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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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Zafirah Ghazali S, Lavoué S, Sukmono T, Habib A, Min Pau T, Azizah Mohd Nor S. Cenozoic colonisation of the Indian Ocean region by the Australian freshwater originating glassperch family Ambassidae (Teleostei). Mol Phylogenet Evol 2023:107832. [PMID: 37263456 DOI: 10.1016/j.ympev.2023.107832] [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: 12/19/2022] [Revised: 03/29/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
We examined the phylogeny and biogeography of the glassperch family Ambassidae (Teleostei), which is widely distributed in the freshwater, brackish and marine coastal habitats across the Indo-West Pacific region. We first built a comprehensive time-calibrated phylogeny of Ambassidae using five genes. We then used this tree to reconstruct the evolution of the salinity preference and ancestral areas. Our results indicate that the two largest genera of Ambassidae, Ambassis and Parambassis, are each not monophyletic. The most recent common ancestor of Ambassidae was freshwater adapted and lived in Australia about 56 million years ago. Three independent freshwater-to-marine transitions are inferred, but no marine-to-freshwater ones. To explain the distribution of ambassids, we hypothesise two long-distance marine dispersal events from Australia. A first event was towards Southeast Asia during the early Cenozoic, followed by a second one towards Africa during mid-Cenozoic. The phylogenetic signal associated with the salinity adaptation of these events was not detected, possibly because of the selective extinction of intermediate marine lineages. The Ambassidae shares two characteristics with other freshwater fish groups distributed in continental regions surrounding the Indian Ocean: They are too young to support the hypothesis that their distribution is the result of the fragmentation of Gondwana, but they did not retain the phylogenetic signal of their marine dispersal.
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Affiliation(s)
- Siti Zafirah Ghazali
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia.
| | - Tedjo Sukmono
- Department of Biology, Universitas Jambi, Jalan Lintas Jambi - Muara Bulian Km15, 36122 Jambi, Sumatra, Indonesia
| | - Ahasan Habib
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Tan Min Pau
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia
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3
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Luis Molina-Quirós J, Hernández-Muñoz S, Antonio Baeza J. The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes. Gene 2022; 845:146847. [PMID: 36058495 DOI: 10.1016/j.gene.2022.146847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/26/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
The roosterfish Nematistius pectoralis is considered as one of the most magnificent sportfishes worldwide. This study developed the first genomic resource for this trophy-fish that is heavily targeted by the fly-fishing industry. The complete mitochondrial genome of N. pectoralis was assembled using short read sequences and analyzed in detail. The mitochondrial genome of N. pectoralis is 16,537 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S and 16S), and 22 transfer RNA genes. A long intergenic space 770 bp in length was assumed to be the D-loop or Control Region (CR). Most of the PCGs and tRNA genes are encoded in the L-strand. All PCGs are under purifying selection and atp8 and nad6 experienced the least selective pressure. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 that lacked the D-arm loop. The D-loop of N. pectoralis exhibits three domains commonly described in other fishes; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the newly recognized order Carangiformes based on all 13 mitochondrial PCGs did not support the monophyly of this clade but recognized several families as monophyletic, including Bothidae, Carangidae, Istiophoridae, Latidae, Paralichthyidae, Polynemidae, and Rhombosoleidae. Nematistius pectoralis was sister to a clade composed of Toxotes chatareus (fam. Toxotidae) + Lactarius lactarius (fam. Lactariidae). This genomic resource developed for N. pectoralis will aid in improving our understanding of the population genomics of and strengthen conservation and management strategies in this remarkable trophy-fish.
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Affiliation(s)
- José Luis Molina-Quirós
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica.
| | - Sebastián Hernández-Muñoz
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica; Sala de Colecciones, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA; Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, IV Región, Chile; Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA
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4
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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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5
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Smith WL, Ghedotti MJ, Domínguez-Domínguez O, McMahan CD, Espinoza E, Martin RP, Girard MG, Davis MP. Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha). NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2021-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.
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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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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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8
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Near TJ, MacGuigan DJ, Boring EL, Simmons JW, Albanese B, Keck BP, Harrington RC, Dinkins GR. A New Species of Bridled Darter Endemic to the Etowah River System in Georgia (Percidae: Etheostomatinae: Percina). BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.3374/014.062.0102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas J. Near
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118 USA —
| | - Daniel J. MacGuigan
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118 USA
| | - Emily L. Boring
- Pierson College and Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Jeffrey W. Simmons
- River and Reservoir Compliance Monitoring, Tennessee Valley Authority, Chattanooga, TN 37402-2881 USA
| | - Brett Albanese
- Wildlife Conservation Section, Georgia Department of Natural Resources, Social Circle, GA 30025 USA
| | - Benjamin P. Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1610 USA
| | - Richard C. Harrington
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; and Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8118 USA
| | - Gerald R. Dinkins
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN 37996-3200 USA
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Koblmüller S, Schöggl CA, Lorber CJ, Van Steenberge M, Kmentová N, Vanhove MPM, Zangl L. African lates perches (Teleostei, Latidae, Lates): Paraphyly of Nile perch and recent colonization of Lake Tanganyika. Mol Phylogenet Evol 2021; 160:107141. [PMID: 33711447 DOI: 10.1016/j.ympev.2021.107141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 11/17/2022]
Abstract
Lates perches of the genus Lates (Latidae) are large piscivorous fishes, with a strikingly disjunct distribution range in coastal areas and estuaries of the Indo-Pacific region and in some large African freshwater systems. Previous phylogenetic hypotheses based on osteological and ontogenetic data suggested paraphyly of the African representatives, or even the small Lake Tanganyika species assemblage, with respect to the remaining Lates species. Based on a multilocus phylogeny, however, we show that extant African lates perches are monophyletic. The Nile perch, L. niloticus, which is widely distributed in the Nilo-Sudan region and Central Africa, comprises three distinct lineages and is paraphyletic with respect to the four endemic Lake Tanganyika species. We find that diversification of extant African Lates happened only as recently as the Pliocene. With the extensive, in part much older fossil record, this suggests repeated extinction and (re-)colonization of hydrological systems. We further find that Lates started to diversify in Lake Tanganyika only in the Pleistocene, which is much more recent than other fish radiations endemic to Lake Tanganyika, implying that they radiated in the presence of other top predators already in this ecosystem.
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Affiliation(s)
- Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria.
| | - Christian A Schöggl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Clemens J Lorber
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Maarten Van Steenberge
- Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium; Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, Helsinki FI-00014, Finland
| | - Lukas Zangl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria; Universalmuseum Joanneum, Studienzentrum Naturkunde, Weinzöttlstraße 16, 8045 Graz, Austria; ÖKOTEAM - Institute for Animal Ecology and Landscape Planning, Bergmanngasse 22, 8010 Graz, Austria
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10
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Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
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11
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McCraney WT, Thacker CE, Alfaro ME. Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria. Mol Phylogenet Evol 2020; 151:106862. [DOI: 10.1016/j.ympev.2020.106862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 01/04/2023]
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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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Abstract
Abstract
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
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Affiliation(s)
- Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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14
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Verma CR, Kumkar P, Raghavan R, Katwate U, Paingankar MS, Dahanukar N. Glass in the water: Molecular phylogenetics and evolution of Indian glassy perchlets (Teleostei: Ambassidae). J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chandani R. Verma
- Department of Zoology; Modern College of Arts, Science and Commerce; Pune India
| | - Pradeep Kumkar
- Department of Zoology; Modern College of Arts, Science and Commerce; Pune India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management; Kerala University of Fisheries and Ocean Studies (KUFOS); Kochi India
| | - Unmesh Katwate
- Bombay Natural History Society (BNHS); Mumbai India
- School of Ocean Science and Technology; Kerala University of Fisheries and Ocean Studies (KUFOS); Kochi India
| | | | - Neelesh Dahanukar
- Indian Institute of Science Education and Research (IISER); Pune India
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15
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Pülmanns N, Castellanos-Galindo GA, Krumme U. Tidal-diel patterns in feeding and abundance of armed snook Centropomus armatus from macrotidal mangrove creeks of the tropical eastern Pacific Ocean. JOURNAL OF FISH BIOLOGY 2018; 93:850-859. [PMID: 30175486 DOI: 10.1111/jfb.13788] [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: 03/23/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
We investigated the influence of temporal and spatial factors on the feeding habits of the armed snook Centropomus armatus (Centropomidae), the most abundant snook species in eastern Pacific mangrove ecosystems. The influence of the combination of semi-diurnal tides and diel cycles and salinity on the intertidal abundance, stomach fullness, diet composition and daily consumption of this species was investigated over 1 year in the macrotidal Colombian Pacific coast (Bahía Málaga). The abundance of juvenile C. armatus (5.6-23.6 cm total length) in the intertidal creeks was highest during neap tide-night conditions and lowest during spring-tide day conditions. Centropomus armatus fed predominantly on crustaceans (Alpheidae and Palaemonidae) and fishes. Stomach fullness index (ISF ), a proxy of feeding activity, was not influenced by salinity, but by tidal-diel conditions. Stomach fullness index was highest during neap tide nocturnal inundations, but lowest during diurnal neap tides. Nevertheless, the total daily consumption was higher at spring tide than at neap tides. Higher water temperatures in creeks during neap tides at night could explain not only high C. armatus abundance, but also greater accessibility to active prey. Comparison with the feeding patterns of fishes from other macrotidal mangrove ecosystems suggest that the habitat use and feeding patterns of intertidal fishes in mangroves are strongly influenced by the combination of spring-neap tide and diel cycles. However, the interaction between mangrove geomorphology and flooding regime of the specific mangrove forest might also play a role and deserves further investigation.
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Affiliation(s)
- Nathalie Pülmanns
- Resource Management, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Gustavo Adolfo Castellanos-Galindo
- Resource Management, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Marine Programme, WWF-Colombia, Cali, Colombia
- Grupo de Investigación en Ecología de Estuarios y Manglares, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Uwe Krumme
- Living Marine Resources, Thünen Institute of Baltic Sea Fisheries, Rostock, Germany
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16
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Smith WL, Everman E, Richardson C. Phylogeny and Taxonomy of Flatheads, Scorpionfishes, Sea Robins, and Stonefishes (Percomorpha: Scorpaeniformes) and the Evolution of the Lachrymal Saber. COPEIA 2018. [DOI: 10.1643/cg-17-669] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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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: 420] [Impact Index Per Article: 60.0] [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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18
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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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19
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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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20
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Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria). Mol Phylogenet Evol 2015; 86:8-23. [PMID: 25769409 DOI: 10.1016/j.ympev.2015.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/21/2015] [Accepted: 03/02/2015] [Indexed: 11/21/2022]
Abstract
Phylogenetic relationships among families within the order Atheriniformes have been difficult to resolve on the basis of morphological evidence. Molecular studies so far have been fragmentary and based on a small number taxa and loci. In this study, we provide a new phylogenetic hypothesis based on sequence data collected for eight molecular markers for a representative sample of 103 atheriniform species, covering 2/3 of the genera in this order. The phylogeny is calibrated with six carefully chosen fossil taxa to provide an explicit timeframe for the diversification of this group. Our results support the subdivision of Atheriniformes into two suborders (Atherinopsoidei and Atherinoidei), the nesting of Notocheirinae within Atherinopsidae, and the monophyly of tribe Menidiini, among others. We propose taxonomic changes for Atherinopsoidei, but a few weakly supported nodes in our phylogeny suggests that further study is necessary to support a revised taxonomy of Atherinoidei. The time-calibrated phylogeny was used to infer ancestral habitat reconstructions to explain the current distribution of marine and freshwater taxa. Based on these results, the current distribution of Atheriniformes is likely due to widespread marine dispersal along the margins of continents, infrequent trans-oceanic dispersal, and repeated invasion of freshwater habitats. This conclusion is supported by post-Gondwanan divergence times among families within the order, and a high probability of a marine ancestral habitat.
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21
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Davis MP. Evolutionary Relationships of the Deep-Sea Pearleyes (Aulopiformes: Scopelarchidae) and a New Genus of Pearleye from Antarctic Waters. COPEIA 2015. [DOI: 10.1643/ci-14-139] [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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22
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Phylogeny and taxonomy of sculpins, sandfishes, and snailfishes (Perciformes: Cottoidei) with comments on the phylogenetic significance of their early-life-history specializations. Mol Phylogenet Evol 2014; 79:332-52. [PMID: 25014569 DOI: 10.1016/j.ympev.2014.06.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/27/2014] [Accepted: 06/30/2014] [Indexed: 11/21/2022]
Abstract
Despite recent progress on the higher-level relationships of the Cottoidei and its familial components, phylogenetic conflict and uncertainty remain within the Cottoidea. We analyzed a dataset composed of 4518 molecular (mitochondrial 12S, tRNA-Val, 16S, and cytochrome b and nuclear TMO-4c4, Histone H3, and 28S) and 72 morphological characters for 69 terminals to address cottoid intrarelationships. The resulting well-resolved phylogeny was used to produce a revised taxonomy that is consistent with the available molecular and morphological data and recognizes six families: Agonidae, Cottidae, Jordaniidae, Psychrolutidae, Rhamphocottidae, and Scorpaenichthyidae. The traditional Agonidae was expanded to include traditional hemitripterids and Hemilepidotus. The traditional Cottidae was restricted to Leptocottus, Trachidermus, and the riverine, lacustrine, and Lake Baikal freshwater cottoids. Jordaniidae (Jordania and Paricelinus) was separated from the traditional cottids; Psychrolutidae was expanded from the traditional grouping to include nearly all traditional marine cottids and the single species of bathylutichthyid. Rhamphocottidae was expanded to include the traditional ereuniids, and Scorpaenichthyidae separated Scorpaenichthys from the traditional cottids. The importance of early-life-history characters to the resulting phylogeny and taxonomy were highlighted.
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23
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de Oliveira JN, Gomes G, do Rêgo PS, Moreira S, Sampaio I, Schneider H, Araripe J. Molecular data indicate the presence of a novel species of Centropomus (Centropomidae - Perciformes) in the Western Atlantic. Mol Phylogenet Evol 2014; 77:275-80. [PMID: 24792089 DOI: 10.1016/j.ympev.2014.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/12/2014] [Accepted: 04/17/2014] [Indexed: 10/25/2022]
Abstract
Centropomus undecimalis is distributed in the coastal waters of the western Atlantic between North Carolina and São Paulo, although very little is known of the genetic structure of its populations. Here, 148 C. undecimalis samples were obtained from six sites in the southwestern Atlantic, representing the Brazilian distribution of this species. Segments of three mitochondrial (Cytb, COI and 16S) and one nuclear (IGF1) gene were sequenced. The results of all analyses indicated the presence of a previously undetected lineage of Centropomus in the northern extreme of Brazil (Amapá) in the region of the Oiapoque estuary. This taxon is genetically distinct from all 12 recognized species of Centropomus. The populations from the Brazilian states of Pará, Maranhão, Ceará, Rio Grande do Norte, Rio de Janeiro and São Paulo were genetically similar to C. undecimalis from coastal areas of the Caribbean and USA. Nucleotide divergence between C. undecimalis and the new Oiapoque taxon are greater than or similar to those found between a number of valid Centropomus species. The estimated time of divergence between C. undecimalis and the new taxon is approximately 2 millionyears. The findings of the present study emphasize the need for a thorough taxonomic revision of this genus.
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Affiliation(s)
- Joiciane N de Oliveira
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros de Bragança, UFPA, Alameda Leandro Ribeiro, SN, Aldeia, Bragança, Pará, Brazil
| | - Grazielle Gomes
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros de Bragança, UFPA, Alameda Leandro Ribeiro, SN, Aldeia, Bragança, Pará, Brazil
| | - Péricles Sena do Rêgo
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros de Bragança, UFPA, Alameda Leandro Ribeiro, SN, Aldeia, Bragança, Pará, Brazil
| | - Sávia Moreira
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros de Bragança, UFPA, Alameda Leandro Ribeiro, SN, Aldeia, Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros de Bragança, UFPA, Alameda Leandro Ribeiro, SN, Aldeia, Bragança, Pará, Brazil
| | - Horacio Schneider
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros de Bragança, UFPA, Alameda Leandro Ribeiro, SN, Aldeia, Bragança, Pará, Brazil
| | - Juliana Araripe
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros de Bragança, UFPA, Alameda Leandro Ribeiro, SN, Aldeia, Bragança, Pará, Brazil.
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24
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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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25
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Sparks JS, Schelly RC, Smith WL, Davis MP, Tchernov D, Pieribone VA, Gruber DF. The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon. PLoS One 2014; 9:e83259. [PMID: 24421880 PMCID: PMC3885428 DOI: 10.1371/journal.pone.0083259] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 10/31/2013] [Indexed: 12/30/2022] Open
Abstract
The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.
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Affiliation(s)
- John S. Sparks
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Robert C. Schelly
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - W. Leo Smith
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Matthew P. Davis
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Dan Tchernov
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Vincent A. Pieribone
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Department of Cellular and Molecular Physiology, The John B. Pierce Laboratory, Inc., Yale University, New Haven, Connecticut, United States of America
| | - David F. Gruber
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Natural Sciences, Baruch College, City University of New York, New York, New York, United States of America
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26
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Campbell MA, Chen WJ, López JA. Are flatfishes (Pleuronectiformes) monophyletic? Mol Phylogenet Evol 2013; 69:664-73. [PMID: 23876291 PMCID: PMC4458374 DOI: 10.1016/j.ympev.2013.07.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/07/2013] [Accepted: 07/12/2013] [Indexed: 02/03/2023]
Abstract
All extant species of flatfish (order Pleuronectiformes) are thought to descend from a common ancestor, and therefore to represent a monophyletic group. This hypothesis is based largely on the dramatic bilateral asymmetry and associated ocular migration characteristics of all flatfish. Yet, molecular-based phylogenetic studies have been inconclusive on this premise. Support for flatfish monophyly has varied with differences in taxonomic and gene region sampling schemes. Notably, the genus Psettodes has been found to be more related to non-flatfishes than to other flatfishes in many recent studies. The polyphyletic nature of the Pleuronectiformes is often inferred to be the result of weak historical signal and/or artifact of phylogenetic inference due to a bias in the data. In this study, we address the question of pleuronectiform monophyly with a broad set of markers (from six phylogenetically informative nuclear loci) and inference methods designed to limit the influence of phylogenetic artifacts. Concomitant with a character-rich analytical strategy, an extensive taxonomic sampling of flatfish and potential close relatives is used to increase power and resolution. Results of our analyses are most consistent with a non-monophyletic Pleuronectiformes with Psettodes always being excluded. A fossil-calibrated Bayesian relaxed clock analysis estimates the age of Pleuronectoidei to be 73 Ma, and the time to most recent common ancestor of Pleuronectoidei, Psettodes, and other relative taxa to be 77 Ma. The ages are much older than the records of any fossil pleuronectiform currently recognized. We discuss our findings in the context of the available morphological evidence and discuss the compatibility of our molecular hypothesis with morphological data regarding extinct and extant flatfish forms.
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Affiliation(s)
- Matthew A. Campbell
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
| | - J. Andrés López
- School of Fisheries and Ocean Sciences, University of Alaska, Fairbanks, AK 99775, USA
- University of Alaska Museum, Fairbanks, AK 99775, USA
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27
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Betancur-R. R, Li C, Munroe TA, Ballesteros JA, Ortí G. Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes). Syst Biol 2013; 62:763-85. [DOI: 10.1093/sysbio/syt039] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ricardo Betancur-R.
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Chenhong Li
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Thomas A. Munroe
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Jesus A. Ballesteros
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, D.C. 20052, USA; 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; and 3National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C. 20013-7012, USA
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28
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Betancur-R R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton Ii JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Ortí G. The tree of life and a new classification of bony fishes. PLOS CURRENTS 2013; 5:ecurrents.tol.53ba26640df0ccaee75bb165c8c26288. [PMID: 23653398 PMCID: PMC3644299 DOI: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288] [Citation(s) in RCA: 351] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
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29
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Abstract
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
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30
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Near TJ, Sandel M, Kuhn KL, Unmack PJ, Wainwright PC, Leo Smith W. Nuclear gene-inferred phylogenies resolve the relationships of the enigmatic Pygmy Sunfishes, Elassoma (Teleostei: Percomorpha). Mol Phylogenet Evol 2012; 63:388-95. [DOI: 10.1016/j.ympev.2012.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/07/2012] [Accepted: 01/13/2012] [Indexed: 12/01/2022]
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