, have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among extant teleostean fishes. This group includes the mooneyes (Hiodontidae), knifefishes (Notopteridae), the abu (Gymnarchidae), elephantfishes (Mormyridae), arawanas and pirarucu (Osteoglossidae), and the African butterfly fish (Pantodontidae). This morphologically heterogeneous group also has a long and diverse fossil record, including taxa from all continents and both freshwater and marine deposits. The phylogenetic relationships among most extant osteoglossomorph families are widely agreed upon. However, there is still much to discover about the systematic biology of these fishes, particularly with regard to the phylogenetic affinities of several fossil taxa, within Mormyridae, and the position of Pantodon. In this paper we review the state of knowledge for osteoglossomorph fishes. We first provide an overview of the diversity of Osteoglossomorpha, and then discuss studies of the phylogeny of Osteoglossomorpha from both morphological and molecular perspectives, as well as biogeographic analyses of the group. Finally, we offer our perspectives on future needs for research on the systematic biology of Osteoglossomorpha.
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Affiliation(s)
| | - Sébastien Lavoué
- National Taiwan University, Taiwan; Universiti Sains Malaysia, Malaysia
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23
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Ribout C, Bech N, Briand MJ, Guyonnet D, Letourneur Y, Brischoux F, Bonnet X. A lack of spatial genetic structure of Gymnothorax chilospilus (moray eel) suggests peculiar population functioning. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- C Ribout
- CEBC, UMR 7372 CNRS-ULR, Villiers en Bois, France
| | - N Bech
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipe ‘Ecologie, Evolution, Symbiose’, Université de Poitiers, Poitiers, France
| | - M J Briand
- Institut Méditerranéen d’Océanologie (MIO), UMR CNRS 7294, Aix-Marseille Université, Marseille Cedex, France
| | - D Guyonnet
- Signalisation et transports ioniques membranaires (STIM), ERL 7368/EA-7349, Université de Poitiers, Poitiers, France
| | - Y Letourneur
- Université de la Nouvelle-Calédonie, Institut ISEA - EA 7484 and LabEx « Corail », Nouméa cedex, New Caledonia
| | - F Brischoux
- CEBC, UMR 7372 CNRS-ULR, Villiers en Bois, France
| | - X Bonnet
- CEBC, UMR 7372 CNRS-ULR, Villiers en Bois, France
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24
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C B Da Silva JP, Johnson GD. Reconsidering pectoral girdle and fin morphology in Anguillidae (Elopomorpha: Anguilliformes). JOURNAL OF FISH BIOLOGY 2018; 93:420-423. [PMID: 29956329 DOI: 10.1111/jfb.13737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
The morphology of the pectoral girdle and fin of Anguillidae is reconsidered via the inclusion of skeletal components that have previously been unassessed. For example, the pectoral girdle and fin in Anguilla were erroneously reported to lack a scapular bone, a cartilaginous scapulocoracoid plate and a cartilaginous propterygium. The pectoral morphology of Anguilla is also compared with the closely related genus Nemichthys, including additional data on the anatomy of this eel family.
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Affiliation(s)
- João Paulo C B Da Silva
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Division of Fishes, Smithsonian Institution, Washington, DC
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25
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Barros-García D, Froufe E, Bañón R, Carlos Arronte J, de Carlos A. Phylogenetic analysis shows the general diversification pattern of deep-sea notacanthiforms (Teleostei: Elopomorpha). Mol Phylogenet Evol 2018; 124:192-198. [PMID: 29551524 DOI: 10.1016/j.ympev.2018.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/02/2018] [Accepted: 03/07/2018] [Indexed: 11/26/2022]
Abstract
The Notacanthiformes is an ancient group of deep-sea ray-finned fishes comprising 27 species in two families; Halosauridae and Notacanthidae. Although many studies have tried to reconstruct the phylogenetic relationships among the major clades of Elopomorpha, little is known about the evolutionary history of notacanthiforms. Molecular and morphological data were used to test previous hypotheses regarding the phylogenetic relationships among notacanthiform taxa, and to unravel the origin and evolution of this group. The molecular analyses of notacanthids showed similar results to those previously obtained employing osteological data, which proposed the existence of the Lipogenyinae (Lipogenys) and Notacanthinae (Notacanthus + Polyacanthonotus) subfamilies. Nevertheless, when the external morphology data is considered Lipogenys is more related to Notacanthus than Polyacanthonotus. The analyses could not fully resolve the inner relationships of the halosaurids. The time-calibrated tree of the order Notacanthiformes shows a long process of diversification spanning from the upper Cretaceous, to 50 million years after the K-Pg extinction, with the gradual emergence of all the modern families and genera of the group. This is the first specific phylogeny of the order Notacanthiformes, combining different analyses and data in order to obtain a wider perspective of the evolution and diversification of this group of fishes.
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Affiliation(s)
- David Barros-García
- Department of Biochemistry, Genetics and Immunology, University of Vigo, C/Fonte das Abelleiras s/n, 36310 Vigo, Spain; Programa de Doctorado en Metodología y Aplicaciones en Ciencias de la Vida, Facultad de Biología. Universidad de Vigo, C/Fonte das Abelleiras s/n, 36310 Vigo, Spain.
| | - Elsa Froufe
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N 4450-208 Matosinhos, Portugal.
| | - Rafael Bañón
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Científicas (IIM-CSIC), C/ Eduardo Cabello, 6, 36208 Vigo, Spain; Grupo de Estudos do Medio Mariño (GEMM), Puerto Deportivo s/n, 15960 Ribeira, A Coruña, Spain.
| | - Juan Carlos Arronte
- Instituto de Hidráulica Ambiental (IH Cantabria), Universidad de Cantabria, PCTCAN, C/Isabel Torres no 15, 390011 Santander, Spain.
| | - Alejandro de Carlos
- Department of Biochemistry, Genetics and Immunology, University of Vigo, C/Fonte das Abelleiras s/n, 36310 Vigo, Spain.
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26
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Nakamura Y, Yasuike M, Mekuchi M, Iwasaki Y, Ojima N, Fujiwara A, Chow S, Saitoh K. Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication. ZOOLOGICAL LETTERS 2017; 3:18. [PMID: 29075512 PMCID: PMC5645911 DOI: 10.1186/s40851-017-0079-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/11/2017] [Indexed: 06/16/2023]
Abstract
BACKGROUND Gene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels' unique life cycle, in which they migrate from rivers or lakes to the sea. These rho genes are apparently paralogous, but the timing of their duplication is unclear due to the deep-branching phylogeny. The aim of the present study is to elucidate the evolutionary origin of the two rho copies in eels using comparative genomics methods. RESULTS In the present study, we sequenced the genome of Japanese eel Anguilla japonica and reconstructed two regions containing rho by de novo assembly. We found a single corresponding region in a non-teleostean primitive ray-finned fish (spotted gar) and two regions in a primitive teleost (Asian arowana). The order of ds-rho and the neighboring genes was highly conserved among the three species. With respect to fw-rho, which was lost in Asian arowana, the neighboring genes were also syntenic between Japanese eel and Asian arowana. In particular, the pattern of gene losses in ds-rho and fw-rho regions was the same as that in Asian arowana, and no discrepancy was found in any of the teleost genomes examined. Phylogenetic analysis supports mutual monophyly of these two teleostean synteny groups, which correspond to the ds-rho and fw-rho regions. CONCLUSIONS Syntenic and phylogenetic analyses suggest that the duplication of rhodopsin gene in Japanese eel predated the divergence of eel (Elopomorpha) and arowana (Osteoglossomorpha). Thus, based on the principle of parsimony, it is most likely that the rhodopsin paralogs were generated through a whole genome duplication in the ancestor of teleosts, and have remained till the present in eels with distinct functional roles. Our result indicates, for the first time, that teleost-specific genome duplication may have contributed to a gene innovation involved in eel-specific migratory life cycle.
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Affiliation(s)
- Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Miyuki Mekuchi
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Nobuhiko Ojima
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Japan Fisheries Research and Education Agency, 2-3-3 Minatomirai, Nishi, Yokohama, Kanagawa 220-6115 Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Seinen Chow
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Kenji Saitoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama, Shiogama, Miyagi 985-0001 Japan
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Hung KW, Russell BC, Chen WJ. Molecular systematics of threadfin breams and relatives (Teleostei, Nemipteridae). ZOOL SCR 2017. [DOI: 10.1111/zsc.12237] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kuo-Wei Hung
- Institute of Oceanography; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Barry C. Russell
- Museum & Art Gallery of the Northern Territory; PO Box 4646 Darwin NT 0801 Australia
| | - Wei-Jen Chen
- Institute of Oceanography; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
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Anibaldi A, Benassi Franciosi C, Massari F, Tinti F, Piccinetti C, Riccioni G. Morphology and Species Composition of Southern Adriatic Sea Leptocephali Evaluated Using DNA Barcoding. PLoS One 2016; 11:e0166137. [PMID: 27893773 PMCID: PMC5125788 DOI: 10.1371/journal.pone.0166137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022] Open
Abstract
Leptocephali are the characteristic larvae of the superorder Elopomorpha that are difficult to identify at the species level. In this study, we used DNA barcoding (i.e. short genetic sequences of DNA used as unique species tags) coupled with classical taxonomic methods to identify leptocephali in the southern Adriatic Sea. This information will provide an assessment of the biodiversity of the eel larvae in this region. A total of 2,785 leptocephali were collected, and using external morphology were assigned to seven morphotypes: Ariosoma balearicum, Conger conger, Gnathophis mystax, Facciolella sp., Nettastoma melanurum, Dalophis imberbis and Chlopsis bicolor. Collectively, these seven morphotypes are considered to be a good proxy for the Anguilliformes community (the main order of the Elopomorpha) in the southern Adriatic Sea (to date, seven families and sixteen species have been recorded in this region). Interestingly, the higher number of G. mystax larvae collected suggests an increased abundance of this genus. To validate the morphological identifications, we sequenced 61 leptocephali (at a 655 bp fragment from the cytochrome oxidase subunit 1 mitochondrial region) and developed barcode vouchers for the seven morphotypes. Using genetic information from reference databases, we validated three of these morphotypes. Where reference sequences were unavailable, we generated barcodes for both adult and juvenile forms to provide additional genetic information. Using this integrated approach allowed us to characterize a new species of Facciolella in the Adriatic Sea for the first time. Moreover, we also revealed a lack of differentiation, at the species level, between G. mistax and G. bathytopos, a western Atlantic Ocean species. Our morphological and barcode data have been published in the Barcoding of the Adriatic Leptocephali database. This work represents the first contribution to a wider project that aims to create a barcode database to support the assessment of leptocephali diversity in the Mediterranean Sea.
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Affiliation(s)
- Alessandra Anibaldi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Laboratory of Marine Biology and Fishery, Fano (PU), Italy
| | - Claudia Benassi Franciosi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Laboratory of Marine Biology and Fishery, Fano (PU), Italy
| | - Francesco Massari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Ravenna, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Laboratory of Marine Biology and Fishery, Fano (PU), Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Ravenna, Italy
- * E-mail:
| | - Corrado Piccinetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Laboratory of Marine Biology and Fishery, Fano (PU), Italy
| | - Giulia Riccioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Laboratory of Marine Biology and Fishery, Fano (PU), Italy
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Chow S, Yanagimoto T, Kurogi H, Appleyard SA, Pogonoski JJ. A giant anguilliform leptocephalus Thalassenchelys foliaceus Castle & Raju is a junior synonym of Congriscus maldivensis (Norman 1939). JOURNAL OF FISH BIOLOGY 2016; 89:2203-2211. [PMID: 27511812 DOI: 10.1111/jfb.13111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
A single specimen of giant leptocephalus Thalassenchelys foliaceus Castle & Raju 1975 was caught in subtropical waters of the western North Pacific Ocean. Mitochondrial coI gene sequence divergence between T. foliaceus and Congriscus maldivensis (Norman 1939) was 0·64 ± 0·27% (mean ± s.e.), and the myomere and vertebral counts of these species were similar, indicating T. foliaceus is a junior synonym of C. maldivensis.
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Affiliation(s)
- S Chow
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanagawa 236-8648, Japan.
| | - T Yanagimoto
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanagawa 236-8648, Japan
| | - H Kurogi
- National Research Institute of Fisheries Science, 6-3-1 Nagai, Kanagawa 238-0316, Japan
| | - S A Appleyard
- Australian National Fish Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), GPO Box 1538, Hobart, Tasmania, 7001, Australia
| | - J J Pogonoski
- Australian National Fish Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), GPO Box 1538, Hobart, Tasmania, 7001, Australia
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Lafont AG, Rousseau K, Tomkiewicz J, Dufour S. Three nuclear and two membrane estrogen receptors in basal teleosts, Anguilla sp.: Identification, evolutionary history and differential expression regulation. Gen Comp Endocrinol 2016; 235:177-191. [PMID: 26654744 DOI: 10.1016/j.ygcen.2015.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/26/2015] [Accepted: 11/29/2015] [Indexed: 12/17/2022]
Abstract
Estrogens interact with classical intracellular nuclear receptors (ESR), and with G-coupled membrane receptors (GPER). In the eel, we identified three nuclear (ESR1, ESR2a, ESR2b) and two membrane (GPERa, GPERb) estrogen receptors. Duplicated ESR2 and GPER were also retrieved in most extant teleosts. Phylogeny and synteny analyses suggest that they result from teleost whole genome duplication (3R). In contrast to conserved 3R-duplicated ESR2 and GPER, one of 3R-duplicated ESR1 has been lost shortly after teleost emergence. Quantitative PCRs revealed that the five receptors are all widely expressed in the eel, but with differential patterns of tissue expression and regulation. ESR1 only is consistently up-regulated in vivo in female eel BPG-liver axis during induced sexual maturation, and also up-regulated in vitro by estradiol in eel hepatocyte primary cultures. This first comparative study of the five teleost estradiol receptors provides bases for future investigations on differential roles that may have contributed to the conservation of multiple estrogen receptors.
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Affiliation(s)
- Anne-Gaëlle Lafont
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCN, Paris, France.
| | - Karine Rousseau
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCN, Paris, France
| | - Jonna Tomkiewicz
- Technical University of Denmark, National Institute of Aquatic Resources, Charlottenlund, Denmark
| | - Sylvie Dufour
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCN, Paris, France.
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31
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Mirande JM. Combined phylogeny of ray-finned fishes (Actinopterygii) and the use of morphological characters in large-scale analyses. Cladistics 2016; 33:333-350. [DOI: 10.1111/cla.12171] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 01/27/2023] Open
Affiliation(s)
- Juan Marcos Mirande
- Unidad Ejecutora Lillo (UEL, Fundación Miguel Lillo-CONICET); San Miguel de Tucumán 4000 Argentina
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32
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Sun BF, Li T, Xiao JH, Jia LY, Liu L, Zhang P, Murphy RW, He SM, Huang DW. Horizontal functional gene transfer from bacteria to fishes. Sci Rep 2015; 5:18676. [PMID: 26691285 PMCID: PMC4687049 DOI: 10.1038/srep18676] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 11/23/2015] [Indexed: 01/06/2023] Open
Abstract
Invertebrates can acquire functional genes via horizontal gene transfer (HGT) from bacteria but fishes are not known to do so. We provide the first reliable evidence of one HGT event from marine bacteria to fishes. The HGT appears to have occurred after emergence of the teleosts. The transferred gene is expressed and regulated developmentally. Its successful integration and expression may change the genetic and metabolic repertoire of fishes. In addition, this gene contains conserved domains and similar tertiary structures in fishes and their putative donor bacteria. Thus, it may function similarly in both groups. Evolutionary analyses indicate that it evolved under purifying selection, further indicating its conserved function. We document the first likely case of HGT of functional gene from prokaryote to fishes. This discovery certifies that HGT can influence vertebrate evolution.
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Affiliation(s)
- Bao-Fa Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences
| | - Jin-Hua Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling-Yi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Liu
- Network &Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Shun-Min He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Da-Wei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, China
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Barros-García D, Bañón R, Arronte JC, Fernández-Peralta L, García R, de Carlos A. DNA barcoding of deep-water notacanthiform fishes (Teleostei, Elopomorpha). ZOOL SCR 2015. [DOI: 10.1111/zsc.12154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- David Barros-García
- Departamento de Bioquímica; Xenética e Inmunoloxía; Universidade de Vigo; Rúa Fonte das Abelleiras s/n Vigo 36310 Spain
- ECIMAT; Estación de Ciencias Mariñas de Toralla (Universidade de Vigo); Isla de Toralla s/n, 36331 Vigo Spain
| | - Rafael Bañón
- Servizo de Planificación; Consellería do Mar e Medio Rural; Xunta de Galicia; Santiago de Compostela Spain
| | - Juan Carlos Arronte
- Instituto Español de Oceanografía; C.O. de Santander, Promontorio San Martín s/n, 39004 Santander Spain
| | | | - Ramón García
- Instituto Español de Oceanografía; CO de Málaga, Puerto pesquero s/n, 29640 Fuengirola Spain
| | - Alejandro de Carlos
- Departamento de Bioquímica; Xenética e Inmunoloxía; Universidade de Vigo; Rúa Fonte das Abelleiras s/n Vigo 36310 Spain
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Freeman MA, Kristmundsson Á. Histozoic myxosporeans infecting the stomach wall of elopiform fishes represent a novel lineage, the Gastromyxidae. Parasit Vectors 2015; 8:517. [PMID: 26453151 PMCID: PMC4600289 DOI: 10.1186/s13071-015-1140-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 10/03/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Traditional studies on myxosporeans have used myxospore morphology as the main criterion for identification and taxonomic classification, and it remains important as the fundamental diagnostic feature used to confirm myxosporean infections in fish and other vertebrate taxa. However, its use as the primary feature in systematics has led to numerous genera becoming polyphyletic in subsequent molecular phylogenetic analyses. It is now known that other features, such as the site and type of infection, can offer a higher degree of congruence with molecular data, albeit with its own inconsistencies, than basic myxospore morphology can reliably provide. METHODS Histozoic gastrointestinal myxosporeans from two elopiform fish from Malaysia, the Pacific tarpon Megalops cyprinoides and the ten pounder Elops machnata were identified and described using morphological, histological and molecular methodologies. RESULTS The myxospore morphology of both species corresponds to the generally accepted Myxidium morphotype, but both had a single nucleus in the sporoplasm and lacked valvular striations. In phylogenetic analyses they were robustly grouped in a discrete clade basal to myxosporeans, with similar shaped myxospores, described from gill monogeneans, which are located at the base of the multivalvulid clade. New genera Gastromyxum and Monomyxum are erected to accommodate these myxosporean taxa from fish and gill monogeneans respectively. Each are placed in a new family, the Gastromyxidae with Gastromyxum as the type genus and Monomyxidae with Monomyxum as the type genus. CONCLUSIONS To improve modern systematics of the myxosporeans it is clear that a combination of biological, ecological, morphological and molecular data should be used in descriptive studies, and the naming and redistribution of taxa and genera is going to be necessary to achieve this. Here we demonstrate why some Myxidium-shaped myxospores should not be included in the family Myxidiidae, and create two new families to accommodate them based on their site of infection, host biology / ecology, DNA sequence data and morphological observations. Subsequent descriptive works need to follow a similar course if we are going to create a prevailing and workable systematic structure for the Myxosporea.
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Affiliation(s)
- Mark A Freeman
- Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies.
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| | - Árni Kristmundsson
- Institute for Experimental Pathology, University of Iceland, Reykjavik, Iceland.
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35
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Springer VG, Johnson GD. The Gill-Arch Musculature ofProtanguilla, the Morphologically Most Primitive Eel (Teleostei: Anguilliformes), Compared with That of Other Putatively Primitive Extant Eels and Other Elopomorphs. COPEIA 2015. [DOI: 10.1643/ci-14-152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Maugars G, Dufour S. Demonstration of the Coexistence of Duplicated LH Receptors in Teleosts, and Their Origin in Ancestral Actinopterygians. PLoS One 2015; 10:e0135184. [PMID: 26271038 PMCID: PMC4536197 DOI: 10.1371/journal.pone.0135184] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/18/2015] [Indexed: 11/18/2022] Open
Abstract
Pituitary gonadotropins, FSH and LH, control gonad activity in vertebrates, via binding to their respective receptors, FSHR and LHR, members of GPCR superfamily. Until recently, it was accepted that gnathostomes possess a single FSHR and a single LHR, encoded by fshr and lhcgr genes. We reinvestigated this question, focusing on vertebrate species of key-phylogenetical positions. Genome analyses supported the presence of a single fshr and a single lhcgr in chondrichthyans, and in sarcopterygians including mammals, birds, amphibians and coelacanth. In contrast, we identified a single fshr but two lhgcr in basal teleosts, the eels. We further showed the coexistence of duplicated lhgcr in other actinopterygians, including a non-teleost, the gar, and other teleosts, e.g. Mexican tetra, platyfish, or tilapia. Phylogeny and synteny analyses supported the existence in actinopterygians of two lhgcr paralogs (lhgcr1/ lhgcr2), which do not result from the teleost-specific whole-genome duplication (3R), but likely from a local gene duplication that occurred early in the actinopterygian lineage. Due to gene losses, there was no impact of 3R on the number of gonadotropin receptors in extant teleosts. Additional gene losses during teleost radiation, led to a single lhgcr (lhgcr1 or lhgcr2) in some species, e.g. medaka and zebrafish. Sequence comparison highlighted divergences in the extracellular and intracellular domains of the duplicated lhgcr, suggesting differential properties such as ligand binding and activation mechanisms. Comparison of tissue distribution in the European eel, revealed that fshr and both lhgcr transcripts are expressed in the ovary and testis, but are differentially expressed in non-gonadal tissues such as brain or eye. Differences in structure-activity relationships and tissue expression may have contributed as selective drives in the conservation of the duplicated lhgcr. This study revises the evolutionary scenario and nomenclature of gonadotropin receptors, and opens new research avenues on the roles of duplicated LHR in actinopterygians.
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Affiliation(s)
- Gersende Maugars
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208-IRD 207-UPMC-UCBN, Paris, France
| | - Sylvie Dufour
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208-IRD 207-UPMC-UCBN, Paris, France
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Morini M, Pasquier J, Dirks R, van den Thillart G, Tomkiewicz J, Rousseau K, Dufour S, Lafont AG. Duplicated leptin receptors in two species of eel bring new insights into the evolution of the leptin system in vertebrates. PLoS One 2015; 10:e0126008. [PMID: 25946034 PMCID: PMC4422726 DOI: 10.1371/journal.pone.0126008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 03/30/2015] [Indexed: 12/19/2022] Open
Abstract
Since its discovery in mammals as a key-hormone in reproduction and metabolism, leptin has been identified in an increasing number of tetrapods and teleosts. Tetrapods possess only one leptin gene, while most teleosts possess two leptin genes, as a result of the teleost third whole genome duplication event (3R). Leptin acts through a specific receptor (LEPR). In the European and Japanese eels, we identified two leptin genes, and for the first time in vertebrates, two LEPR genes. Synteny analyses indicated that eel LEPRa and LEPRb result from teleost 3R. LEPRb seems to have been lost in the teleost lineage shortly after the elopomorph divergence. Quantitative PCRs revealed a wide distribution of leptins and LEPRs in the European eel, including tissues involved in metabolism and reproduction. Noticeably, leptin1 was expressed in fat tissue, while leptin2 in the liver, reflecting subfunctionalization. Four-month fasting had no impact on the expression of leptins and LEPRs in control European eels. This might be related to the remarkable adaptation of silver eel metabolism to long-term fasting throughout the reproductive oceanic migration. In contrast, sexual maturation induced differential increases in the expression of leptins and LEPRs in the BPG-liver axis. Leptin2 was strikingly upregulated in the liver, the central organ of the reproductive metabolic challenge in teleosts. LEPRs were differentially regulated during sexual maturation, which may have contributed to the conservation of the duplicated LEPRs in this species. This suggests an ancient and positive role of the leptin system in the vertebrate reproductive function. This study brings new insights on the evolutionary history of the leptin system in vertebrates. Among extant vertebrates, the eel represents a unique case of duplicated leptins and leptin receptors as a result of 3R.
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Affiliation(s)
- Marina Morini
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCBN, Paris, France
| | - Jérémy Pasquier
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCBN, Paris, France
| | - Ron Dirks
- ZF-screens B.V., Leiden, The Netherlands
| | - Guido van den Thillart
- ZF-screens B.V., Leiden, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Jonna Tomkiewicz
- Technical University of Denmark, National Institute of Aquatic Resources, Charlottenlund, Denmark
| | - Karine Rousseau
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCBN, Paris, France
| | - Sylvie Dufour
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCBN, Paris, France
| | - Anne-Gaëlle Lafont
- Muséum National d'Histoire Naturelle, Sorbonne Universités, Research Unit BOREA, Biology of Aquatic Organisms and Ecosystems, CNRS 7208, IRD207, UPMC, UCBN, Paris, France
- * E-mail:
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Dornburg A, Friedman M, Near TJ. Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei). Mol Phylogenet Evol 2015; 89:205-18. [PMID: 25899306 DOI: 10.1016/j.ympev.2015.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/31/2015] [Accepted: 04/07/2015] [Indexed: 02/05/2023]
Abstract
Elopomorpha is one of the three main clades of living teleost fishes and includes a range of disparate lineages including eels, tarpons, bonefishes, and halosaurs. Elopomorphs were among the first groups of fishes investigated using Hennigian phylogenetic methods and continue to be the object of intense phylogenetic scrutiny due to their economic significance, diversity, and crucial evolutionary status as the sister group of all other teleosts. While portions of the phylogenetic backbone for Elopomorpha are consistent between studies, the relationships among Albula, Pterothrissus, Notacanthiformes, and Anguilliformes remain contentious and difficult to evaluate. This lack of phylogenetic resolution is problematic as fossil lineages are often described and placed taxonomically based on an assumed sister group relationship between Albula and Pterothrissus. In addition, phylogenetic studies using morphological data that sample elopomorph fossil lineages often do not include notacanthiform or anguilliform lineages, potentially introducing a bias toward interpreting fossils as members of the common stem of Pterothrissus and Albula. Here we provide a phylogenetic analysis of DNA sequences sampled from multiple nuclear genes that include representative taxa from Albula, Pterothrissus, Notacanthiformes and Anguilliformes. We integrate our molecular dataset with a morphological character matrix that spans both living and fossil elopomorph lineages. Our results reveal substantial uncertainty in the placement of Pterothrissus as well as all sampled fossil lineages, questioning the stability of the taxonomy of fossil Elopomorpha. However, despite topological uncertainty, our integration of fossil lineages into a Bayesian time calibrated framework provides divergence time estimates for the clade that are consistent with previously published age estimates based on the elopomorph fossil record and molecular estimates resulting from traditional node-dating methods.
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Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae). Mol Phylogenet Evol 2015; 88:132-43. [PMID: 25848970 DOI: 10.1016/j.ympev.2015.03.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/26/2015] [Accepted: 03/28/2015] [Indexed: 11/20/2022]
Abstract
Widely distributed groups of living animals, such as the predominantly marine fish family Sciaenidae, have always attracted the attention of biogeographers to document the origins and patterns of diversification in time and space. In this study, the historical biogeography of the global Sciaenidae is reconstructed within a molecular phylogenetic framework to investigate their origin and to test the hypotheses explaining the present-day biogeographic patterns. Our data matrix comprises six mitochondrial and nuclear genes in 93 globally sampled sciaenid species from 52 genera. Within the inferred phylogenetic tree of the Sciaenidae, we identify 15 main and well-supported lineages; some of which have not been recognized previously. Reconstruction of habitat preferences shows repeated habitat transitions between marine and euryhaline environments. This implies that sciaenids can easily adapt to some variations in salinity, possibly as the consequence of their nearshore habitats and migratory life history. Conversely, complete marine/euryhaline to freshwater transitions occurred only three times, in South America, North America and South Asia. Ancestral range reconstruction analysis concomitant with fossil evidence indicates that sciaenids first originated and diversified in the tropical America during the Oligocene to Early Miocene before undergoing two range expansions, to Eastern Atlantic and to the Indo-West Pacific where a maximum species richness is observed. The uncommon biogeographic pattern identified is discussed in relation to current knowledge on origin of gradients of marine biodiversity toward the center of origin hypothesis in the Indo-West Pacific.
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Churcher AM, Hubbard PC, Marques JP, Canário AVM, Huertas M. Deep sequencing of the olfactory epithelium reveals specific chemosensory receptors are expressed at sexual maturity in the European eel Anguilla anguilla. Mol Ecol 2015; 24:822-34. [PMID: 25580852 DOI: 10.1111/mec.13065] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/19/2014] [Accepted: 12/30/2014] [Indexed: 01/02/2023]
Abstract
Vertebrate genomes encode a diversity of G protein-coupled receptor (GPCR) that belong to large gene families and are used by olfactory systems to detect chemical cues found in the environment. It is not clear however, if individual receptors from these large gene families have evolved roles that are specific to certain life stages. Here, we used deep sequencing to identify differentially expressed receptor transcripts in the olfactory epithelia (OE) of freshwater, seawater and sexually mature male eels (Anguilla anguilla). This species is particularly intriguing because of its complex life cycle, extreme long-distance migrations and early-branching position within the teleost phylogeny. In the A. anguillaOE, we identified full-length transcripts for 13, 112, 6 and 38 trace amine-associated receptors, odorant receptors (OR) and type I and type II vomeronasal receptors (V1R and V2R). Most of these receptors were expressed at similar levels at different life stages and a subset of OR and V2R-like transcripts was more abundant in sexually mature males suggesting that ORs and V2R-like genes are important for reproduction. We also identified a set of GPCR signal transduction genes that were differentially expressed indicating that eels make use of different GPCR signal transduction genes at different life stages. The finding that a diversity of chemosensory receptors is expressed in the olfactory epithelium and that a subset is differentially expressed suggests that most receptors belonging to large chemosensory gene families have functions that are important at multiple life stages, while a subset has evolved specific functions at different life stages.
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Affiliation(s)
- Allison M Churcher
- Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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Kück P, Longo GC. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front Zool 2014; 11:81. [PMID: 25426157 PMCID: PMC4243772 DOI: 10.1186/s12983-014-0081-x] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/21/2014] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Phylogenetic and population genetic studies often deal with multiple sequence alignments that require manipulation or processing steps such as sequence concatenation, sequence renaming, sequence translation or consensus sequence generation. In recent years phylogenetic data sets have expanded from single genes to genome wide markers comprising hundreds to thousands of loci. Processing of these large phylogenomic data sets is impracticable without using automated process pipelines. Currently no stand-alone or pipeline compatible program exists that offers a broad range of manipulation and processing steps for multiple sequence alignments in a single process run. RESULTS Here we present FASconCAT-G, a system independent editor, which offers various processing options for multiple sequence alignments. The software provides a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation between nucleotide and amino acid states, consensus generation of specific sequence blocks, sequence concatenation, model selection of amino acid replacement with ProtTest, two types of RY coding as well as site exclusions and extraction of parsimony informative sites. Convieniently, most options can be invoked in combination and performed during a single process run. Additionally, FASconCAT-G prints useful information regarding alignment characteristics and editing processes such as base compositions of single in- and outfiles, sequence areas in a concatenated supermatrix, as well as paired stem and loop regions in secondary structure sequence strings. CONCLUSIONS FASconCAT-G is a command-line driven Perl program that delivers computationally fast and user-friendly processing of multiple sequence alignments for phylogenetic and population genetic applications and is well suited for incorporation into analysis pipelines.
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Affiliation(s)
- Patrick Kück
- />Zoologisches Forschungsmuseum A. Koenig, Adenauerallee 160-163, Bonn, 53113 Germany
| | - Gary C Longo
- />Center for Ocean Health, 100 Shaffer Road, Santa Cruz, 95060 CA USA
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Multiple thyrotropin β-subunit and thyrotropin receptor-related genes arose during vertebrate evolution. PLoS One 2014; 9:e111361. [PMID: 25386660 PMCID: PMC4227674 DOI: 10.1371/journal.pone.0111361] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/01/2014] [Indexed: 01/09/2023] Open
Abstract
Thyroid-stimulating hormone (TSH) is composed of a specific β subunit and an α subunit that is shared with the two pituitary gonadotropins. The three β subunits derive from a common ancestral gene through two genome duplications (1R and 2R) that took place before the radiation of vertebrates. Analysis of genomic data from phylogenetically relevant species allowed us to identify an additional Tshβ subunit-related gene that was generated through 2R. This gene, named Tshβ2, present in cartilaginous fish, little skate and elephant shark, and in early lobe-finned fish, coelacanth and lungfish, was lost in ray-finned fish and tetrapods. The absence of a second type of TSH receptor (Tshr) gene in these species suggests that both TSHs act through the same receptor. A novel Tshβ sister gene, named Tshβ3, was generated through the third genomic duplication (3R) that occurred early in the teleost lineage. Tshβ3 is present in most teleost groups but was lostin tedraodontiforms. The 3R also generated a second Tshr, named Tshrb. Interestingly, the new Tshrb was translocated from its original chromosomic position after the emergence of eels and was then maintained in its new position. Tshrb was lost in tetraodontiforms and in ostariophysians including zebrafish although the latter species have two TSHs, suggesting that TSHRb may be dispensable. The tissue distribution of duplicated Tshβs and Tshrs was studied in the European eel. The endocrine thyrotropic function in the eel would be essentially mediated by the classical Tshβ and Tshra, which are mainly expressed in the pituitary and thyroid, respectively. Tshβ3 and Tshrb showed a similar distribution pattern in the brain, pituitary, ovary and adipose tissue, suggesting a possible paracrine/autocrine mode of action in these non-thyroidal tissues. Further studies will be needed to determine the binding specificity of the two receptors and how these two TSH systems are interrelated.
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Campbell MA, Chen WJ, López JA. Molecular data do not provide unambiguous support for the monophyly of flatfishes (Pleuronectiformes): A reply to Betancur-R and Ortí. Mol Phylogenet Evol 2014; 75:149-53. [DOI: 10.1016/j.ympev.2014.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/11/2014] [Accepted: 02/16/2014] [Indexed: 11/24/2022]
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