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Lü Z, Li H, Jiang H, Luo H, Wang W, Kong X, Li Y. Reply to: Phylogenomic and comparative genomic analyses support a single evolutionary origin of flatfish asymmetry. Nat Genet 2024; 56:1073-1074. [PMID: 38802565 DOI: 10.1038/s41588-024-01783-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Affiliation(s)
- Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Hairong Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Xiaoyu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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2
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Kundu S, Palimirmo FS, Kang HE, Kim AR, Lee SR, Gietbong FZ, Song SH, Kim HW. Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean. BIOLOGY 2023; 12:1317. [PMID: 37887027 PMCID: PMC10604034 DOI: 10.3390/biology12101317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.
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Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Flandrianto Sih Palimirmo
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Se Hyun Song
- Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyun-Woo Kim
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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3
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Bitencourt JA, Affonso PRAM, Ramos RTC, Schneider H, Sampaio I. Phylogenetic relationships and the origin of New World soles (Teleostei: Pleuronectiformes: Achiridae): The role of estuarine habitats. Mol Phylogenet Evol 2023; 178:107631. [PMID: 36162736 DOI: 10.1016/j.ympev.2022.107631] [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: 05/08/2022] [Revised: 09/08/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
Even though the monophyletic status of Achiridae has been supported by morphological and molecular data, the interrelationships within the representatives of this family are poorly resolved. In the present study, we carried out the most complete molecular phylogenetic analysis of this group, encompassing all genera and employing both nuclear (Rhodopsin, Recombination activator [Rag 1], Mixed - lineage Leukemia [MLL] and Early Growth Response Protein 3 [EGR3]) and mitochondrial (Cytochrome C Oxidase Subunit I [COI], Cytochrome B [CytB], ATPase 6.8, 16S and 12S RNAr) genes. All topologies based on Maximum Likelihood, Bayesian inferences and Bayesian Inference of the Multispecies Coalescent confirmed the monophyletism of Achiridae, in spite of some incongruences in relation to Achirus mucuri, A. lineatus, Apionichthys finis and Trinectes microphthalmus. In fact, Achirus and Trinectes proved to be non-monophyletic genera while Hypoclinemus mentalis was closely related to A. achirus, suggesting this species should be reevaluated. We provided evidence that Achiridae has first arisen in estuaries (about 23.5 million years ago) and some lineages have evolved independently to either marine or freshwater habitats. Furthermore, we propose a diversification scenario of New World soles involving at least two events of marine incursions during Miocene and Pliocene - Pleistocene associated with natural geographic barriers (Victoria-Trindade chain), the width and exposure of continental shelf and headwater capture along the Amazon basin. Finally, the evolutionary dependence of Achirid soles on estuaries, characterized as highly dynamic environments, has probably driven the recent divergence of many species of Achiridae.
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Affiliation(s)
- Jamille A Bitencourt
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Campus Jequié, Av. José Moreira Sobrinho, S/N, Jequiezinho, 45208-190 Jequié, BA, Brazil.
| | - Paulo R A M Affonso
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Campus Jequié, Av. José Moreira Sobrinho, S/N, Jequiezinho, 45208-190 Jequié, BA, Brazil
| | - Robson T C Ramos
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Campus I Lot. Cidade Universitária, 58051-900 João Pessoa, PB, Brazil
| | - Horacio Schneider
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança, Alameda Leandro Ribeiro, 68600-000 Bragança, PA, Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança, Alameda Leandro Ribeiro, 68600-000 Bragança, PA, Brazil
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Ramírez D, Rodríguez ME, Cross I, Arias-Pérez A, Merlo MA, Anaya M, Portela-Bens S, Martínez P, Robles F, Ruiz-Rejón C, Rebordinos L. Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis. Int J Mol Sci 2022; 23:ijms23105353. [PMID: 35628170 PMCID: PMC9140517 DOI: 10.3390/ijms23105353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/28/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions.
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Affiliation(s)
- Daniel Ramírez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - María Esther Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Alberto Arias-Pérez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Manuel Alejandro Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Marco Anaya
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Universidad de Santiago de Compostela, 27002 Lugo, Spain;
| | - Francisca Robles
- Departamento de Genética, Universidad de Granada, 18071 Granada, Spain; (F.R.); (C.R.-R.)
| | - Carmelo Ruiz-Rejón
- Departamento de Genética, Universidad de Granada, 18071 Granada, Spain; (F.R.); (C.R.-R.)
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
- Correspondence: ; Tel.: +34-956-016181
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5
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Girard MG, Davis MP, Tan HH, Wedd DJ, Chakrabarty P, Ludt WB, Summers AP, Smith WL. Phylogenetics of archerfishes (Toxotidae) and evolution of the toxotid shooting apparatus. Integr Org Biol 2022; 4:obac013. [PMID: 35814192 PMCID: PMC9259087 DOI: 10.1093/iob/obac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/11/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Archerfishes (Toxotidae) are variously found in the fresh- and brackish-water environments of Asia Pacific and are well known for their ability to shoot water at terrestrial prey. These shots of water are intended to strike their prey and cause it to fall into the water for capture and consumption. While this behavior is well known, there are competing hypotheses (blowpipe vs. pressure tank hypothesis) of how archerfishes shoot and which oral structures are involved. Current understanding of archerfish shooting structures is largely based on two species, Toxotes chatareus and T. jaculatrix. We do not know if all archerfishes possess the same oral structures to shoot water, if anatomical variation is present within these oral structures, or how these features have evolved. Additionally, there is little information on the evolution of the Toxotidae as a whole, with all previous systematic works focusing on the interrelationships of the family. We first investigate the limits of archerfish species using new and previously published genetic data. Our analyses highlight that the current taxonomy of archerfishes does not conform to the relationships we recover. Toxotes mekongensis and T. siamensis are placed in synonymy of T. chatareus, Toxotes carpentariensis is recognized as a species and removed from synonymy of T. chatareus, and the genus Protoxotes is recognized for T. lorentzi based on the results of our analyses. We then take an integrative approach, using a combined analysis of discrete hard- and soft-tissue morphological characters with genetic data, to construct a phylogeny of the Toxotidae. Using the resulting phylogenetic hypothesis, we then characterize the evolutionary history and anatomical variation within the archerfishes. We discuss the variation in the oral structures and the evolution of the mechanism with respect to the interrelationships of archerfishes, and find that the oral structures of archerfishes support the blowpipe hypothesis but soft-tissue oral structures may also play a role in shooting. Finally, by comparing the morphology of archerfishes to their sister group, we find that the Leptobramidae has relevant shooting features in the oral cavity, suggesting that some components of the archerfish shooting mechanism are examples of co-opted or exapted traits.
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Affiliation(s)
- M G Girard
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, 20560, USA
| | - M P Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, MN, 56301, USA
| | - H H Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, 117377, SGP
| | - D J Wedd
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0810, AUS
| | - P Chakrabarty
- Ichthyology Section, Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - W B Ludt
- Department of Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA
| | - A P Summers
- Department of Biology and SAFS, University of Washington's Friday Harbor Laboratories, Friday Harbor, WA, 98250, USA
| | - W L Smith
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
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Tripathy PK, Seth JK, Dixit PK. Geometric morphometric analysis of flatfishes of Gopalpur-on-Sea, Odisha coast, India. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-021-00061-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Atta CJ, Yuan H, Li C, Arcila D, Betancur-R R, Hughes LC, Ortí G, Tornabene L. Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei). Mol Phylogenet Evol 2021; 166:107315. [PMID: 34537325 DOI: 10.1016/j.ympev.2021.107315] [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: 12/19/2020] [Revised: 05/12/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
There is an extensive collection of literature on the taxonomy and phylogenetics of flatfishes (Pleuronectiformes) that extends over two centuries, but consensus on many of their evolutionary relationships remains elusive. Phylogenetic uncertainty stems from highly divergent results derived from morphological and genetic characters, and between various molecular datasets. Deciphering relationships is complicated by rapid diversification early in the Pleuronectiformes tree and an abundance of studies that incompletely and inconsistently sample taxa and genetic markers. We present phylogenies based on a genome-wide dataset (4,434 nuclear markers via exon-capture) and wide taxon sampling (86 species spanning 12 of 16 families) of the largest flatfish suborder (Pleuronectoidei). Nine different subsets of the data and two tree construction approaches (eighteen phylogenies in total) are remarkably consistent with other recent molecular phylogenies, and show strong support for the monophyly of all families included except Pleuronectidae. Analyses resolved a novel phylogenetic hypothesis for the family Rhombosoleidae as being within the Pleuronectoidea rather than the Soleoidea, and failed to support the subfamily Hippoglossinae as a monophyletic group. Our results were corroborated with evidence from previous phylogenetic studies to outline regions of persistent phylogenetic uncertainty and identify groups in need of further phylogenetic inference.
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Affiliation(s)
- Calder J Atta
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA.
| | - Hao Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Dahiana Arcila
- Sam Noble Oklahoma Museum of Natural History, The University of Oklahoma, Norman, OK 73072, USA; Department of Biology, The University of Oklahoma, Norman, OK 73072, USA
| | - Ricardo Betancur-R
- Sam Noble Oklahoma Museum of Natural History, The University of Oklahoma, Norman, OK 73072, USA; Department of Biology, The University of Oklahoma, Norman, OK 73072, USA
| | - Lily C Hughes
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Guillermo Ortí
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA
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8
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Lü Z, Gong L, Ren Y, Chen Y, Wang Z, Liu L, Li H, Chen X, Li Z, Luo H, Jiang H, Zeng Y, Wang Y, Wang K, Zhang C, Jiang H, Wan W, Qin Y, Zhang J, Zhu L, Shi W, He S, Mao B, Wang W, Kong X, Li Y. Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan. Nat Genet 2021; 53:742-751. [PMID: 33875864 PMCID: PMC8110480 DOI: 10.1038/s41588-021-00836-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/05/2021] [Indexed: 11/09/2022]
Abstract
The evolutionary and genetic origins of the specialized body plan of flatfish are largely unclear. We analyzed the genomes of 11 flatfish species representing 9 of the 14 Pleuronectiforme families and conclude that Pleuronectoidei and Psettodoidei do not form a monophyletic group, suggesting independent origins from different percoid ancestors. Genomic and transcriptomic data indicate that genes related to WNT and retinoic acid pathways, hampered musculature and reduced lipids might have functioned in the evolution of the specialized body plan of Pleuronectoidei. Evolution of Psettodoidei involved similar but not identical genes. Our work provides valuable resources and insights for understanding the genetic origins of the unusual body plan of flatfishes.
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Affiliation(s)
- Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yongjiu Chen
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xianqing Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zhenzhu Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hairong Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Yan Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yifan Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Chen Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Haifeng Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenting Wan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yanli Qin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jianshe Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Liang Zhu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Xiaoyu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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9
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Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis. Int J Mol Sci 2021; 22:ijms22041614. [PMID: 33562667 PMCID: PMC7915175 DOI: 10.3390/ijms22041614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 12/18/2022] Open
Abstract
Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of Solea senegalensis. S. senegalensis is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (FISH-BAC) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (Cynoglossus semilaevis, Scophthalmus maximus, Sparus aurata, Gasterosteus aculeatus, Xiphophorus maculatus, Oryzias latipes, Danio rerio, and Lepisosteus oculatus) for comparison, showed that the BACs of these two chromosomes of S. senegalensis were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (C. semilaevis, S. maximus, O. latipes, and D. rerio) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to S. senegalensis, like S. maximus and C. semilaevis. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs.
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Wang C, Chen H, Tian S, Yang C, Chen X. Novel Gene Rearrangement and the Complete Mitochondrial Genome of Cynoglossus monopus: Insights into the Envolution of the Family Cynoglossidae (Pleuronectiformes). Int J Mol Sci 2020; 21:E6895. [PMID: 32962212 PMCID: PMC7555148 DOI: 10.3390/ijms21186895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 11/26/2022] Open
Abstract
Cynoglossus monopus, a small benthic fish, belongs to the Cynoglossidae, Pleuronectiformes. It was rarely studied due to its low abundance and cryptical lifestyle. In order to understand the mitochondrial genome and the phylogeny in Cynoglossidae, the complete mitogenome of C. monopus has been sequenced and analyzed for the first time. The total length is 16,425 bp, typically containing 37 genes with novel gene rearrangements. The tRNA-Gln gene is inverted from the light to the heavy strand and translocated from the downstream of tRNA-Ile gene to its upstream. The control region (CR) translocated downstream to the 3'-end of ND1 gene adjoining to inverted to tRNA-Gln and left a 24 bp trace fragment in the original position. The phylogenetic trees were reconstructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 32 tonguefish species and two outgroups. The results support the idea that Cynoglossidae is a monophyletic group and indicate that C. monopus has the closest phylogenetic relationship with C. puncticeps. By combining fossil records and mitogenome data, the time-calibrated evolutionary tree of families Cynoglossidae and Soleidae was firstly presented, and it was indicated that Cynoglossidae and Soleidae were differentiated from each other during Paleogene, and the evolutionary process of family Cynoglossidae covered the Quaternary, Neogene and Paleogene periods.
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Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
| | - Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Silin Tian
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
| | - Cheng Yang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; (C.W.); (S.T.); (C.Y.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China
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Campbell MA, Tongboonkua P, Chanet B, Chen WJ. The distribution of the recessus orbitalis across flatfishes (order: Pleuronectiformes). JOURNAL OF FISH BIOLOGY 2020; 97:293-297. [PMID: 32333611 DOI: 10.1111/jfb.14356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
The recessus orbitalis is an accessory organ of flatfishes functioning in the protrusion of the eyes. This character, along with cranial asymmetry and a forward insertion of the dorsal fin, have been considered synapomorphies for the Pleuronectiformes. New dissections and examination of images taken in the wild show that the recessus orbitalis is present in all representatives of Pleuronectoidei examined but is absent in the single species of Psettoidei dissected. Psettoidei, the most primitive pleuronectiform lineage, contains three recognized species; thus, the absence of the recessus orbitalis in this whole lineage is unclear without further dissections. Ancestral character estimation at the family level for the recessus orbitalis indicates that the recessus orbitalis was likely absent in the common ancestor of Pleuronectiformes but was most likely present in the common ancestor of the Pleuronectoidei. Given that so few species of flatfishes have been assessed for the recessus orbitalis to date, additional characterization of the distribution of the recessus orbitalis across flatfishes will further inform what states this character may have and if it is a synapomorphy of Pleuronectiformes or simply a derived character state of Pleuronectoidei.
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Affiliation(s)
| | | | - Bruno Chanet
- Équipe Homologies, Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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12
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Girard MG, Davis MP, Smith WL. The Phylogeny of Carangiform Fishes: Morphological and Genomic Investigations of a New Fish Clade. COPEIA 2020. [DOI: 10.1643/ci-19-320] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Matthew G. Girard
- Biodiversity Institute, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, Kansas 66045; (MGG) . Send reprint requests to MGG
| | - Matthew P. Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota 56301
| | - W. Leo Smith
- Biodiversity Institute, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, Kansas 66045; (MGG) . Send reprint requests to MGG
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13
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Black CR, Berendzen PB. Shared ecological traits influence shape of the skeleton in flatfishes (Pleuronectiformes). PeerJ 2020; 8:e8919. [PMID: 32280569 PMCID: PMC7134016 DOI: 10.7717/peerj.8919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/16/2020] [Indexed: 11/23/2022] Open
Abstract
In the age of phylogenetic comparative methods, evolutionary biologists have been able to explore evolutionary trends in form in unique and extraordinarily diverse groups of animals. Pleuronectiformes, commonly known as flatfishes, is a diverse and specialized order of fishes that have remarkable asymmetry induced by ocular migration and a benthic life style. Although flatfishes are unique from other fishes, species within the group are morphologically diverse. The origin of ocular migration has been a primary focus of research; however, little is known about overall shape diversification among the flatfishes. In this study, we use integrative methods to examine how body shape evolved within the flatfishes. Shape was quantified from X-rays using geometric morphometrics for 389 individuals across 145 species. The most recent and robust phylogeny was overlaid onto the morphospace and phylogenetic signal was calculated to ascertain convergence in the morphospace. In addition, phylogenetic linear models were employed to determine if ecological traits were correlated with shape and if size had an effect on overall body shape. Results revealed that the majority of variation evolved recently, within the past 15–10-million-years in the middle Miocene, and is highly variable within the flatfishes. These changes are best summarized by body depth, jaw length and medial fin length. Dorsal and anal fin length are correlated, which may be due to the unique mode of locomotion used by flatfishes. A phylogenetic linear model and phylomorphospace analysis suggested that several ecological traits are correlated with shape, which indicates an ecological role in the diversification of flatfishes.
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Affiliation(s)
- Corinthia R Black
- Department of Biological Sciences, Auburn University, Auburn, AL, USA.,Department of Biology, University of Northern Iowa, Cedar Falls, IA, USA
| | - Peter B Berendzen
- Department of Biology, University of Northern Iowa, Cedar Falls, IA, USA
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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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García-Angulo A, Merlo MA, Portela-Bens S, Rodríguez ME, García E, Al-Rikabi A, Liehr T, Rebordinos L. Evidence for a Robertsonian fusion in Solea senegalensis (Kaup, 1858) revealed by zoo-FISH and comparative genome analysis. BMC Genomics 2018; 19:818. [PMID: 30428854 PMCID: PMC6236887 DOI: 10.1186/s12864-018-5216-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/31/2018] [Indexed: 11/16/2022] Open
Abstract
Background Solea senegalensis (Kaup, 1858) is a commercially important flatfish species, belonging to the Pleuronectiformes order. The taxonomy of this group has long been controversial, and the karyotype of the order presents a high degree of variability in diploid number, derived from chromosomal rearrangements such as Robertsonian fusions. Previously it has been proposed that the large metacentric chromosome of S. senegalensis arises from this kind of chromosome rearrangement and that this is a proto-sex chromosome. Results In this work, the Robertsonian origin of the large metacentric chromosome of S. senegalensis has been tested by the Zoo-FISH technique applied to two species of the Soleidae family (Dicologlossa cuneata and Dagetichthys lusitanica), and by comparative genome analysis with Cynoglossus semilaevis. From the karyotypic analysis we were able to determine a chromosome complement comprising 2n = 50 (FN = 54) in D. cuneata and 2n = 42 (FN = 50) in D. lusitanica. The large metacentric painting probe gave consistent signals in four acrocentric chromosomes of the two Soleidae species; and the genome analysis proved a common origin with four chromosome pairs of C. semilaevis. As a result of the genomic analysis, up to 61 genes were annotated within the thirteen Bacterial Artificial Chromosome clones analysed. Conclusions These results confirm that the large metacentric chromosome of S. senegalensis originated from a Robertsonian fusion and provide new data about the chromosome evolution of S. senegalensis in particular, and of Pleuronectiformes in general. Electronic supplementary material The online version of this article (10.1186/s12864-018-5216-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aglaya García-Angulo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel A Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María E Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Emilio García
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ahmed Al-Rikabi
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain.
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16
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Maroso F, Hermida M, Millán A, Blanco A, Saura M, Fernández A, Dalla Rovere G, Bargelloni L, Cabaleiro S, Villanueva B, Bouza C, Martínez P. Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly. DNA Res 2018; 25:439-450. [PMID: 29897548 PMCID: PMC6105115 DOI: 10.1093/dnares/dsy015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/05/2018] [Indexed: 12/26/2022] Open
Abstract
Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.
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Affiliation(s)
| | - M Hermida
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | | | - A Blanco
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - M Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - A Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - S Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, Spain
| | - B Villanueva
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - C Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - P Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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17
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Campbell MA, Sado T, Shinzato C, Koyanagi R, Okamoto M, Miya M. Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships. Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Shi W, Chen S, Kong X, Si L, Gong L, Zhang Y, Yu H. Flatfish monophyly refereed by the relationship of Psettodes in Carangimorphariae. BMC Genomics 2018; 19:400. [PMID: 29801430 PMCID: PMC5970519 DOI: 10.1186/s12864-018-4788-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/14/2018] [Indexed: 11/18/2022] Open
Abstract
Background The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained. Results The mitogenomes of five flatfishes were determined. Select mitogenomes of representative carangimorph species were further employed for phylogenetic and molecular clock analyses. Our phylogenetic results do not fully support Psettodes as a sister group to pleuronectoids or other carangimorphs. And results also supported the evidence of long-branch attraction between Psettodes and the adjacent clades. Two chronograms, derived from Bayesian relaxed-clock methods, suggest that over a short period in the early Paleocene, a series of important evolutionary events occurred in carangimorphs. Conclusion Based on insights provided by the molecular clock, we propose the following evolutionary explanation for the difficulty in determining the phylogenetic position of Psettodes: The initial diversification of Psettodes was very close in time to the initial diversification of carangimorphs, and the primary diversification time of pleuronectoids, the other suborder of flatfishes, occurred later than that of some percomorph taxa. Additionally, the clade of Psettodes is long and naked branch, which supports the uncertainty of its phylogenetic placement. Finally, we confirmed the monophyly of flatfishes, which was accepted by most ichthyologists. Electronic supplementary material The online version of this article (10.1186/s12864-018-4788-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Shi
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Shixi Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
| | - Lizhen Si
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Li Gong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Yanchun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Hui Yu
- College of Life Science, Foshan University, Foshan, 528231, Guangdong, China.
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Vinnikov KA, Thomson RC, Munroe TA. Revised classification of the righteye flounders (Teleostei: Pleuronectidae) based on multilocus phylogeny with complete taxon sampling. Mol Phylogenet Evol 2018. [PMID: 29535031 DOI: 10.1016/j.ympev.2018.03.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Members of the family Pleuronectidae are common representatives of the marine benthic fauna inhabiting northern regions of the Atlantic and Pacific oceans. The most recent comprehensive classification of the family, based entirely on morphological synapomorphies, recognized five subfamilies, 23 genera, and 61 extant species. However, several subsequent molecular studies have shown that many synapomorphic characters discovered in the morphological study might represent homoplasies, thereby questioning the reliance on these characters with the warning that they may provide misleading information for testing other morphology-based evolutionary hypotheses. In the present study, we propose a comprehensive taxonomic reassessment of the family Pleuronectidae based on the molecular phylogeny reconstructed from four nuclear and three mitochondrial loci and represented by complete taxon sampling of all but one valid species currently assigned to this family. To check for robustness of the phylogenetic hypothesis, we analyzed the effect of base compositional heterogeneity on phylogenetic signal for each locus and compared six different gene partitioning schemes. The final dataset, comprising 14 partitions and 154 individuals, was used to reconstruct phylogenetic trees in RAxML, MrBayes and BEAST2. Alternative topologies for several questionable nodes were compared using Bayes factors. The topology with the highest marginal likelihood was selected as the final phylogenetic tree for inferring pleuronectid relationships and character evolution. Based on our results, we recognize the Pleuronectidae comprising five subfamilies, 24 genera and 59 species. Our new phylogeny comprises five major monophyletic groups within the family, which we define as the subfamilies within the family: Atheresthinae, Pleuronichthyinae, Microstominae, Hippoglossinae and Pleuronectinae. Taxonomic composition of most of these subfamilies is different from that proposed in previous classifications. We also re-assess hypotheses proposed in earlier studies regarding intra-relationships of species of each lineage. Results of the current study contribute to better understanding of the evolutionary relationships of pleuronectid flatfishes based on molecular evidence, and they also provide the framework towards future comprehensive morphological revision of constituent lineages within the family Pleuronectidae.
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Affiliation(s)
- Kirill A Vinnikov
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA; Department of Marine Biodiversity and Bioresources, Far Eastern Federal University, Vladivostok 690091, Russia.
| | - Robert C Thomson
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Thomas A Munroe
- National Systematics Laboratory, NOAA's National Marine Fisheries Service, Office of Science and Technology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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20
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Drinan DP, Loher T, Hauser L. Identification of Genomic Regions Associated With Sex in Pacific Halibut. J Hered 2017; 109:326-332. [DOI: 10.1093/jhered/esx102] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/07/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniel P Drinan
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, Washington
| | - Timothy Loher
- International Pacific Halibut Commission, Seattle, Washington
| | - Lorenz Hauser
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, Washington
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21
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Betancur-R R, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, Lecointre G, Ortí G. Phylogenetic classification of bony fishes. BMC Evol Biol 2017; 17:162. [PMID: 28683774 PMCID: PMC5501477 DOI: 10.1186/s12862-017-0958-3] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/26/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. RESULTS The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. CONCLUSIONS This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras, P.O. Box 23360, San Juan, PR 00931 USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Edward O. Wiley
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS USA
- Sam Houston State Natural History Collections, Sam Houston State University, Huntsville, Texas USA
| | - Gloria Arratia
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS USA
| | - Arturo Acero
- Universidad Nacional de Colombia sede Caribe, Cecimar, El Rodadero, Santa Marta, Magdalena Colombia
| | - Nicolas Bailly
- FishBase Information and Research Group, Los Baños, Philippines
| | - Masaki Miya
- Department Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Guillaume Lecointre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Department of Biology, The George Washington University, Washington, DC USA
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Abstract
Most phylogenetic methods are model-based and depend on models of evolution designed to approximate the evolutionary processes. Several methods have been developed to identify suitable models of evolution for phylogenetic analysis of alignments of nucleotide or amino acid sequences and some of these methods are now firmly embedded in the phylogenetic protocol. However, in a disturbingly large number of cases, it appears that these models were used without acknowledgement of their inherent shortcomings. In this chapter, we discuss the problem of model selection and show how some of the inherent shortcomings may be identified and overcome.
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Affiliation(s)
| | - Vivek Jayaswal
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Faisal M Ababneh
- Department of Mathematics & Statistics, Al-Hussein Bin Talal University, Ma'an, Jordan
| | - John Robinson
- School of Mathematics & Statistics, University of Sydney, Sydney, NSW, Australia
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Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol Biol 2016; 16:224. [PMID: 27769164 PMCID: PMC5073739 DOI: 10.1186/s12862-016-0786-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/30/2016] [Indexed: 11/26/2022] Open
Abstract
Background Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes. Results We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years. Conclusions The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0786-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard C Harrington
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK. .,Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA.
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77553, USA
| | - W Leo Smith
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK.,Museum of Paleontology and Department of Earth and Environmental Science, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA
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24
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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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25
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Si LZ, Gong L, Shi W, Yang M, Kong XY. The complete mitochondrial genome of Pseudorhombus dupliocellatus (Pleuronectiformes: Paralichthyidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:58-59. [PMID: 26681344 DOI: 10.3109/19401736.2015.1110797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Pseudorhombus dupliocellatus belongs to family Paralichthyidae of Pleuronectiformes. In this study, the complete mitochondrial genome of P. dupliocellatus is determined and described. The mitogenome is 16 621 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, a control region, and a L-strand replication origin. The arrangement of the mitogenome is identical to that of the typical teleost. The overall base composition is 26.9%, 25.3%, 31.0%, and 16.8% for A, T, C, and G, respectively, with a slight bias on A+T content (52.2%). The phylogenetic tree of 13 species all in Pleuronectiformes demonstrated that P. dupliocellatus, as well as the other Paralichthyidae fishes containing Paralichthys olivaceus and Pseudorhombus cinnamoneus, clustered in a clade and had a closer relationship with Pleuronectidae species than Bothidae ones. This study is expected to contributing to the systematic evolution of Paralichthyidae and further Pleuronectiformes.
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Affiliation(s)
- Li-Zhen Si
- a Key Laboratory of Tropical Marine Bio-Resources and Ecology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , PR China , and.,b University of Chinese Academy of Sciences , Beijing , PR China
| | - Li Gong
- a Key Laboratory of Tropical Marine Bio-Resources and Ecology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , PR China , and.,b University of Chinese Academy of Sciences , Beijing , PR China
| | - Wei Shi
- a Key Laboratory of Tropical Marine Bio-Resources and Ecology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , PR China , and
| | - Min Yang
- a Key Laboratory of Tropical Marine Bio-Resources and Ecology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , PR China , and.,b University of Chinese Academy of Sciences , Beijing , PR China
| | - Xiao-Yu Kong
- a Key Laboratory of Tropical Marine Bio-Resources and Ecology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , PR China , and
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26
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Sanciangco MD, Carpenter KE, Betancur-R R. Phylogenetic placement of enigmatic percomorph families (Teleostei: Percomorphaceae). Mol Phylogenet Evol 2015; 94:565-576. [PMID: 26493227 DOI: 10.1016/j.ympev.2015.10.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 11/26/2022]
Abstract
Percomorphs are a large and diverse group of spiny-finned fishes that have come to be known as the "bush at the top" due to their persistent lack of phylogenetic resolution. Recently, the broader Euteleost Tree of Life project (EToL) inferred a well-supported phylogenetic hypothesis that groups the diversity of percomorphs into nine well-supported series (supraordinal groups): Ophidiaria, Batrachoidaria, Gobiaria, Syngnatharia, Pelagiaria, Anabantaria, Carangaria, Ovalentaria, and Eupercaria. The EToL also provided, for the first time, a monophyletic definition of Perciformes - the largest order of vertebrates. Despite significant progress made in accommodating the diversity of percomorph taxa into major clades, some 62 families (most previously placed in "Perciformes", as traditionally defined) were not examined by the EToL. Here, we provide evidence for the phylogenetic affinities of 10 of those 62 families, seven of which have largely remained enigmatic. This expanded taxonomic sampling also provides further support for the nine EToL supraordinal series. We examined sequences from 21 genes previously used by the EToL and added two fast-evolving mitochondrial markers in an attempt to increase resolution within the rapid percomorph radiations. We restricted the taxonomic sampling to 1229 percomorph species, including expanded sampling from recent studies. Results of maximum likelihood analysis revealed that bathyclupeids (Bathyclupeidae), galjoen fishes (Dichistiidae), kelpfishes (Chironemidae), marblefishes (Aplodactylidae), trumpeters (Latridae), barbeled grunters (Hapalogenyidae), slopefishes (Symphysanodontidae), and picarel porgies (formerly Centracanthidae) are members of the series Eupercaria ("new bush at the top"). The picarel porgies and porgies (Sparidae) are now placed in the same family (Sparidae). Our analyses suggest a close affinity between the orders Spariformes (including Lethrinidae, Nemipteridae and Sparidae) and Lobotiformes (including the tripletails or Lobotidae, the barbeled grunters, and tigerperches or Datnioididae), albeit support for this group is low. None of the newly examined families belong in the order Perciformes, as recently defined. Finally, we confirm results from other recent studies that place the Australasian salmons (Arripidae) within Pelagiaria, and the false trevallies (Lactariidae) close to flatfishes, jacks, and trevallies, within Carangaria.
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Affiliation(s)
| | - Kent E Carpenter
- Department of Biology, Old Dominion University, Norfolk, VA 23529, USA
| | - Ricardo Betancur-R
- Department of Biology, University of Puerto Rico - Río Piedras, P.O. Box 23360, San Juan 00931, Puerto Rico.
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27
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Li DH, Shi W, Munroe TA, Gong L, Kong XY. Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes). PLoS One 2015; 10:e0134580. [PMID: 26237419 PMCID: PMC4523187 DOI: 10.1371/journal.pone.0134580] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 07/12/2015] [Indexed: 12/20/2022] Open
Abstract
Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.
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Affiliation(s)
- Dong-He Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Shi
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, China
- * E-mail: (WS); (XYK)
| | - Thomas A. Munroe
- National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C., 20013–7012, United States of America
| | - Li Gong
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Yu Kong
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- * E-mail: (WS); (XYK)
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28
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Buser TJ, Andrés López J. Molecular phylogenetics of sculpins of the subfamily Oligocottinae (Cottidae). Mol Phylogenet Evol 2015; 86:64-74. [PMID: 25791911 DOI: 10.1016/j.ympev.2015.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 10/23/2022]
Abstract
The sculpin subfamily Oligocottinae includes 18-20 species of nearshore benthic fishes with a diverse array of reproductive strategies. As a first step toward understanding the evolution of that diversity, we conducted a phylogenetic study based on DNA sequences from eight genomic regions from 31 sculpin species aimed at testing monophyly and relationships of the Oligocottinae. Representatives from the perciform families Agonidae, Cottidae, Hemitripteridae, Hexagrammidae, Psychrolutidae, and Rhamphocottidae served as outgroups. The sequence data were analyzed in maximum likelihood and Bayesian phylogenetic inference frameworks. Results of these analyses show that a systematic revision of the group is warranted. The genus Clinocottus is a polyphyletic assemblage of three distinct lineages, which should be indicated by resurrection of the subgenera Blennicottus, Clinocottus, and Oxycottus; Leiocottus hirundo is more closely related to Clinocottus analis than C. analis is related to any other member of Clinocottus; the composition of the tribe Oligocottini should be revised to include only the genera Oligocottus, Clinocottus, and Orthonopias; and the genus Sigmistes should be removed from the subfamily Oligocottinae.
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Affiliation(s)
- Thaddaeus J Buser
- School of Fisheries and Ocean Sciences, 905 N. Koyukuk Drive, University of Alaska, Fairbanks, AK 99775, USA; Department of Fisheries and Wildlife, 104 Nash Hall, Oregon State University, Corvallis, OR 97331, USA.
| | - J Andrés López
- School of Fisheries and Ocean Sciences, 905 N. Koyukuk Drive, University of Alaska, Fairbanks, AK 99775, USA; University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA.
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29
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Britz R, Conway KW, Rüber L. Miniatures, morphology and molecules: Paedocypris and its phylogenetic position (Teleostei, Cypriniformes). Zool J Linn Soc 2014. [DOI: 10.1111/zoj12184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralf Britz
- Department of Zoology, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX, 77843, USA
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland
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30
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Britz R, Conway KW, Rüber L. Miniatures, morphology and molecules:Paedocyprisand its phylogenetic position (Teleostei, Cypriniformes). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralf Britz
- Department of Zoology; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections; Texas A&M University; College Station TX 77843 USA
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15 3005 Bern Switzerland
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31
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Mitochondrial genomic investigation of flatfish monophyly. Gene 2014; 551:176-82. [PMID: 25172210 DOI: 10.1016/j.gene.2014.08.053] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/11/2014] [Accepted: 08/26/2014] [Indexed: 11/21/2022]
Abstract
We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.
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32
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Fine mapping and evolution of the major sex determining region in turbot (Scophthalmus maximus). G3-GENES GENOMES GENETICS 2014; 4:1871-80. [PMID: 25106948 PMCID: PMC4199694 DOI: 10.1534/g3.114.012328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fish sex determination (SD) systems are varied, suggesting evolutionary changes including either multiple evolution origins of genetic SD from nongenetic systems (such as environmental SD) and/or turnover events replacing one genetic system by another. When genetic SD is found, cytological differentiation between the two members of the sex chromosome pair is often minor or undetectable. The turbot (Scophthalmus maximus), a valuable commercial flatfish, has a ZZ/ZW system and a major SD region on linkage group 5 (LG5), but there are also other minor genetic and environmental influences. We here report refined mapping of the turbot SD region, supported by comparative mapping with model fish species, to identify the turbot master SD gene. Six genes were located to the SD region, two of them associated with gonad development (sox2 and dnajc19). All showed a high association with sex within families (P = 0), but not at the population level, so they are probably partially sex-linked genes, but not SD gene itself. Analysis of crossovers in LG5 using two families confirmed a ZZ/ZW system in turbot and suggested a revised map position for the master gene. Genetic diversity and differentiation for 25 LG5 genetic markers showed no differences between males and females sampled from a wild population, suggesting a recent origin of the SD region in turbot. We also analyzed associations with markers of the most relevant sex-related linkage groups in brill (S. rhombus), a closely related species to turbot; the data suggest that an ancient XX/XY system in brill changed to a ZZ/ZW mechanism in turbot.
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33
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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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34
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Molecular evidence for the monophyly of flatfishes (Carangimorpharia: Pleuronectiformes). Mol Phylogenet Evol 2014; 73:18-22. [DOI: 10.1016/j.ympev.2014.01.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 11/18/2022]
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35
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Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones. Chromosoma 2014; 123:281-91. [PMID: 24473579 DOI: 10.1007/s00412-014-0452-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.
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