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Yu TS, Park K, Han KH, Kwak IS. Morphological and genetic analysis for the diversity conservation of rare species, Thamnaconus multilineatus (Tetraodontiformes: Monacanthidae). PLoS One 2024; 19:e0292916. [PMID: 38422090 PMCID: PMC10903791 DOI: 10.1371/journal.pone.0292916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 03/02/2024] Open
Abstract
Climate changes have altered biodiversity and ultimately induced community changes that have threatened the survival of certain aquatic organisms such as fish species. Obtaining biological and genetic information on endangered fish species is critical for ecological population management. Thamnaconus multilineatus, registered as an endangered species by the IUCN in 2019, is a Data Deficient (DD) species with a remarkably small number of habitats worldwide and no known information other than its habitat and external form. In this study, we characterized the external and osteological morphology of a T. multilineatus specimen collected from eastern Jeju Island, South Korea, in 2020. We also investigated the phylogenetic relationships among related fish species through complete mitochondrial DNA (mtDNA) analysis of the T. multilineatus specimen. The external and skeletal characteristics of T. multilineatus were similar to those of previous reports describing other fish of the genus Thamnaconus, making it difficult to classify T. multilineatus as a similar species based only on morphological characteristics. As a result of analyzing the complete mtDNA of T. multilineatus, the length of the mtDNA was determined to be 16,435 bp, and the mitochondrial genome was found to have 37 CDCs, including 13 PCGs, 22 tRNAs, and 2 rRNAs. In the phylogenetic analysis within the suborder Balistoidei, T. multilineatus mtDNA formed a cluster with fish of the genus Thamnaconus. This study is the first to report on the skeletal structure and complete mtDNA of T. multilineatus. Since the current research on T. multilineatus has only been reported on morphology, the results of this study will be utilized as important information for the management and restoration of T. multilineatus as an endangered species and significant fishery resource.
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Affiliation(s)
- Tae-Sik Yu
- Fisheries Science Institute, Chonnam National University, Yeosu, Republic of Korea
| | - Kiyun Park
- Fisheries Science Institute, Chonnam National University, Yeosu, Republic of Korea
| | - Kyeong-Ho Han
- Department of Aquaculture, Chonnam National University, Yeosu, Republic of Korea
| | - Ihn-Sil Kwak
- Fisheries Science Institute, Chonnam National University, Yeosu, Republic of Korea
- Department of Ocean Integrated Science, Chonnam National University, Yeosu, Republic of Korea
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Hunt EP, Willis SC, Conway KW, Portnoy DS. Interrelationships and biogeography of the New World pufferfish genus Sphoeroides (Tetraodontiformes: Tetraodontidae) inferred using ultra-conserved DNA elements. Mol Phylogenet Evol 2023; 189:107935. [PMID: 37778529 DOI: 10.1016/j.ympev.2023.107935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Colonization of the New World by marine taxa has been hypothesized to have occurred through the Tethys Sea or by crossing the East Pacific Barrier. To better understand patterns and timing of diversification, geological events can be coupled with time calibrated phylogenetic hypotheses to infer major drivers of diversification. Phylogenetic relationships among members of Sphoeroides, a genus of four toothed pufferfishes (Tetraodontiformes: Tetraodontidae) which are found nearly exclusively in the New World (eastern Pacific and western Atlantic), were reconstructed using sequences from ultra-conserved DNA elements, nuclear markers with clear homology among many vertebrate taxa. Hypotheses derived from concatenated maximum-likelihood and species tree summary methods support a paraphyletic Sphoeroides, with Colomesus deeply nested within the genus. Analyses also revealed S. pachygaster, a pelagic species with a cosmopolitan distribution, as the sister taxon to the remainder of Sphoeroides and recovered distinct lineages within S. pachygaster, indicating that this cosmopolitan species may represent a species complex. Ancestral range reconstruction may suggest the genus colonized the New World through the eastern Pacific before diversifying in the western Atlantic, though date estimates for these events are uncertain due to the lack of reliable fossil record for the genus.
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Affiliation(s)
- Elizabeth P Hunt
- Department of Life Sciences, Texas A&M University - Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412, USA.
| | - Stuart C Willis
- Department of Life Sciences, Texas A&M University - Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412, USA; Columbia River Inter-Tribal Fish Commission - Hagerman Genetics Lab, 3059-F National Fish Hatchery Road, Hagerman, ID 83332, USA
| | - Kevin W Conway
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University, 534 John Kimbrough Blvd., College Station, TX 77843, USA
| | - David S Portnoy
- Department of Life Sciences, Texas A&M University - Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412, USA
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Momota K, Doi H, Obata H, Sakai H. Tandem spawning and development in the African freshwater pufferfish Tetraodon schoutedeni. Zoo Biol 2023; 42:357-363. [PMID: 36604841 DOI: 10.1002/zoo.21752] [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: 07/06/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023]
Abstract
To advance breeding techniques for the African freshwater pufferfish Tetraodon schoutedeni and observe tandem spawning closely, we monitored the reproduction of captive individuals. Eight spawning sessions (stable water temperature 24-25°C; daily light period 07:00-19:00) occurred between May 2016 and November 2017. After 65-150 min of tandem swimming (the male biting and clinging to the female's abdomen), 3-50 spherical, weakly adhesive eggs were spawned, being scattered onto the sandy substrate or water plants. The removal of cohabitants (potentially eating spawned eggs) and provision of small initial food items, such as small-type Brachionus spp., for larval fish were essential for successful breeding.
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Affiliation(s)
| | | | | | - Harumi Sakai
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Yamaguchi, Japan
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4
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Milec LJM, Vanhove MPM, Bukinga FM, De Keyzer ELR, Kapepula VL, Masilya PM, Mulimbwa N, Wagner CE, Raeymaekers JAM. Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation. BMC Ecol Evol 2022; 22:127. [PMID: 36329403 PMCID: PMC9635120 DOI: 10.1186/s12862-022-02085-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Background The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecessor of the Malagarasi–Congo River and only 5–6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissatanganicae and Limnothrissamiodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids. Results We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S.tanganicae and L.miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissaobtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P.obtusirostris around 10.92 MYA [95% CI: 6.37–15.48]. Conclusions These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi–Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe, e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02085-8.
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Affiliation(s)
- Leona J. M. Milec
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway ,grid.12155.320000 0001 0604 5662Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Maarten P. M. Vanhove
- grid.12155.320000 0001 0604 5662Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Déberiotstraat 32, 3000 Leuven, Belgium
| | - Fidel Muterezi Bukinga
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo
| | - Els L. R. De Keyzer
- grid.5596.f0000 0001 0668 7884Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Déberiotstraat 32, 3000 Leuven, Belgium ,grid.5284.b0000 0001 0790 3681Evolutionary Ecology Group (EVECO), Universiteit Antwerpen, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Vercus Lumami Kapepula
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo ,grid.7942.80000 0001 2294 713XUniversité Catholique de Louvain, Place Sainte Barbe 2, 1348 Louvain-la-Neuve, Belgium
| | - Pascal Mulungula Masilya
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo ,Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée (UERHA)-ISP/Bukavu, Bukavu, Sud-Kivu Democratic Republic of Congo
| | - N’Sibula Mulimbwa
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo
| | - Catherine E. Wagner
- grid.135963.b0000 0001 2109 0381University of Wyoming, 1000 E University Ave, Laramie, WY 82071 USA
| | - Joost A. M. Raeymaekers
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway
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Yang Y, Liu Y, Song H, Wang X, Liu C, Hu Y, Mu X. The complete mitochondrial genome of longhorn cowfish, Lactoria cornuta. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3767-3768. [PMID: 33367093 PMCID: PMC7671596 DOI: 10.1080/23802359.2020.1835570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We determined the complete mitochondrial genome of Lactoria cornuta, which is 16,495 bp in length with an A + T content of 57.37%, and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a complete control region. The total base composition of the mitogenome is 28.2% T, 26.7% C, 29.2% A and 15.9% G. Of the 13 protein-coding genes, 12 genes start with an ATG codon, except for COX1 with GTG. Ten genes use TAA or AGA as the termination codon, whereas three (COX2, ND4, and Cyt b) have incomplete stop codon T. This study would provide useful genetic information for phylogenetic and species idenfication of the family Ostraciidae.
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Affiliation(s)
- Yexin Yang
- Key Laboratry of Leisure Fisheries, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yi Liu
- Key Laboratry of Leisure Fisheries, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongmei Song
- Key Laboratry of Leisure Fisheries, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xuejie Wang
- Key Laboratry of Leisure Fisheries, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chao Liu
- Key Laboratry of Leisure Fisheries, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yinchang Hu
- Key Laboratry of Leisure Fisheries, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xidong Mu
- Key Laboratry of Leisure Fisheries, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Martínez-Aquino A, García-Teh JG, Ceccarelli FS, Aguilar-Aguilar R, Vidal-Martinez VM, Leopoldina Aguirre-Macedo M. New morphological and molecular data for Xystretrum solidum (Gorgoderidae, Gorgoderinae) from Sphoeroides testudineus (Tetraodontiformes, Tetraodontidae) in Mexican waters. Zookeys 2020; 925:141-161. [PMID: 32317854 PMCID: PMC7160187 DOI: 10.3897/zookeys.925.49503] [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: 12/19/2019] [Accepted: 02/21/2020] [Indexed: 11/12/2022] Open
Abstract
Adults of trematodes in the genus Xystretrum Linton, 1910 (Gorgoderidae, Gorgoderinae) are parasites found exclusively in the urinary bladders of tetraodontiform fishes. However, limited and unclear morphological data were used to describe the type species, X. solidum Linton, 1910. Here, we present the first detailed morphological information for a member of Xystretrum. Morphological characters were described using light and scanning electron microscopy (SEM) of Xystretrum specimens from Sphoeroides testudineus (Linnaeus) (Tetraodontiformes, Tetraodontidae), collected at six localities off the northern Yucatan Peninsula coast of the Gulf of Mexico. We also compared sequence fragments of the 28S (region D1–D3) ribosomal DNA and mitochondrial Cytochrome c oxidase subunit 1 (COI) gene with those available for other gorgoderine taxa. We assigned these Xystretrum specimens to X. solidum, despite the incompleteness of published descriptions. The data provide a foundation for future work to validate the identities of X. solidum, X. papillosum Linton, 1910 and X. pulchrum (Travassos, 1920) with new collections from the type localities and hosts. Comparisons of 28S and COI regions described here also provide an opportunity to evaluate the monophyletic status of Xystretrum.
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7
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Jackson LM, Fernando PC, Hanscom JS, Balhoff JP, Mabee PM. Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. Syst Biol 2018; 67:559-575. [PMID: 29325126 PMCID: PMC6005059 DOI: 10.1093/sysbio/syx098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 11/24/2022] Open
Abstract
Data synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes. We developed a bioinformatics pipeline to identify the presence and absence of pectoral and pelvic fins of 12,582 species. To do this, we integrated a synthetic morphological supermatrix of phenotypic data for the pectoral and pelvic fins for teleost fishes from the Phenoscape Knowledgebase (two presence/absence characters for 3047 taxa) with a species-level tree for teleost fishes from the Open Tree of Life project (38,419 species). The integration method detailed herein harnessed a new combined approach by utilizing data based on ontological inference, as well as phylogenetic propagation, to reduce overall data loss. Using inference enabled by ontology-based annotations, missing data were reduced from 98.0% to 85.9%, and further reduced to 34.8% by phylogenetic data propagation. These methods allowed us to extend the data to an additional 11,293 species for a total of 12,582 species with trait data. The pectoral fin appears to have been independently lost in a minimum of 19 lineages and the pelvic fin in 48. Though interpretation is limited by lack of phylogenetic resolution at the species level, it appears that following loss, both pectoral and pelvic fins were regained several (3) to many (14) times respectively. Focused investigation into putative regains of the pectoral fin, all within one clade (Anguilliformes), showed that the pectoral fin was regained at least twice following loss. Overall, this study points to specific teleost clades where strategic phylogenetic resolution and genetic investigation will be necessary to understand the pattern and frequency of pectoral fin reversals.
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Affiliation(s)
- Laura M Jackson
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - Pasan C Fernando
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - Josh S Hanscom
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive Suite 540, Chapel Hill, NC 27517, USA
| | - Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA
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Molecular phylogeny of Macrosiphini (Hemiptera: Aphididae): An evolutionary hypothesis for the Pterocomma-group habitat adaptation. Mol Phylogenet Evol 2018; 121:12-22. [DOI: 10.1016/j.ympev.2017.12.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 10/25/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
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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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Sun Z, Cheng Y, Zhang J. MITOSCISSOR: A Useful Tool for Auto-Assembly of Mitogenomic Datasets in the Evolutionary Analysis of Fishes. Evol Bioinform Online 2015; 11:115-20. [PMID: 26106259 PMCID: PMC4467657 DOI: 10.4137/ebo.s22340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/10/2015] [Accepted: 02/16/2015] [Indexed: 11/05/2022] Open
Abstract
As a result of the development of rapid and efficient sequencing technologies, complete sequences of numerous mitochondrial genomes are now available. Mitochondrial genomes have been widely used to evaluate relationships between species in several fields, including evolutionary and population genetics, as well as in forensic identification and in the study of mitochondrial diseases in humans. However, the creation of mitochondrial genomes is extremely time consuming. In this paper, we present a new tool, MITOSCISSOR, which is a rapid method for parsing and formatting dozens of complete mitochondrial genome sequences. With the aid of MITOSCISSOR, complete mitochondrial genome sequences of 103 species from Tetraodontiformes (a difficult-to-classify order of fish) were easily parsed and formatted. It typically takes several days to produce similar results when relying upon manual editing. This tool could open the .gb file of Genbank directly and help us to use existing mitogenomic data. In the present study, we established the first clear and robust molecular phylogeny of 103 tetraodontiform fishes, a goal that has long eluded ichthyologists. MITOSCISSOR greatly increases the efficiency with which DNA data files can be parsed and annotated, and thus has the potential to greatly facilitate evolutionary analysis using mitogenomic data. This software is freely available for noncommercial users at http://www.filedropper.com/mitoscissor.
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Affiliation(s)
- Zheng Sun
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P.R. China. ; Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P.R. China
| | - Yuanzhi Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P.R. China
| | - Junbin Zhang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, P.R. China
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11
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Uehara M, Hosaka YZ, Doi H, Sakai H. The shortened spinal cord in tetraodontiform fishes. J Morphol 2014; 276:290-300. [PMID: 25388857 DOI: 10.1002/jmor.20338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 09/27/2014] [Accepted: 10/17/2014] [Indexed: 11/09/2022]
Abstract
In teleosts, the spinal cord generally extends along the entire vertebral canal. The Tetraodontiformes, in which the spinal cord is greatly reduced in length with a distinct long filum terminale and cauda equina, have been regarded as an aberration. The aims of this study are: 1) to elucidate whether the spinal cord in all tetraodontiform fishes shorten with the filum terminale, and 2) to describe the gross anatomical and histological differences in the spinal cord among all families of the Tetraodontiformes. Representative species from all families of the Tetraodontiformes, and for comparison the carp as a common teleost, were investigated. In the Triacanthodidae, Triacanthidae, and Triodontidae, which are the more ancestral taxa of the Tetraodontiformes, the spinal cord extends through the entire vertebral canal. In the Triacanthidae and Triodontidae, the caudal half or more spinal segments of the spinal cord, however, lack gray matter and consist largely of nerve fibers. In the other tetraodontiform families, the spinal cord is shortened forming a filum terminale with the cauda equina, which is prolonged as far as the last vertebra. The shortened spinal cord is divided into three groups. In the Ostraciidae and Molidae, the spinal cord tapers abruptly at the cranium or first vertebra forming a cord-like filum terminale. In the Monacanthidae, Tetraodontidae, and Diodontidae, it abruptly flattens at the rostral vertebrae forming a flat filum terminale. The spinal cord is relatively longer in the Monacanthidae than that in the other two families. It is suggested by histological features of the flat filum terminale that shortening of the spinal cord in this group progresses in order of the Monacanthidae, Tetraodontidae, and Diodontidae. In the Balistidae and Aracanidae, the cord is relatively long and then gradually decreased in dorso-ventral thickness.
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Affiliation(s)
- Masato Uehara
- Department of Veterinary Anatomy, Faculty of Agriculture, Tottori University, Tottori, 680-8553, Japan
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12
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Arcila D, Alexander Pyron R, Tyler JC, Ortí G, Betancur-R R. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol Phylogenet Evol 2014; 82 Pt A:131-45. [PMID: 25462998 DOI: 10.1016/j.ympev.2014.10.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new fossilized birth-death process model for node dating (implemented in the program DPPDiv), and the other using a total-evidence or tip-dating method (implemented in MrBayes and BEAST). These methods are applied herein to tetraodontiform fishes, a diverse group of living and extinct taxa that features one of the most extensive fossil records among teleosts. Previous estimates of time-calibrated phylogenies of tetraodontiforms using node-dating methods reported disparate estimates for their age of origin, ranging from the late Jurassic to the early Paleocene (ca. 150-59Ma). We analyzed a comprehensive dataset with 16 loci and 210 morphological characters, including 131 taxa (95 extant and 36 fossil species) representing all families of fossil and extant tetraodontiforms, under different molecular clock calibration approaches. Results from node-dating methods produced consistently younger ages than the tip-dating approaches. The older ages inferred by tip dating imply an unlikely early-late Jurassic (ca. 185-119Ma) origin for this order and the existence of extended ghost lineages in their fossil record. Node-based methods, by contrast, produce time estimates that are more consistent with the stratigraphic record, suggesting a late Cretaceous (ca. 86-96Ma) origin. We show that the precision of clade age estimates using tip dating increases with the number of fossils analyzed and with the proximity of fossil taxa to the node under assessment. This study suggests that current implementations of tip dating may overestimate ages of divergence in calibrated phylogenies. It also provides a comprehensive phylogenetic framework for tetraodontiform systematics and future comparative studies.
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Affiliation(s)
- Dahiana Arcila
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States.
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - James C Tyler
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States; Department of Biology, University of Puerto Rico - Río Piedras, P.O. Box 23360, San Juan 00931, Puerto Rico
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Lavoué S, Nakayama K, Jerry DR, Yamanoue Y, Yagishita N, Suzuki N, Nishida M, Miya M. Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis. Gene 2014; 549:46-57. [PMID: 25026502 DOI: 10.1016/j.gene.2014.07.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/03/2014] [Accepted: 07/11/2014] [Indexed: 10/25/2022]
Abstract
Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.
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Affiliation(s)
- Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan.
| | - Kouji Nakayama
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto 606-8502, Japan
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Yusuke Yamanoue
- Atmosphere Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan
| | - Naoki Yagishita
- Faculty of Agriculture, Kinki University, 3327-204 Naka-machi, Nara 631-8505, Japan
| | - Nobuaki Suzuki
- Research Center of Sub-tropical Fisheries, Seikai National Fisheries Research Institute, Fisheries Research Agency, Fukai-Ota 148-446, Ishigaki, Okinawa 907-0451, Japan
| | - Mutsumi Nishida
- Atmosphere Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan
| | - Masaki Miya
- Department of Zoology, Natural History Museum & Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan
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Chanet B, Guintard C, Lecointre G. The gas bladder of puffers and porcupinefishes (Acanthomorpha: Tetraodontiformes): phylogenetic interpretations. J Morphol 2014; 275:894-901. [PMID: 24634057 DOI: 10.1002/jmor.20266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/17/2014] [Accepted: 02/21/2014] [Indexed: 11/10/2022]
Abstract
The anatomy of the gas bladder of Diodontidae (porcupinefishes) and Tetraodontidae (pufferfishes) was studied on the basis of dissections and magnetic resonance imaging. Among the examined taxa of Tetraodontiformes, only puffers and porcupinefishes possess a thick walled and dorsally U-shaped or crescent-moon-shaped gas bladder. In the tetraodontid genus Lagocephalus the gas bladder is reduced to a rudiment. The species belonging to the genera Canthigaster, Arothron, and some species of Tetraodon differ in the positioning of their crescent-moon-shaped gas bladder. These observations confirm the close relationship of: (i) Diodontidae and Tetraodontidae and (ii) Canthigaster, Arothron, and some species of Tetraodon. The heterogeneity of the genus Tetraodon is supported by the gas bladder morphology, as previously suggested by molecular studies.
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Affiliation(s)
- Bruno Chanet
- Département Systématique et Evolution, ISYEB, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, CP 50, 57 rue Cuvier, 75005, Paris, France
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15
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Santini F, Sorenson L, Alfaro ME. A new multi-locus timescale reveals the evolutionary basis of diversity patterns in triggerfishes and filefishes (Balistidae, Monacanthidae; Tetraodontiformes). Mol Phylogenet Evol 2013; 69:165-76. [DOI: 10.1016/j.ympev.2013.05.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/19/2013] [Accepted: 05/20/2013] [Indexed: 12/01/2022]
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16
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Bergsten J, Nilsson AN, Ronquist F. Bayesian tests of topology hypotheses with an example from diving beetles. Syst Biol 2013; 62:660-73. [PMID: 23628960 PMCID: PMC3739882 DOI: 10.1093/sysbio/syt029] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/16/2013] [Accepted: 04/23/2013] [Indexed: 01/18/2023] Open
Abstract
We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.
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Affiliation(s)
- Johannes Bergsten
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Anders N. Nilsson
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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Santini F, Sorenson L, Alfaro ME. A new phylogeny of tetraodontiform fishes (Tetraodontiformes, Acanthomorpha) based on 22 loci. Mol Phylogenet Evol 2013; 69:177-87. [PMID: 23727595 DOI: 10.1016/j.ympev.2013.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
Tetraodontiform fishes represent one of the most peculiar radiations of teleost fishes. In spite of this, we do not currently have a consensus on the phylogenetic relationships among the major tetraodontiform lineages, with different morphological and molecular datasets all supporting contrasting relationships. In this paper we present the results of the analysis of tetraodontiform interrelationships based on two mitochondrial and 20 nuclear loci for 40 species of tetraodontiforms (representing all of the 10 currently recognized families), as well as three outgroups. Bayesian and maximum likelihood analyses of the concatenated dataset (18,682 nucleotides) strongly support novel relationships among the major tetraodontiform lineages. Our results recover two large clades already found in mitogenomic analyses (although the position of triacanthids differ), while they strongly conflict with hypotheses of tetraodontiform relationships inferred by previous studies based on morphology, as well as studies of higher-level teleost relationships based on nuclear loci, which included multiple tetraodontiform lineages. A parsimony gene-tree, species-tree analysis recovers relationships that are mostly congruent with the analyses of the concatenated dataset, with the significant exception of the position of the pufferfishes+porcupine fishes clade. Our findings suggest that while the phylogenetic placement of some tetraodontiform lineages (triacanthids, molids) remains problematic even after sequencing 22 loci, an overall molecular consensus is beginning to emerge regarding the existence of several major clades. This new hypothesis will require a re-evaluation of the phylogenetic usefulness of several morphological features, such as the fusion of several jaw bones into a parrot-like beak, or the reduction and loss of some of the fins, which may have occurred independently more times than previously thought.
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Affiliation(s)
- Francesco Santini
- University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E. Young Drive South, Los Angeles, CA 90095, USA.
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18
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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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19
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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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20
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Santini F, Nguyen MTT, Sorenson L, Waltzek TB, Lynch Alfaro JW, Eastman JM, Alfaro ME. Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae). J Evol Biol 2013; 26:1003-18. [DOI: 10.1111/jeb.12112] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 12/18/2012] [Accepted: 12/19/2012] [Indexed: 11/28/2022]
Affiliation(s)
- F. Santini
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - M. T. T. Nguyen
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - L. Sorenson
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - T. B. Waltzek
- Department of Infectious Diseases and Pathology; College of Veterinary Medicine, University of Florida; Gainesville FL USA
| | - J. W. Lynch Alfaro
- Institute for Society and Genetics & Department of Anthropology; University of California Los Angeles; Los Angeles CA USA
| | - J. M. Eastman
- Department of Biological Sciences & the Institute of Bioinformatics and Evolutionary Study; University of Idaho; Moscow ID USA
| | - M. E. Alfaro
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
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21
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Santini F, Sorenson L, Marcroft T, Dornburg A, Alfaro ME. A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes). Mol Phylogenet Evol 2013; 66:153-60. [DOI: 10.1016/j.ympev.2012.09.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 09/10/2012] [Accepted: 09/17/2012] [Indexed: 11/27/2022]
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Meynard CN, Mouillot D, Mouquet N, Douzery EJP. A phylogenetic perspective on the evolution of Mediterranean teleost fishes. PLoS One 2012; 7:e36443. [PMID: 22590545 PMCID: PMC3348158 DOI: 10.1371/journal.pone.0036443] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 04/04/2012] [Indexed: 11/18/2022] Open
Abstract
The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ∼100–80 Mya, and most Perciformes families originated 80–50 Mya. Two important clade origin events were detected. The first at 100–80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.
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Affiliation(s)
- Christine N Meynard
- Institut des Sciences de l'Evolution, UMR 5554-CNRS-IRD, Université de Montpellier II, Place Eugene Bataillon, CC065, Montpellier, France.
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23
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Arima S, Tardella L. Improved harmonic mean estimator for phylogenetic model evidence. J Comput Biol 2012; 19:418-38. [PMID: 22414153 DOI: 10.1089/cmb.2010.0139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bayesian phylogenetic methods are generating noticeable enthusiasm in the field of molecular systematics. Many phylogenetic models are often at stake, and different approaches are used to compare them within a Bayesian framework. The Bayes factor, defined as the ratio of the marginal likelihoods of two competing models, plays a key role in Bayesian model selection. We focus on an alternative estimator of the marginal likelihood whose computation is still a challenging problem. Several computational solutions have been proposed, none of which can be considered outperforming the others simultaneously in terms of simplicity of implementation, computational burden and precision of the estimates. Practitioners and researchers, often led by available software, have privileged so far the simplicity of the harmonic mean (HM) estimator. However, it is known that the resulting estimates of the Bayesian evidence in favor of one model are biased and often inaccurate, up to having an infinite variance so that the reliability of the corresponding conclusions is doubtful. We consider possible improvements of the generalized harmonic mean (GHM) idea that recycle Markov Chain Monte Carlo (MCMC) simulations from the posterior, share the computational simplicity of the original HM estimator, but, unlike it, overcome the infinite variance issue. We show reliability and comparative performance of the improved harmonic mean estimators comparing them to approximation techniques relying on improved variants of the thermodynamic integration.
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Affiliation(s)
- Serena Arima
- Dipartimento di Metodi e Modelli per l'Economia, il Territorio e la Finanza, Sapienza Università di Roma, Rome, Italy.
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Cheng J, Ma GQ, Miao ZQ, Shui BN, Gao TX. Complete mitochondrial genome sequence of the spinyhead croaker Collichthys lucidus (Perciformes, Sciaenidae) with phylogenetic considerations. Mol Biol Rep 2011; 39:4249-59. [PMID: 21786157 DOI: 10.1007/s11033-011-1211-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 07/14/2011] [Indexed: 11/29/2022]
Abstract
The complete mitochondrial genome of the spinyhead croaker Collichthys lucidus was determined using long-PCR and primer walking methods. It is a circular molecule of 16,451 bp in length with a standard set of 22 tRNAs, 2 rRNAs, 13 protein-coding genes as well as a non-coding control region in the same order as those of the other bony fishes. C. lucidus mitogenome exhibited a clear strand-specific bias in nucleotide composition, as evidence by a GC- skew of the H-strand of -0.319. The strand-specific bias was also reflected in the codon usage of genes oriented in opposite directions. All tRNA genes except for tRNA( Ser(AGY)) harbored the typical cloverleaf secondary structures and possessed anticodons that matched the vertebrate mitochondrial genetic code. Contrary to the typical structure of control region consistig of TAS, central, and CSB domains, there were no central conserved blocks available in C. lucidus mitogenome. Despite extensive studies based on both morphology and molecules, phylogenetic position of C. lucidus with Sciaenidae is still controversial. Our phylogenetic results provided more evidence to support previous morphological studies and consistently placed C. lucidus as a sister taxon to Collichthys niveatus, with both of these taxa forming the monophyletic Collichthys.
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Affiliation(s)
- Jiao Cheng
- Fisheries College, Ocean University of China, Qingdao, 266003, China
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25
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Konstantinidis P, Johnson GD. Ontogeny of the jaw apparatus and suspensorium of the Tetraodontiformes. ACTA ZOOL-STOCKHOLM 2011. [DOI: 10.1111/j.1463-6395.2011.00509.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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de Lima LCB, Martinez PA, Molina WF. Cytogenetic characterization of three Balistoidea fish species from the Atlantic with inferences on chromosomal evolution in the families Monacanthidae and Balistidae. COMPARATIVE CYTOGENETICS 2011; 5:61-69. [PMID: 24260619 PMCID: PMC3833730 DOI: 10.3897/compcytogen.v5i1.1141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/23/2010] [Indexed: 06/02/2023]
Abstract
The Tetraodontiformes are the most derived group of teleostean fish. Among other apomorphies, they are characterized by a high degree of fusions or significant bone loss in the head and body. In the early phylogenetic proposals presented for this order, the families Balistidae and Monacanthidae have been unanimously considered to be closely related. Although they have moderate species diversity, they are scarcely known in cytogenetic aspect and chromosomal pattern comparisons between these groups have yet to be established. The species Cantherhines macrocerus (Hollard,1853), Cantherhines pullus (Ranzani, 1842) (Monacanthidae) and Melichthys niger (Bloch, 1786) (Balistidae) were cytogenetically analyzed using conventional (Ag-impregnation, C-banding, CMA3- and DAPI-fluorescence) and molecular (FISH with an 18S rDNA probe) cytogenetic protocols. The karyotypes of all three species were very similar possessing diploid chromosome numbers 2n = 40 and composed exclusively of acrocentric chromosomes. Single NOR-bearing pair as well as positive heterochromatic blocks at pericentromeric regions were identified in the karyotypes of the three species studied. NOR-bearing sites were positively labeled after Ag-impregnation, C-banding, CMA3-fluorescence and FISH with an 18S rDNA probe but were negative after DAPI-fluorescence. Such remarkable shared conspicuous chromosomal characters corroborate either close phylogenetic relationship of these families, previously established by morphological and molecular data, or rather conservative nature of karyotype differentiation processes. The later hypothesis, however, appears less probable due to centric or in tandem fusions documented for another Balistoidea species.
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Affiliation(s)
- Lorena Corina Bezerra de Lima
- />Department of Cell Biology and Genetics, Centro de Biociências, Universidade Federal do io Grande do Norte, Campus Universitário, 59078 – 970 Natal, RN, Brazil
| | - Pablo Ariel Martinez
- />Department of Cell Biology and Genetics, Centro de Biociências, Universidade Federal do io Grande do Norte, Campus Universitário, 59078 – 970 Natal, RN, Brazil
| | - Wagner Franco Molina
- />Department of Cell Biology and Genetics, Centro de Biociências, Universidade Federal do io Grande do Norte, Campus Universitário, 59078 – 970 Natal, RN, Brazil
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Yamanoue Y, Miya M, Doi H, Mabuchi K, Sakai H, Nishida M. Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective. PLoS One 2011; 6:e17410. [PMID: 21364898 PMCID: PMC3045446 DOI: 10.1371/journal.pone.0017410] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 01/30/2011] [Indexed: 11/30/2022] Open
Abstract
Pufferfishes of the Family Tetraodontidae are the most speciose group in the Order Tetraodontiformes and mainly inhabit coastal waters along continents. Although no members of other tetraodontiform families have fully discarded their marine lives, approximately 30 tetraodontid species spend their entire lives in freshwaters in disjunct tropical regions of South America, Central Africa, and Southeast Asia. To investigate the interrelationships of tetraodontid pufferfishes and thereby elucidate the evolutionary origins of their freshwater habitats, we performed phylogenetic analysis based on whole mitochondrial genome sequences from 50 tetraodontid species and closely related species (including 31 newly determined sequences). The resulting phylogenies reveal that the family is composed of four major lineages and that freshwater species from the different continents are independently nested in two of the four lineages. A monophyletic origin of the use of freshwater habitats was statistically rejected, and ancestral habitat reconstruction on the resulting tree demonstrates that tetraodontids independently entered freshwater habitats in different continents at least three times. Relaxed molecular-clock Bayesian divergence time estimation suggests that the timing of these invasions differs between continents, occurring at 0–10 million years ago (MA) in South America, 17–38 MA in Central Africa, and 48–78 MA in Southeast Asia. These timings are congruent with geological events that could facilitate adaptation to freshwater habitats in each continent.
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Affiliation(s)
- Yusuke Yamanoue
- Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Chiba, Japan.
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28
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Konstantinidis P, Johnson GD. A comparative ontogenetic study of the tetraodontiform caudal complex. ACTA ZOOL-STOCKHOLM 2010. [DOI: 10.1111/j.1463-6395.2010.00490.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yamanoue Y, Setiamarga DHE, Matsuura K. Pelvic fins in teleosts: structure, function and evolution. JOURNAL OF FISH BIOLOGY 2010; 77:1173-1208. [PMID: 21039499 DOI: 10.1111/j.1095-8649.2010.02674.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The pelvic fins of teleosts are paired appendages that are considered to be homologous to the hind limbs of tetrapods. Because they are less important for swimming, their morphology and function can be flexibly modified, and such modifications have probably facilitated the adaptations of teleosts to various environments. Recently, among these modifications, pelvic-fin loss has gained attention in evolutionary developmental biology. Pelvic-fin loss, however, has only been investigated in a few model species, and various biological aspects of pelvic fins in teleosts in general remain poorly understood. This review summarizes the current state of knowledge regarding pelvic fins, such as their structure, function and evolution, to elucidate their contribution to the considerable diversity of teleosts. This information could be invaluable for future investigations into various aspects of pelvic fins, which will provide clues to understanding the evolution, diversity and adaptations of teleosts.
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Affiliation(s)
- Y Yamanoue
- Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
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Yasuike M, Jantzen S, Cooper GA, Leder E, Davidson WS, Koop BF. Grayling (Thymallinae) phylogeny within salmonids: complete mitochondrial DNA sequences of Thymallus arcticus and Thymallus thymallus. JOURNAL OF FISH BIOLOGY 2010; 76:395-400. [PMID: 20738715 DOI: 10.1111/j.1095-8649.2009.02494.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The phylogenetic relationships among the three subfamilies (Salmoninae, Coregoninae and Thymallinae) in the Salmonidae have not been addressed extensively at the molecular level. In this study, the whole mitochondrial genomes of two Thymallinae species, Thymallus arcticus and Thymallus thymallus were sequenced, and the published mitochondrial genome sequences of other salmonids were used for Bayesian and maximum-likelihood phylogenetic analyses. These results support an ancestral Coregoninae, branching within the Salmonidae, with Thymallinae as the sister group to Salmoninae.
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Affiliation(s)
- M Yasuike
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, British Columbia, V8W 3N5 Canada
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31
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Catanese G, Manchado M, Infante C. Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species. Gene 2009; 452:35-43. [PMID: 20035845 DOI: 10.1016/j.gene.2009.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 12/11/2009] [Accepted: 12/12/2009] [Indexed: 11/29/2022]
Abstract
Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.
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Affiliation(s)
- Gaetano Catanese
- IFAPA Centro El Toruño, Junta de Andalucía, 11500 El Puerto de Santa María (Cádiz), Spain
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32
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Abstract
Absolute barriers to dispersal are not common in marine systems, and the prevalence of planktonic larvae in marine taxa provides potential for gene flow across large geographic distances. These observations raise the fundamental question in marine evolutionary biology as to whether geographic and oceanographic barriers alone can account for the high levels of species diversity observed in marine environments such as coral reefs, or whether marine speciation also operates in the presence of gene flow between diverging populations. In this respect, the ecological hypothesis of speciation, in which reproductive isolation results from divergent or disruptive natural selection, is of particular interest because it may operate in the presence of gene flow. Although important insights into the process of ecological speciation in aquatic environments have been provided by the study of freshwater fishes, comparatively little is known about the possibility of ecological speciation in marine teleosts. In this study, the evidence consistent with different aspects of the ecological hypothesis of speciation is evaluated in marine fishes. Molecular approaches have played a critical role in the development of speciation hypotheses in marine fishes, with a role of ecology suggested by the occurrence of sister clades separated by ecological factors, rapid cladogenesis or the persistence of genetically and ecologically differentiated species in the presence of gene flow. Yet, ecological speciation research in marine fishes is still largely at an exploratory stage. Cases where the major ingredients of ecological speciation, namely a source of natural divergent or disruptive selection, a mechanism of reproductive isolation and a link between the two have been explicitly documented are few. Even in these cases, specific predictions of the ecological hypothesis of speciation remain largely untested. Recent developments in the study of freshwater fishes illustrate the potential for molecular approaches to address specific questions related to the ecological hypothesis of speciation such as the nature of the genes underlying key ecological traits, the magnitude of their effect on phenotype and the mechanisms underlying their differential expression in different ecological contexts. The potential provided by molecular studies is fully realized when they are complemented with alternative (e.g. ecological, theoretical) approaches.
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Affiliation(s)
- O Puebla
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Ancon, Republic of Panama.
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Yamanoue Y, Miya M, Matsuura K, Sakai H, Katoh M, Nishida M. Unique patterns of pelvic fin evolution: A case study of balistoid fishes (Pisces: Tetraodontiformes) based on whole mitochondrial genome sequences. Mol Phylogenet Evol 2009; 50:179-89. [DOI: 10.1016/j.ympev.2008.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 10/15/2008] [Accepted: 10/20/2008] [Indexed: 11/17/2022]
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Yamanoue Y, Miya M, Matsuura K, Miyazawa S, Tsukamoto N, Doi H, Takahashi H, Mabuchi K, Nishida M, Sakai H. Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology. Mol Biol Evol 2008; 26:623-9. [PMID: 19074759 DOI: 10.1093/molbev/msn283] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although the fugu Takifugu rubripes has attracted attention as a model organism for genomic studies because of its compact genome, it is not generally appreciated that there are approximately 25 closely related species with limited distributions in the waters of East Asia. We performed molecular phylogenetic analyses and constructed a time tree using whole mitochondrial genome sequences from 15 Takifugu species together with 10 outgroups to examine patterns of diversification. The resultant time tree showed that the modern Takifugu species underwent explosive speciation during the Pliocene 1.8-5.3 Ma, which is comparable with that of the Malawi cichlids and tropheine cichlids in Lake Tanganyika. Considering their limited distributions and remarkable variations in coloration, morphology, and behavior, the results of the present study strongly suggest that Takifugu species are strong candidates as a model system for evolutionary studies of speciation mechanisms in marine environments where few such organisms are available.
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Affiliation(s)
- Yusuke Yamanoue
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
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