1
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da Silva JPCB. The morphology of the branchial skeleton of heterocongrines (Anguilliformes: Congridae) and its relation to their diet. ZOOLOGY 2024; 165:126185. [PMID: 38908325 DOI: 10.1016/j.zool.2024.126185] [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: 10/23/2023] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Members of the subfamily Heterocongrinae (Congridae) are a peculiar group of anguilliform eels that construct sandy borrows, form large colonies, and are popularly recognized as garden eels. They live with most of their bodies inside self-constructed borrows exposing their heads and trunk to feed on zooplankton, preferably copepods, that are brought passively by currents. As plankton feeders there was a suspicion that their branchial skeleton would have structures that could aid in the filtering process, such as highly developed or modified branchial rakers, which are observed in other suspension-feeding fishes, such as anchovies and sardines. Branchial rakers, however, were considered to be absent across Anguilliformes (except for Protanguilla). Nonetheless, specimens that were examined using clearing and staining and computed tomography showed, in all cases, branchial rakers associated with their gill arches. Heterocongrines have branchial rakers across their first to fourth branchial arches. These rakers are conical and apparently unossified, but further studies are necessary to attest its degree of ossification or its complete absence. Their pharyngeal tooth plates are reduced, a condition that may reflect their preference for smaller food items. Additionally, they may use crossflow filtering to feed, although detailed studies are necessary to clarify if hydrosol sieving may also aid in food capture. Furthermore, the present study proposes that the presence of branchial rakers should be better investigated in Anguilliformes with similar feeding habits as heterocongrines, considering that these structures may be more widespread within the group than previously considered.
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Affiliation(s)
- João Paulo Capretz Batista da Silva
- Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Castelo Branco, João Pessoa, PB 58051-900, Brazil.
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2
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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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3
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Chen J, Zeng H, Lv W, Sun N, Wang C, Xu W, Hu M, Gan X, He L, He S, Fang C. Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2251-8. [PMID: 36648612 DOI: 10.1007/s11427-022-2251-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 01/18/2023]
Abstract
High hydrostatic pressure, low temperature, and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments. Here, we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel (MAE, Ilyophis brunneus, captured below a depth of 3,500 m) by using Illumina, PacBio, and Hi-C sequencing. We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes. The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes. Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species, European eel, ∼111.9 Mya and experienced a rapid evolution. The genome evolutionary analyses primarily revealed the following: (i) under high hydrostatic pressure, the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability; ACOX1 may enhance the fluidity of cell membrane and maintain transport activity; the expansion of ABCC12 gene family may enhance the integrity of DNA; (ii) positively selected HARS likely maintain the transcription ability at low temperatures; and (iii) energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and mTOR signaling pathways.
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Affiliation(s)
- Jie Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Xu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingliang Hu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lisheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Chengchi Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Lemopoulos A, Montoya-Burgos JI. From scales to armor: Scale losses and trunk bony plate gains in ray-finned fishes. Evol Lett 2021; 5:240-250. [PMID: 34136272 PMCID: PMC8190451 DOI: 10.1002/evl3.219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/04/2021] [Indexed: 11/25/2022] Open
Abstract
Actinopterygians (ray‐finned fishes) are the most diversified group of vertebrates and are characterized by a variety of protective structures covering their integument, the evolution of which has intrigued biologists for decades. Paleontological records showed that the first mineralized vertebrate skeleton was composed of dermal bony plates covering the body, including odontogenic and skeletogenic components. Later in evolution, the exoskeleton of actinopterygian's trunk was composed of scale structures. Although scales are nowadays a widespread integument cover, some contemporary lineages do not have scales but bony plates covering their trunk, whereas other lineages are devoid of any such structures. To understand the evolution of the integument coverage and particularly the transition between different structures, we investigated the pattern of scale loss events along with actinopterygian evolution and addressed the functional relationship between the scaleless phenotype and the ecology of fishes. Furthermore, we examined whether the emergence of trunk bony plates was dependent over the presence or absence of scales. To this aim, we used two recently published actinopterygian phylogenies, one including >11,600 species, and by using stochastic mapping and Bayesian methods, we inferred scale loss events and trunk bony plate acquisitions. Our results reveal that a scaled integument is the most frequent state in actinopterygians, but multiple independent scale loss events occurred along their phylogeny with essentially no scale re‐acquisition. Based on linear mixed models, we found evidence supporting that after a scale loss event, fishes tend to change their ecology and adopt a benthic lifestyle. Furthermore, we show that trunk bony plates appeared independently multiple times along the phylogeny. By using fitted likelihood models for character evolution, we show that trunk bony plate acquisitions were dependent on a previous scale loss event. Overall, our findings support the hypothesis that integument cover is a key evolutionary trait underlying actinopterygian radiation.
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Affiliation(s)
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution University of Geneva Geneva Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva Geneva Switzerland
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5
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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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6
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Coluccia E, Deidda F, Lobina C, Melis R, Porcu C, Agus B, Salvadori S. Chromosome Mapping of 5S Ribosomal Genes in Indo-Pacific and Atlantic Muraenidae: Comparative Analysis by Dual Colour Fluorescence In Situ Hybridisation. Genes (Basel) 2020; 11:genes11111319. [PMID: 33172170 PMCID: PMC7694744 DOI: 10.3390/genes11111319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 11/16/2022] Open
Abstract
The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending the karyology of this fish group, the chromosomal mapping of the 5S ribosomal gene family was performed on seven species belonging to the genera Muraena and Gymnothorax from both the Atlantic and Pacific oceans. Fluorescence in situ hybridisation (FISH) experiments were realized using species-specific 5S rDNA probes; in addition, two-colour FISH was performed to investigate the possible association with the 45S ribosomal gene family. Multiple 5S rDNA clusters, located either in species-specific or in possibly homoeologous chromosomes, were found. Either a syntenic or different chromosomal location of the two ribosomal genes was detected. Our results revealed variability in the number and location of 5S rDNA clusters and confirmed a substantial conservation of the number and location of the 45S rDNA.
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7
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Liu ZQ, Shen YZ, Zhao M, Wang W, Chen W, Ma CY, Zhang FY, Ma LB. Characterization of the complete mitochondrial DNA sequence of the Ariosoma meeki (Anguilliformes, Congridae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2539-2541. [PMID: 33457855 PMCID: PMC7782183 DOI: 10.1080/23802359.2020.1781557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
In this study, the complete mitochondrial genome of Ariosoma meeki was sequenced, assembled and annotated. The circular genome is 16,154 bp in length with nucleotide composition is 28.42% A, 26.53% T, 19.65% G, and 25.40% C and contains 13 protein-coding genes (PCGs), 21 transfer RNA genes (tRNAs), 2 ribosomal RNA unit genes and a large non-coding region (putative control region). To further explore the evolution relationship of the Anguilliformes, we constructed the phylogenetic tree and found that the A. meeki had closer relationship with Ariosoma shiroanago. This study provided the valuable evidence on phylogenetic relationship of the A. meeki at the molecular level and essential resource for further study the molecular phylogenetic, biogeography and adaptive evolution of this lineage.
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Affiliation(s)
- Zhi-Qiang Liu
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Yao-Zhong Shen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Ming Zhao
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Wang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Wei Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Chun-Yan Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Feng-Ying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Ling-Bo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
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8
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Martinez-Villegas L, Assis-Geraldo J, Koerich LB, Collier TC, Lee Y, Main BJ, Rodrigues NB, Orfano AS, Pires ACAM, Campolina TB, Nacif-Pimenta R, Baia-da-Silva DC, Duarte APM, Bahia AC, Rios-Velásquez CM, Lacerda MVG, Monteiro WM, Lanzaro GC, Secundino NFC, Pimenta PFP. Characterization of the complete mitogenome of Anopheles aquasalis, and phylogenetic divergences among Anopheles from diverse geographic zones. PLoS One 2019; 14:e0219523. [PMID: 31479460 PMCID: PMC6720026 DOI: 10.1371/journal.pone.0219523] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/25/2019] [Indexed: 11/18/2022] Open
Abstract
Whole mitogenome sequences (mtDNA) have been exploited for insect ecology studies, using them as molecular markers to reconstruct phylogenies, or to infer phylogeographic relationships and gene flow. Recent Anopheles phylogenomic studies have provided information regarding the time of deep lineage divergences within the genus. Here we report the complete 15,393 bp mtDNA sequences of Anopheles aquasalis, a Neotropical human malaria vector. When comparing its structure and base composition with other relevant and available anopheline mitogenomes, high similarity and conserved genomic features were observed. Furthermore, 22 mtDNA sequences comprising anopheline and Dipteran sibling species were analyzed to reconstruct phylogenies and estimate dates of divergence between taxa. Phylogenetic analysis using complete mtDNA sequences suggests that A. aquasalis diverged from the Anopheles albitarsis complex ~28 million years ago (MYA), and ~38 MYA from Anopheles darlingi. Bayesian analysis suggests that the most recent ancestor of Nyssorhynchus and Anopheles + Cellia was extant ~83 MYA, corroborating current estimates of ~79–100 MYA. Additional sampling and publication of African, Asian, and North American anopheline mitogenomes would improve the resolution of the Anopheles phylogeny and clarify early continental dispersal routes.
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Affiliation(s)
- Luis Martinez-Villegas
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Juliana Assis-Geraldo
- Biosystems Informatics and Genomics Group, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Leonardo B Koerich
- Laboratory of Physiology of Haematophagous Insects, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Travis C Collier
- Daniel K. Inouye US Pacific Basin Agricultural Research Center (PBARC), United States Department of Agriculture, Agricultural Research Service, Hilo, Hawaii, United States of America
| | - Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Bradley J Main
- Davis Arbovirus Research and Training, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Nilton B Rodrigues
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Alessandra S Orfano
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Ana C A M Pires
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Thais B Campolina
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Rafael Nacif-Pimenta
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
| | - Djane C Baia-da-Silva
- Institute of Clinical Research Borborema, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
- Graduation Program in Tropical Medicine, Amazonas State University, Manaus, AM, Brazil
- Foundation of Tropical Medicine Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Ana P M Duarte
- Institute of Clinical Research Borborema, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
- Graduation Program in Tropical Medicine, Amazonas State University, Manaus, AM, Brazil
- Foundation of Tropical Medicine Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Ana C Bahia
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Marcus V G Lacerda
- Institute of Clinical Research Borborema, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
- Graduation Program in Tropical Medicine, Amazonas State University, Manaus, AM, Brazil
- Foundation of Tropical Medicine Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
- Institute Leonidas and Maria Deane, Oswaldo Cruz Foundation, FIOCRUZ, Manaus, AM, Brazil
| | - Wuelton M Monteiro
- Institute of Clinical Research Borborema, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
- Graduation Program in Tropical Medicine, Amazonas State University, Manaus, AM, Brazil
- Foundation of Tropical Medicine Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Gregory C Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Nagila F C Secundino
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
- Graduation Program in Tropical Medicine, Amazonas State University, Manaus, AM, Brazil
- Foundation of Tropical Medicine Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Paulo F P Pimenta
- Laboratory of Medical Entomology, Institute René Rachou, Oswaldo Cruz Foundation, Minas Gerais, FIOCRUZ, Belo Horizonte, MG, Brazil
- Institute of Clinical Research Borborema, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
- Graduation Program in Tropical Medicine, Amazonas State University, Manaus, AM, Brazil
- Foundation of Tropical Medicine Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
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9
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Dale KE, Tinker MT, Mehta RS. Larval morphology predicts geographical dispersal range of Eastern Pacific eels. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe geographical range of many marine species is strongly influenced by the dispersal potential of propagules such as eggs and larvae. Here, we investigate morphological diversity and the effect of body shape on geographical range of leptocephali, the unique, laterally compressed larvae of eels (order Anguilliformes). We used phylogenetically informed analyses to examine the morphological variation of larvae for 17 Eastern Pacific eel species from three adult habitats. We also investigated whether morphological traits of leptocephali could predict larval latitudinal range, hypothesizing that body shape may influence passive dispersal via currents. We found that no two species shared the same multivariate growth trajectories, with the size and scaling of pectoral fin length and snout-to-anus length being particularly variable. Larvae with longer relative predorsal and snout-to-anus lengths at median sizes exhibited wider larval geographical ranges. Body aspect ratio and maximum body length at metamorphosis, two traits we hypothesized to be important for passive transport, were not significant predictors of maximal larval range. We discovered an increase in phylogenetic signal over larval development as eels approach metamorphosis, potentially due to similar selective pressures between related species (such as juvenile habitat or adult morphology). Lastly, we conclude that larval body shape is probably influenced by adult habitat and adult morphology.
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Affiliation(s)
| | - M Timothy Tinker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Rita S Mehta
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
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10
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Macaluso L, Carnevale G, Casu R, Pietrocola D, Villa A, Delfino M. Structural and environmental constraints on reduction of paired appendages among vertebrates. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractBurrowing habits or complex environments have generally been considered as potential drivers acting on reduction and loss of the appendicular skeleton among vertebrates. Herein, we suggest that this might be the case for lissamphibians and squamates, but that fin loss in fishes is usually prevented by important structural constraints, because pectoral fins are commonly used to control rolling and pitching. We provide an overview of the distribution of paired appendage reduction across vertebrates while examining the ecological affinities of finless and limbless clades. We analysed the correlation between lifestyle and fin or limb loss using the discrete comparative analysis. The resulting Bayesian factors indicate strong evidence of correlation between: (1) pectoral-fin loss and coexistence of anguilliform elongation and burrowing habits or complex habitat in teleost fishes; and (2) limb loss and a burrowing or grass-swimming lifestyle in squamate reptiles and lissamphibians. These correlations suggest that a complex environment or a fossorial habit is a driving force leading to appendage loss. The only style of locomotion that is functional even in the absence of paired appendages is the undulatory one, which is typical of all elongated reptiles and lissamphibians, but certainly less common in teleost fishes.
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Affiliation(s)
- Loredana Macaluso
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Raffaello Casu
- Dipartimento di Fisica, Università degli Studi di Torino, Via Pietro Giuria, Torino, Italy
| | - Daniel Pietrocola
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Andrea Villa
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße, München, Germany
| | - Massimo Delfino
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici Z (ICTA-ICP), Carrer de les Columnes s/n, Campus de la UAB, Cerdanyola del Valles, Barcelona, Spain
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11
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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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12
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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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13
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Kindl GH, O'Quin KE. On Intraspecific and Interspecific Variation in Teleost Scleral Ossification. Anat Rec (Hoboken) 2019; 302:1238-1249. [PMID: 30737901 DOI: 10.1002/ar.24080] [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: 12/08/2017] [Revised: 10/03/2018] [Accepted: 10/23/2018] [Indexed: 11/08/2022]
Abstract
Scleral ossicles are bony elements found along the eyes of many fishes, amphibians, and reptiles. These bones provide a superficial layer of support to the eye and may facilitate visual acuity. Previous research has shown that scleral ossicle diversity is generally limited among teleosts, but that scleral ossicles have been lost numerous times among teleosts inhabiting benthopelagic habitats (Franz-Odendaal. Anat Rec 291 (2008) 161-168). In this study, we further investigate these patterns of intraspecific and interspecific variation by examining eyes from multiple individuals of 10 riverine teleosts native to Kentucky as well as one population of the Mexican blind cavefish, Astyanax mexicanus, and by re-analyzing a quantitative database of scleral ossicle number and depth preference from over 100 teleosts using newly resolved teleost phylogenies. Consistent with the limited diversity of most teleost families, we find that intraspecific variation in scleral ossicle number and size is virtually nonexistent among the species sampled, although we do find evidence of additional interspecific variation among the Cyprinodontiformes, as well as dramatic intrapopulation variation among cavefish from Chica Cave. Although our data replicates the negative relationship between scleral ossicle number and the depth preference previously found among teleosts (Franz-Odendaal. Anat Rec 291 (2008) 161-168), even when accounting for phylogenetic relationships, our results further reveal that this relationship is relatively weak. We conclude that further sampling may reveal additional interspecific and even intraspecific variation among some groups of teleosts, and that depth could serve as a proxy for other life history traits that more directly influence teleost scleral ossicle diversity such as prey-capture strategies. Anat Rec, 302:1238-1249, 2019. © 2019 Wiley Periodicals, Inc.
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14
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Du TY, Tissandier SC, Larsson HCE. Integration and modularity of teleostean pectoral fin shape and its role in the diversification of acanthomorph fishes. Evolution 2019; 73:401-411. [PMID: 30593658 DOI: 10.1111/evo.13669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/09/2018] [Indexed: 12/30/2022]
Abstract
Phenotypic integration and modularity describe the strength and pattern of interdependencies between traits. Integration and modularity have been proposed to influence the trajectory of evolution, either acting as constraints or facilitators. Here, we examine trends in the integration and modularity of pectoral fin morphology in teleost fishes using geometric morphometrics. We compare the fin shapes of the highly diverse radiation of acanthomorph fishes to lower teleosts. Integration and modularity are measured using two-block partial least squares analysis and the covariance ratio coefficient between the radial bones and lepidotrichia of the pectoral fins. We show that the fins of acanthomorph fishes are more tightly integrated but also more morphologically diverse and faster evolving compared to nonacanthomorph fishes. The main pattern of shape covariation in nonacanthomorphs is concordant with the main trajectory of evolution between nonacanthomorphs and acanthomorphs. Our findings support a facilitating role for integration during the acanthomorph diversification. Potential functional consequences and developmental mechanisms of fin integration are discussed.
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Affiliation(s)
- Trina Y Du
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada.,Current Address: Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - Sylvie C Tissandier
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada.,Current Address: Edmonton, Alberta, Canada
| | - Hans C E Larsson
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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15
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Mohapatra A, Kundu S, Mohanty SR, Mishra SS, Kumar V, Tripathy B, Chandra K. DNA barcoding adjudicate two different morphs of Bascanichthys deraniyagalai (Anguilliformes: Ophichthidae): re-description and first record from Chilika lagoon, India. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1598298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anil Mohapatra
- Zoological Survey of India, Estuarine Biology Regional Centre, Ganjam, India
| | - Shantanu Kundu
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
| | - Swarup R. Mohanty
- Zoological Survey of India, Estuarine Biology Regional Centre, Ganjam, India
| | | | - Vikas Kumar
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
| | - Basudev Tripathy
- Malacology Division, Zoological Survey of India, New Alipore, Kolkata, India
| | - Kailash Chandra
- Zoological Survey of India, Estuarine Biology Regional Centre, Ganjam, India
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
- Marine Fish Section, Zoological Survey of India, Kolkata, India
- Malacology Division, Zoological Survey of India, New Alipore, Kolkata, India
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16
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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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17
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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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18
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Poulsen JY, Miller MJ, Sado T, Hanel R, Tsukamoto K, Miya M. Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic gene orders. PLoS One 2018; 13:e0199982. [PMID: 30044814 PMCID: PMC6059418 DOI: 10.1371/journal.pone.0199982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/14/2018] [Indexed: 11/24/2022] Open
Abstract
Deep-sea midwater "saccopharyngiform" eels of the families Cyematidae, Monognathidae, Eurypharyngidae and Saccopharyngidae (order Anguilliformes) are extraordinary fishes having major skeletal reductions and modifications compared to the general anguilliform body structure. Little is known about most aspects of the systematics, phylogeny, and ecology of these families, and few of the approximately 30 species described from adult specimens have been matched with their leptotocephalus larvae. Based on mitogenomic sequence data from rare new specimens, we show that the long-speculated-about larval form referred to as "Leptocephalus holti", which was thought to possibly be the larva of the rare orange-colored eels of Neocyema (5 known specimens; speculated to belong to the Cyematidae) are actually the larvae of the one-jaw eels of the family Monognathidae. One of the 5 types of L. holti larvae that were collected in the Pacific is genetically matched with Monognathus jesperseni, but multiple species exist based on larval sequence data and the morphology of adult specimens. A rare leptocephalus from the Sargasso Sea, with unique morphological characteristics including many small orange spots on the gut, was found to be the larva of Neocyema, which is presently only known from the Atlantic Ocean. We demonstrate that Neocyema constitutes a separate family being most closely related to Eurypharyngidae and Saccopharyngidae based on mitogenomic DNA sequences and unique mitochondrial gene orders.
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Affiliation(s)
- Jan Y. Poulsen
- Department of Fish and Shellfish, Greenland Institute of Natural Resources, Kivioq, Nuuk, Greenland
- Fish Section, Australian Museum, Sydney NSW, Australia
| | - Michael J. Miller
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Aoba-cho, Chuo-ku, Chiba, Japan
| | | | - Katsumi Tsukamoto
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Masaki Miya
- Thunen-Institute of Fisheries Ecology, Hamburg, Germany
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19
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Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Syst Biol 2018; 67:559-575. [PMID: 29325126 PMCID: PMC6005059 DOI: 10.1093/sysbio/syx098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 11/24/2022] Open
Abstract
Data synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes. We developed a bioinformatics pipeline to identify the presence and absence of pectoral and pelvic fins of 12,582 species. To do this, we integrated a synthetic morphological supermatrix of phenotypic data for the pectoral and pelvic fins for teleost fishes from the Phenoscape Knowledgebase (two presence/absence characters for 3047 taxa) with a species-level tree for teleost fishes from the Open Tree of Life project (38,419 species). The integration method detailed herein harnessed a new combined approach by utilizing data based on ontological inference, as well as phylogenetic propagation, to reduce overall data loss. Using inference enabled by ontology-based annotations, missing data were reduced from 98.0% to 85.9%, and further reduced to 34.8% by phylogenetic data propagation. These methods allowed us to extend the data to an additional 11,293 species for a total of 12,582 species with trait data. The pectoral fin appears to have been independently lost in a minimum of 19 lineages and the pelvic fin in 48. Though interpretation is limited by lack of phylogenetic resolution at the species level, it appears that following loss, both pectoral and pelvic fins were regained several (3) to many (14) times respectively. Focused investigation into putative regains of the pectoral fin, all within one clade (Anguilliformes), showed that the pectoral fin was regained at least twice following loss. Overall, this study points to specific teleost clades where strategic phylogenetic resolution and genetic investigation will be necessary to understand the pattern and frequency of pectoral fin reversals.
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Affiliation(s)
- Laura M Jackson
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - Pasan C Fernando
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - Josh S Hanscom
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive Suite 540, Chapel Hill, NC 27517, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
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20
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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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21
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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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22
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Pfaff C, Zorzin R, Kriwet J. Evolution of the locomotory system in eels (Teleostei: Elopomorpha). BMC Evol Biol 2016; 16:159. [PMID: 27514517 PMCID: PMC4981956 DOI: 10.1186/s12862-016-0728-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/25/2016] [Indexed: 11/28/2022] Open
Abstract
Background Living anguilliform eels represent a distinct clade of elongated teleostean fishes inhabiting a wide range of habitats. Locomotion of these fishes is highly influenced by the elongated body shape, the anatomy of the vertebral column, and the corresponding soft tissues represented by the musculotendinous system. Up to now, the evolution of axial elongation in eels has been inferred from living taxa only, whereas the reconstruction of evolutionary patterns and functional ecology in extinct eels still is scarce. Rare but excellently preserved fossil eels from the Late Cretaceous and Cenozoic were investigated here to gain a better understanding of locomotory system evolution in anguilliforms and, consequently, their habitat occupations in deep time. Results The number of vertebrae in correlation with the body length separates extinct and extant anguilliforms. Even if the phylogenetic signal cannot entirely be excluded, the analyses performed here reveal a continuous shortening of the vertebral column with a simultaneous increase in vertebral numbers in conjunction with short lateral tendons throughout the order. These anatomical changes contradict previous hypotheses based on extant eels solely. Conclusions The body curvatures of extant anguilliforms are highly flexible and can be clearly distinguished from extinct species. Anatomical changes of the vertebral column and musculotendinous system through time and between extinct and extant anguilliforms correlate with changes of the body plan and swimming performance and reveal significant shifts in habitat adaptation and thus behaviour. Evolutionary changes in the skeletal system of eels established here also imply that environmental shifts were triggered by abiotic rather than biotic factors (e.g., K/P boundary mass extinction event). Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0728-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cathrin Pfaff
- Department of Palaeontology, University of Vienna, Faculty of Earth Sciences, Geozentrum, UZA II, Althanstraße 14, 1090, Vienna, Austria.
| | - Roberto Zorzin
- Museo civico di Storia Naturale, Palazzo Pompei, Lungadige Porta Vittoria 9, 37129, Verona, Italy
| | - Jürgen Kriwet
- Department of Palaeontology, University of Vienna, Faculty of Earth Sciences, Geozentrum, UZA II, Althanstraße 14, 1090, Vienna, Austria
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Coluccia E, Deidda F, Cannas R, Lobina C, Cuccu D, Deiana AM, Salvadori S. Comparative cytogenetics of six Indo-Pacific moray eels (Anguilliformes: Muraenidae) by chromosomal banding and fluorescence in situ hybridization. JOURNAL OF FISH BIOLOGY 2015; 87:634-645. [PMID: 26242690 DOI: 10.1111/jfb.12737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 06/09/2015] [Indexed: 06/04/2023]
Abstract
A comparative cytogenetic analysis, using both conventional staining techniques and fluorescence in situ hybridization, of six Indo-Pacific moray eels from three different genera (Gymnothorax fimbriatus, Gymnothorax flavimarginatus, Gymnothorax javanicus, Gymnothorax undulatus, Echidna nebulosa and Gymnomuraena zebra), was carried out to investigate the chromosomal differentiation in the family Muraenidae. Four species displayed a diploid chromosome number 2n = 42, which is common among the Muraenidae. Two other species, G. javanicus and G. flavimarginatus, were characterized by different chromosome numbers (2n = 40 and 2n = 36). For most species, a large amount of constitutive heterochromatin was detected in the chromosomes, with species-specific C-banding patterns that enabled pairing of the homologous chromosomes. In all species, the major ribosomal genes were localized in the guanine-cytosine-rich region of one chromosome pair, but in different chromosomal locations. The (TTAGGG)n telomeric sequences were mapped onto chromosomal ends in all muraenid species studied. The comparison of the results derived from this study with those available in the literature confirms a substantial conservation of the diploid chromosome number in the Muraenidae and supports the hypothesis that rearrangements have occurred that have diversified their karyotypes. Furthermore, the finding of two species with different diploid chromosome numbers suggests that additional chromosomal rearrangements, such as Robertsonian fusions, have occurred in the karyotype evolution of the Muraenidae.
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Affiliation(s)
- E Coluccia
- Dipartimento di Scienze della Vita e dell'Ambiente, sezione Biologia Animale ed Ecologia, Università degli Studi di Cagliari, via T. Fiorelli, 1, 09126, Cagliari, Italy
| | - F Deidda
- Dipartimento di Scienze della Vita e dell'Ambiente, sezione Biologia Animale ed Ecologia, Università degli Studi di Cagliari, via T. Fiorelli, 1, 09126, Cagliari, Italy
| | - R Cannas
- Dipartimento di Scienze della Vita e dell'Ambiente, sezione Biologia Animale ed Ecologia, Università degli Studi di Cagliari, via T. Fiorelli, 1, 09126, Cagliari, Italy
| | - C Lobina
- Dipartimento di Scienze della Vita e dell'Ambiente, sezione Biologia Animale ed Ecologia, Università degli Studi di Cagliari, via T. Fiorelli, 1, 09126, Cagliari, Italy
| | - D Cuccu
- Dipartimento di Scienze della Vita e dell'Ambiente, sezione Biologia Animale ed Ecologia, Università degli Studi di Cagliari, via T. Fiorelli, 1, 09126, Cagliari, Italy
| | - A M Deiana
- Dipartimento di Scienze della Vita e dell'Ambiente, sezione Biologia Animale ed Ecologia, Università degli Studi di Cagliari, via T. Fiorelli, 1, 09126, Cagliari, Italy
| | - S Salvadori
- Dipartimento di Scienze della Vita e dell'Ambiente, sezione Biologia Animale ed Ecologia, Università degli Studi di Cagliari, via T. Fiorelli, 1, 09126, Cagliari, Italy
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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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25
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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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26
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Jacobsen MW, Pujolar JM, Hansen MM. Relationship between amino acid changes in mitochondrial ATP6 and life-history variation in anguillid eels. Biol Lett 2015; 11:rsbl.2015.0014. [PMID: 25788489 DOI: 10.1098/rsbl.2015.0014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial genes are part of the oxidative phosphorylation pathway and important for energy production. Although evidence for positive selection at the mitochondrial level exists, few studies have investigated the link between amino acid changes and phenotype. Here we test the hypothesis that differences in two life-history related traits, migratory distance between spawning and foraging areas and larval phase duration, are associated with divergent selection within the mitochondrial ATP6 gene in anguillid eels. We compare amino acid changes among 18 species with the sequence of the putative ancestral species, believed to have shown short migratory distance and larval phase duration. We find positive correlations between both life-history related traits and (i) the number of amino acid changes and (ii) the strength of the combined physico-chemical and structural changes at positions previously identified as candidates for positive selection. This supports a link between genotype and phenotype driven by positive selection at ATP6.
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Affiliation(s)
- Magnus W Jacobsen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C 8000, Denmark
| | - José Martin Pujolar
- Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C 8000, Denmark
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C 8000, Denmark
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Santini F, Carnevale G, Sorenson L. First timetree of Sphyraenidae (Percomorpha) reveals a Middle Eocene crown age and an Oligo–Miocene radiation of barracudas. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/11250003.2014.962630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Chen JN, López JA, Lavoué S, Miya M, Chen WJ. Phylogeny of the Elopomorpha (Teleostei): Evidence from six nuclear and mitochondrial markers. Mol Phylogenet Evol 2014; 70:152-61. [DOI: 10.1016/j.ympev.2013.09.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/04/2013] [Indexed: 12/15/2022]
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