1
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Dimens PV, Jones KL, Margulies D, Scholey V, Cusatti S, McPeak B, Hildahl TE, Saillant EAE. Genomic resources for the Yellowfin tuna Thunnus albacares. Mol Biol Rep 2024; 51:232. [PMID: 38281308 DOI: 10.1007/s11033-023-09117-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND The Yellowfin tuna (Thunnus albacares) is a large tuna exploited by major fisheries in tropical and subtropical waters of all oceans except the Mediterranean Sea. Genomic studies of population structure, adaptive variation or of the genetic basis of phenotypic traits are needed to inform fisheries management but are currently limited by the lack of a reference genome for this species. Here we report a draft genome assembly and a linkage map for use in genomic studies of T. albacares. METHODS AND RESULTS Illumina and PacBio SMRT sequencing were used in combination to generate a hybrid assembly that comprises 743,073,847 base pairs contained in 2,661 scaffolds. The assembly has a N50 of 351,587 and complete and partial BUSCO scores of 86.47% and 3.63%, respectively. Double-digest restriction associated DNA (ddRAD) was used to genotype the 2 parents and 164 of their F1 offspring resulting from a controlled breeding cross, retaining 19,469 biallelic single nucleotide polymorphism (SNP) loci. The SNP loci were used to construct a linkage map that features 24 linkage groups that represent the 24 chromosomes of yellowfin tuna. The male and female maps span 1,243.8 cM and 1,222.9 cM, respectively. The map was used to anchor the assembly in 24 super-scaffolds that contain 79% of the yellowfin tuna genome. Gene prediction identified 46,992 putative genes 20,203 of which could be annotated via gene ontology. CONCLUSIONS The draft reference will be valuable to interpret studies of genome wide variation in T. albacares and other Scombroid species.
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Affiliation(s)
- Pavel V Dimens
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | | | - Daniel Margulies
- Inter-American Tropical Tuna Commission, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Vernon Scholey
- Inter-American Tropical Tuna Commission, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Susana Cusatti
- Inter-American Tropical Tuna Commission, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Brooke McPeak
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | - Tami E Hildahl
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | - Eric A E Saillant
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA.
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2
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Friedman M, Feilich KL, Beckett HT, Alfaro ME, Faircloth BC, Černý D, Miya M, Near TJ, Harrington RC. A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean. Proc Biol Sci 2019; 286:20191502. [PMID: 31506051 PMCID: PMC6742994 DOI: 10.1098/rspb.2019.1502] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/14/2019] [Indexed: 11/12/2022] Open
Abstract
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of 'core' Stromateoidei, and a clade comprising 'Gempylidae' and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae + Tetragonurus). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene-Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes.
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Affiliation(s)
- Matt Friedman
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Kara L. Feilich
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
| | | | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Brant C. Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - David Černý
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Aoba-cho, Chuo-ku, Chiba, Japan
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Peabody Museum, Yale University, New Haven, CT, USA
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3
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Ciezarek AG, Osborne OG, Shipley ON, Brooks EJ, Tracey SR, McAllister JD, Gardner LD, Sternberg MJE, Block B, Savolainen V. Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas. Mol Biol Evol 2019; 36:84-96. [PMID: 30364966 PMCID: PMC6340463 DOI: 10.1093/molbev/msy198] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas are commercially important fishes worldwide, and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain in warm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large-scale industrial fisheries. Despite the importance of these traits to not only fisheries but also habitat utilization and responses to climate change, little is known of the genetic processes underlying the diversification of tunas. In collecting and analyzing sequence data across 29,556 genes, we found that parallel selection on standing genetic variation is associated with the evolution of endothermy in bluefin tunas. This includes two shared substitutions in genes encoding glycerol-3 phosphate dehydrogenase, an enzyme that contributes to thermogenesis in bumblebees and mammals, as well as four genes involved in the Krebs cycle, oxidative phosphorylation, β-oxidation, and superoxide removal. Using phylogenetic techniques, we further illustrate that the eight Thunnus species are genetically distinct, but found evidence of mitochondrial genome introgression across two species. Phylogeny-based metrics highlight conservation needs for some of these species.
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Affiliation(s)
- Adam G Ciezarek
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Owen G Osborne
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
| | - Oliver N Shipley
- Shark Research and Conservation Program, The Cape Eleuthera Institute, Rock Sound, Eleuthera, The Bahamas
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, NY
| | - Edward J Brooks
- Shark Research and Conservation Program, The Cape Eleuthera Institute, Rock Sound, Eleuthera, The Bahamas
| | - Sean R Tracey
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Jaime D McAllister
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Luke D Gardner
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, Kensington, London, United Kingdom
| | - Barbara Block
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom
- Corresponding author: E-mail:
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4
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Wainwright DK, Ingersoll S, Lauder GV. Scale diversity in bigeye tuna (Thunnus obesus): Fat-filled trabecular scales made of cellular bone. J Morphol 2018. [PMID: 29537097 DOI: 10.1002/jmor.20814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tunas of the genus Thunnus possess many morphological and physiological adaptations for their high-performance epipelagic ecology. Although Thunnus anatomy has been studied, there are no quantitative studies on the structure of their scales. We investigated the scales of bigeye tuna (Thunnus obesus) from ten regions of the body using micro computed tomography (µCT)-scanning and histology to quantitatively and qualitatively compare regional scale morphology. We found a diversity of scale sizes and shapes across the body of bigeye tuna and discriminant function analysis on variables derived from µCT-data showed that scales across the body differ quantitatively in shape and size. We also report the discovery of a novel scale type in corselet, tail, and cheek regions. These modified scales are ossified shells supported by internal trabeculae, filled with fat, and possessing an internal blood supply. Histological analysis showed that the outer lamellar layers of these thickened scales are composed of cellular bone, unexpected for a perciform fish in which bone is typically acellular. In the fairing region of the anterior body, these fat-filled scales are stacked in layers up to five scales deep, forming a thickened bony casing. Cheek scales also possess a fat-filled internal trabecular structure, while most posterior body scales are more plate-like and similar to typical teleost scales. While the function of these novel fat-filled scales is unknown, we explore several possible hypotheses for their function.
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Affiliation(s)
- Dylan K Wainwright
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | - Sam Ingersoll
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | - George V Lauder
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
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5
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Frédérich B, Marramà G, Carnevale G, Santini F. Non-reef environments impact the diversification of extant jacks, remoras and allies (Carangoidei, Percomorpha). Proc Biol Sci 2016; 283:20161556. [PMID: 27807262 PMCID: PMC5124091 DOI: 10.1098/rspb.2016.1556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/07/2016] [Indexed: 11/12/2022] Open
Abstract
Various factors may impact the processes of diversification of a clade. In the marine realm, it has been shown that coral reef environments have promoted diversification in various fish groups. With the exception of requiem sharks, all the groups showing a higher level of diversity in reefs than in non-reef habitats have diets based predominantly on plankton, algae or benthic invertebrates. Here we explore the pattern of diversification of carangoid fishes, a clade that includes numerous piscivorous species (e.g. trevallies, jacks and dolphinfishes), using time-calibrated phylogenies as well as ecological and morphological data from both extant and fossil species. The study of carangoid morphospace suggests that reef environments played a role in their early radiation during the Eocene. However, contrary to the hypothesis of a reef-association-promoting effect, we show that habitat shifts to non-reef environments have increased the rates of morphological diversification (i.e. size and body shape) in extant carangoids. Piscivory did not have a major impact on the tempo of diversification of this group. Through the ecological radiation of carangoid fishes, we demonstrate that non-reef environments may sustain and promote processes of diversification of different marine fish groups, at least those including a large proportion of piscivorous species.
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Affiliation(s)
- Bruno Frédérich
- Laboratoire de Morphologie Fonctionnelle et Evolutive, AFFISH Research Center, Université de Liège, 4000 Liège, Belgium
- Laboratoire d'Océanologie, MARE Center, Université de Liège, 4000 Liège, Belgium
| | - Giuseppe Marramà
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino 10125, Italy
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino 10125, Italy
| | - Francesco Santini
- Associazione Italiana per lo Studio della Biodiversità, Pisa 56100, Italy
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6
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Ciezarek AG, Dunning LT, Jones CS, Noble LR, Humble E, Stefanni SS, Savolainen V. Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biol Evol 2016; 8:3011-3021. [PMID: 27614233 PMCID: PMC5630876 DOI: 10.1093/gbe/evw211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite 400–450 million years of independent evolution, a strong phenotypic convergence has occurred between two groups of fish: tunas and lamnid sharks. This convergence is characterized by centralization of red muscle, a distinctive swimming style (stiffened body powered through tail movements) and elevated body temperature (endothermy). Furthermore, both groups demonstrate elevated white muscle metabolic capacities. All these traits are unusual in fish and more likely evolved to support their fast-swimming, pelagic, predatory behavior. Here, we tested the hypothesis that their convergent evolution was driven by selection on a set of metabolic genes. We sequenced white muscle transcriptomes of six tuna, one mackerel, and three shark species, and supplemented this data set with previously published RNA-seq data. Using 26 species in total (including 7,032 tuna genes plus 1,719 shark genes), we constructed phylogenetic trees and carried out maximum-likelihood analyses of gene selection. We inferred several genes relating to metabolism to be under selection. We also found that the same one gene, glycogenin-1, evolved under positive selection independently in tunas and lamnid sharks, providing evidence of convergent selective pressures at gene level possibly underlying shared physiology.
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Affiliation(s)
- Adam G Ciezarek
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK
| | - Luke T Dunning
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK Present address: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Catherine S Jones
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, Scotland, UK
| | - Leslie R Noble
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, Scotland, UK
| | - Emily Humble
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK Present address: Department of Animal Behaviour, University of Bielefeld, Postfach 100131, Bielefeld, Germany
| | | | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK
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7
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Díaz-Arce N, Arrizabalaga H, Murua H, Irigoien X, Rodríguez-Ezpeleta N. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas. Mol Phylogenet Evol 2016; 102:202-7. [DOI: 10.1016/j.ympev.2016.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
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8
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The historical biogeography of groupers: Clade diversification patterns and processes. Mol Phylogenet Evol 2016; 100:21-30. [PMID: 26908372 DOI: 10.1016/j.ympev.2016.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 11/20/2022]
Abstract
Groupers (family Epinephelidae) are a clade of species-rich, biologically diverse reef fishes. Given their ecological variability and widespread distribution across ocean basins, it is important to scrutinize their evolutionary history that underlies present day distributions. This study investigated the patterns and processes by which grouper biodiversity has been generated and what factors have influenced their present day distributions. We reconstructed a robust, time-calibrated molecular phylogeny of Epinephelidae with comprehensive (∼87%) species sampling, whereby diversification rates were estimated and ancestral ranges were reconstructed. Our results indicate that groupers originated in what is now the East Atlantic during the mid-Eocene and diverged successively to form six strongly supported main clades. These clades differ in age (late Oligocene to mid-Miocene), geographic origin (West Atlantic to West Indo-Pacific) and temporal-spatial diversification pattern, ranging from constant rates of diversification to episodes of rapid radiation. Overall, divergence within certain biogeographic regions was most prevalent in groupers, while vicariant divergences were more common in Tropical Atlantic and East Pacific groupers. Our findings reveal that both biological and geographical factors have driven grouper diversification. They also underscore the importance of scrutinizing group-specific patterns to better understand reef fish evolution.
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9
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Jondeung A, Karinthanyakit W. Mitochondrial DNA control region of three mackerels, genus Rastrelliger: structure, molecular diversity and phylogenetic relationship. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2395-400. [PMID: 26119119 DOI: 10.3109/19401736.2015.1028047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial control regions (CR) of three mackerels (Rastrelliger spp.) were examined and analyzed. The CR contained three domains, in which three termination-associated sequences (TAS-I, TAS-II and TAS-III), two central conserved sequence blocks (CSB-E, CSB-D), three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and a putative promoter were detected. Molecular indices analyses of the aligned complete CR sequences showed high level of haplotype diversities and genetic divergences among the three species. The intraspecific divergence among species of this genus ranked from 0.25% to 1.62% and interspecific divergence from 1.90% to 4.30%. The phylogenetic tree shows monophyly with R. brachysoma as a basal species of Rastrelliger. Applying the average divergence rate for fish control regions, the results suggest that the time of separation among Rastrelligers could have occurred in the middle Pleistocene era.
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Affiliation(s)
- Amnuay Jondeung
- a Department of Genetics , Kasetsart University , Bangkok , Thailand and
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10
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First multilocus and densely sampled timetree of trevallies, pompanos and allies (Carangoidei, Percomorpha) suggests a Cretaceous origin and Eocene radiation of a major clade of piscivores. Mol Phylogenet Evol 2015; 83:33-9. [DOI: 10.1016/j.ympev.2014.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/21/2014] [Accepted: 10/23/2014] [Indexed: 11/15/2022]
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11
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Santini F, Carnevale G, Sorenson L. First timetree of Sphyraenidae (Percomorpha) reveals a Middle Eocene crown age and an Oligo–Miocene radiation of barracudas. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/11250003.2014.962630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Sorenson L, Santini F, Alfaro ME. The effect of habitat on modern shark diversification. J Evol Biol 2014; 27:1536-48. [DOI: 10.1111/jeb.12405] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 03/24/2014] [Indexed: 02/06/2023]
Affiliation(s)
- L. Sorenson
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
| | - F. Santini
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
| | - M. E. Alfaro
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
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13
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Santini F, Carnevale G, Sorenson L. First multi-locus timetree of seabreams and porgies (Percomorpha: Sparidae). ACTA ACUST UNITED AC 2014. [DOI: 10.1080/11250003.2013.878960] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Santini F, Sorenson L. First molecular timetree of billfishes (Istiophoriformes: Acanthomorpha) shows a Late Miocene radiation of marlins and allies. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/11250003.2013.848945] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Miya M, Friedman M, Satoh TP, Takeshima H, Sado T, Iwasaki W, Yamanoue Y, Nakatani M, Mabuchi K, Inoue JG, Poulsen JY, Fukunaga T, Sato Y, Nishida M. Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families. PLoS One 2013; 8:e73535. [PMID: 24023883 PMCID: PMC3762723 DOI: 10.1371/journal.pone.0073535] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/22/2013] [Indexed: 11/25/2022] Open
Abstract
Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae “Pelagia” in reference to the common habitat preference that links the 15 families.
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Affiliation(s)
- Masaki Miya
- Natural History Museum and Institute, Chiba, Chiba, Japan
- * E-mail:
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
| | - Takashi P. Satoh
- National Museum of Nature and Science, Tsukuba-shi, Ibaraki, Japan
| | - Hirohiko Takeshima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Chiba, Japan
| | - Wataru Iwasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yusuke Yamanoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Masanori Nakatani
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Kohji Mabuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Jun G. Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Jan Yde Poulsen
- Natural History Collections, Bergen Museum, University of Bergen, Bergen, Norway
| | - Tsukasa Fukunaga
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yukuto Sato
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
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16
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Norris RD, Turner SK, Hull PM, Ridgwell A. Marine Ecosystem Responses to Cenozoic Global Change. Science 2013; 341:492-8. [DOI: 10.1126/science.1240543] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- R. D. Norris
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - S. Kirtland Turner
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - P. M. Hull
- Department of Geology and Geophysics, Yale University, New Haven, CT 06520, USA
| | - A. Ridgwell
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
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