1
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Gilmour KM, Turko AJ. Effects of structural remodelling on gill physiology. J Comp Physiol B 2024:10.1007/s00360-024-01558-0. [PMID: 38758304 DOI: 10.1007/s00360-024-01558-0] [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: 03/01/2024] [Revised: 03/01/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024]
Abstract
The complex relationships between the structure and function of fish gills have been of interest to comparative physiologists for many years. Morphological plasticity of the gill provides a dynamic mechanism to reversibly alter its structure in response to changes in the conditions experienced by the fish. The best known example of gill remodelling is the growth or retraction of cell masses between the lamellae, a rapid process that alters the lamellar surface area that is exposed to the water (i.e. the functional lamellar surface area). Decreases in environmental O2 availability and/or increases in metabolic O2 demand stimulate uncovering of the lamellae, presumably to increase the capacity for O2 uptake. This review addresses four questions about gill remodelling: (1) what types of reversible morphological changes occur; (2) how do these changes affect physiological function from the gill to the whole animal; (3) what factors regulate reversible gill plasticity; and (4) is remodelling phylogenetically widespread among fishes? We address these questions by surveying the current state of knowledge of gill remodelling in fishes, with a focus on identifying gaps in our understanding that future research should consider.
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Affiliation(s)
- Kathleen M Gilmour
- Department of Biology, University of Ottawa, 30 Marie Curie Pvt, Ottawa, ON, K1N 6N5, Canada.
| | - Andy J Turko
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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2
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Papa Y, Wellenreuther M, Morrison MA, Ritchie PA. Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus). G3 (BETHESDA, MD.) 2022; 13:6883520. [PMID: 36477875 PMCID: PMC9911067 DOI: 10.1093/g3journal/jkac315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022]
Abstract
Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management. Here, we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi [Nemadactylus macropterus (Forster, 1801)], a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq reads were obtained to assist in gene annotation. The final genome assembly was 568 Mb long with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared with the same values reported for other fishes. Iso-Seq analysis recovered 91,313 unique transcripts from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly and the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics and comparative eco-evolutionary studies in teleosts and related organisms.
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Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Maren Wellenreuther
- Seafood Production Group, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand,School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Mark A Morrison
- National Institute of Water and Atmospheric Research, Auckland 1010, New Zealand
| | - Peter A Ritchie
- Corresponding author: Te Toki A Rata, Gate 7, Kelburn Parade, Wellington 6012, New Zealand.
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3
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Johnson BD, Anderson AP, Small CM, Rose E, Flanagan SP, Hendrickson-Rose C, Jones AG. The evolution of the testis transcriptome in pregnant male pipefishes and seahorses. Evolution 2022; 76:2162-2180. [PMID: 35863060 DOI: 10.1111/evo.14579] [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: 01/10/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
In many animals, sperm competition and sexual conflict are thought to drive the rapid evolution of male-specific genes, especially those expressed in the testes. A potential exception occurs in the male pregnant pipefishes, where females transfer eggs to the males, eliminating testes from participating in these processes. Here, we show that testis-related genes differ dramatically in their rates of molecular evolution and expression patterns in pipefishes and seahorses (Syngnathidae) compared to other fish. Genes involved in testis or sperm function within syngnathids experience weaker selection in comparison to their orthologs in spawning and livebearing fishes. An assessment of gene turnover and expression in the testis transcriptome suggests that syngnathids have lost (or significantly reduced expression of) important classes of genes from their testis transcriptomes compared to other fish. Our results indicate that more than 50 million years of male pregnancy have removed syngnathid testes from the molecular arms race that drives the rapid evolution of male reproductive genes in other taxa.
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Affiliation(s)
| | | | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
| | - Emily Rose
- Department of Biology, Valdosta State University, Valdosta, Georgia, 31698
| | - Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, 8041, New Zealand
| | | | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, 83844
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4
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Samayoa AP, Struthers CD, Trnski T, Roberts CD, Liggins L. Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific. Mol Phylogenet Evol 2022; 176:107584. [PMID: 35843570 DOI: 10.1016/j.ympev.2022.107584] [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: 02/25/2022] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
Abstract
Remote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitāhua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.
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Affiliation(s)
- André P Samayoa
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand.
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Thomas Trnski
- Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
| | - Clive D Roberts
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand; Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
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5
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Jeffries DL, Mee JA, Peichel CL. Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback. J Evol Biol 2022; 35:1683-1695. [PMID: 35816592 PMCID: PMC10083969 DOI: 10.1111/jeb.14034] [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: 01/07/2022] [Revised: 04/07/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. mammals, birds) but so labile in others (e.g. teleosts, amphibians). To identify general mechanisms driving transitions in sex determination systems or forces which favour their conservation, we first require empirical data on sex chromosome systems from multiple lineages. Stickleback fishes are a valuable model lineage for the study of sex chromosome evolution due to variation in sex chromosome systems between closely-related species. Here, we identify the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole-genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex-linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.
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Affiliation(s)
- Daniel L Jeffries
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jonathan A Mee
- Department of Biology, Mount Royal University, Calgary, Alberta, Canada
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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6
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Girard MG, Davis MP, Tan HH, Wedd DJ, Chakrabarty P, Ludt WB, Summers AP, Smith WL. Phylogenetics of archerfishes (Toxotidae) and evolution of the toxotid shooting apparatus. Integr Org Biol 2022; 4:obac013. [PMID: 35814192 PMCID: PMC9259087 DOI: 10.1093/iob/obac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/11/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Archerfishes (Toxotidae) are variously found in the fresh- and brackish-water environments of Asia Pacific and are well known for their ability to shoot water at terrestrial prey. These shots of water are intended to strike their prey and cause it to fall into the water for capture and consumption. While this behavior is well known, there are competing hypotheses (blowpipe vs. pressure tank hypothesis) of how archerfishes shoot and which oral structures are involved. Current understanding of archerfish shooting structures is largely based on two species, Toxotes chatareus and T. jaculatrix. We do not know if all archerfishes possess the same oral structures to shoot water, if anatomical variation is present within these oral structures, or how these features have evolved. Additionally, there is little information on the evolution of the Toxotidae as a whole, with all previous systematic works focusing on the interrelationships of the family. We first investigate the limits of archerfish species using new and previously published genetic data. Our analyses highlight that the current taxonomy of archerfishes does not conform to the relationships we recover. Toxotes mekongensis and T. siamensis are placed in synonymy of T. chatareus, Toxotes carpentariensis is recognized as a species and removed from synonymy of T. chatareus, and the genus Protoxotes is recognized for T. lorentzi based on the results of our analyses. We then take an integrative approach, using a combined analysis of discrete hard- and soft-tissue morphological characters with genetic data, to construct a phylogeny of the Toxotidae. Using the resulting phylogenetic hypothesis, we then characterize the evolutionary history and anatomical variation within the archerfishes. We discuss the variation in the oral structures and the evolution of the mechanism with respect to the interrelationships of archerfishes, and find that the oral structures of archerfishes support the blowpipe hypothesis but soft-tissue oral structures may also play a role in shooting. Finally, by comparing the morphology of archerfishes to their sister group, we find that the Leptobramidae has relevant shooting features in the oral cavity, suggesting that some components of the archerfish shooting mechanism are examples of co-opted or exapted traits.
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Affiliation(s)
- M G Girard
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, 20560, USA
| | - M P Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, MN, 56301, USA
| | - H H Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, 117377, SGP
| | - D J Wedd
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0810, AUS
| | - P Chakrabarty
- Ichthyology Section, Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - W B Ludt
- Department of Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA
| | - A P Summers
- Department of Biology and SAFS, University of Washington's Friday Harbor Laboratories, Friday Harbor, WA, 98250, USA
| | - W L Smith
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
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7
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Girard MG, Davis MP, Baldwin CC, Dettaï A, Martin RP, Smith WL. Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements. JOURNAL OF FISH BIOLOGY 2022; 100:793-810. [PMID: 35137410 DOI: 10.1111/jfb.14997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/24/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral-fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved-element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad-scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.
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Affiliation(s)
- Matthew G Girard
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Matthew P Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota, USA
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Agnès Dettaï
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Paris, FRA
| | - Rene P Martin
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - W Leo Smith
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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8
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Smith WL, Ghedotti MJ, Domínguez-Domínguez O, McMahan CD, Espinoza E, Martin RP, Girard MG, Davis MP. Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha). NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2021-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.
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9
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Stervander M, Cresko WA. A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae). G3 (BETHESDA, MD.) 2021; 11:jkab306. [PMID: 34849773 PMCID: PMC8664458 DOI: 10.1093/g3journal/jkab306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022]
Abstract
The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons-the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole-genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.
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Affiliation(s)
- Martin Stervander
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
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10
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Dornburg A, Near TJ. The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-122120-122554] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina 28223, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511, USA
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11
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Havelka M, Sawayama E, Saito T, Yoshitake K, Saka D, Ineno T, Asakawa S, Takagi M, Goto R, Matsubara T. Chromosome-Scale Genome Assembly and Transcriptome Assembly of Kawakawa Euthynnus affinis; A Tuna-Like Species. Front Genet 2021; 12:739781. [PMID: 34616435 PMCID: PMC8489456 DOI: 10.3389/fgene.2021.739781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Miloš Havelka
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
| | - Eitaro Sawayama
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Taiju Saito
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
| | - Kazutoshi Yoshitake
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Daiki Saka
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshinao Ineno
- Aquaculture Research Institute, Kindai University, Shingu, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Motohiro Takagi
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
| | - Rie Goto
- South Ehime Fisheries Research Center, Ehime University, Ainan, Japan
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12
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Pastana MNL, Johnson GD, Datovo A. Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Abstract
More than half the ray-finned fishes and about one-quarter of all living vertebrates belong to Percomorphacea. Among its 30 orders, Stromateiformes encompass 77 species in 16 genera and six families. Stromateiform monophyly has never been tested using morphology, and it has been rejected by molecular analyses. This comprehensive revision of Stromateiformes includes all its valid genera of all percomorph families previously aligned with the order. We sampled 207 phenotypic characters in 66 terminal taxa representing 14 orders and 46 acanthopterygian families. This dataset significantly surpasses all previous phenotype-based phylogenies of Stromateiformes, which analysed only a fraction of these characters. Stromateiformes is recovered as monophyletic, supported by eight unequivocal synapomorphies. Amarsipidae is the sister group of all other Stromateiformes (= Stromateoidei). Centrolophidae is paraphyletic, with three of its genera allocated into an early-diverging clade and the other four appearing as successive sister groups to a lineage containing the remaining stromateiforms. All other stromateoid families are monophyletic, with the following cladistic arrangement: (Nomeidae (Stromateidae (Tetragonuridae, Ariommatidae))). Our analysis convincingly refutes recent molecular phylogenetic interpretations that fail to recover a monophyletic Stromateiformes. These findings call into question large-scale conclusions of percomorph relationships and trait evolution based solely on molecular data.
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Affiliation(s)
- Murilo N L Pastana
- Division of Fishes, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
| | - G David Johnson
- Division of Fishes, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Aléssio Datovo
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
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13
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Harvey VL, Keating JN, Buckley M. Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201955. [PMID: 34430038 PMCID: PMC8355665 DOI: 10.1098/rsos.201955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/20/2021] [Indexed: 05/12/2023]
Abstract
Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250-283 Ma and ∼120-133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.
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Affiliation(s)
- Virginia L. Harvey
- Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester M13 9PL, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Joseph N. Keating
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Michael Buckley
- Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester M13 9PL, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Abstract
Abstract
Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are seahorses (Hippocampus spp.: 14/42 species, with an additional 17 that are Data Deficient) or freshwater pipefishes of the genus Microphis (2/18 species, with seven additional that are Data Deficient). Two species are Near Threatened. Nearly one-third of syngnathiformes (97 species) are Data Deficient and could potentially be threatened, requiring further field research and evaluation. Most species (61%) were, however, evaluated as Least Concern. Primary threats to syngnathids are (1) overexploitation, primarily by non-selective fisheries, for which most assessments were determined by criterion A (Hippocampus) and/or (2) habitat loss and degradation, for which assessments were determined by criterion B (Microphis and some Hippocampus). Threatened species occurred in most regions but more are found in East and South-east Asia and in South African estuaries. Vital conservation action for syngnathids, including constraining fisheries, particularly non-selective extraction, and habitat protection and rehabilitation, will benefit many other aquatic species.
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15
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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16
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Santaquiteria A, Siqueira AC, Duarte-Ribeiro E, Carnevale G, White W, Pogonoski J, Baldwin CC, Ortí G, Arcila D, Betancur RR. Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences. Syst Biol 2021; 70:1145-1162. [PMID: 33892493 DOI: 10.1093/sysbio/syab028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/14/2022] Open
Abstract
The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.
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Affiliation(s)
- Aintzane Santaquiteria
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Emanuell Duarte-Ribeiro
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10125, Torino, Italy
| | - William White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - John Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - Guillermo Ortí
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA.,Department of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.,Sam Noble Oklahoma Museum of Natural History, 2401 Chautauqua Ave, Norman, OK 73072, USA
| | - Ricardo R Betancur
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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17
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Oh DJ, Lee JC, Ham YM, Jung YH. The mitochondrial genome of Stereolepis doederleini (Pempheriformes: Polyprionidae) and mitogenomic phylogeny of Pempheriformes. Genet Mol Biol 2021; 44:e20200166. [PMID: 33661273 PMCID: PMC7931504 DOI: 10.1590/1678-4685-gmb-2020-0166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 01/19/2021] [Indexed: 11/22/2022] Open
Abstract
The complete mitochondrial (mt) genome of Stereolepis doederleini was sequenced from a specimen collected in a commercial aquarium in Jeju Island. The sequence was 16,513 base pairs in length and, similar to other vertebrate mt genomes, included 37 mt genes and a noncoding control region; the gene order was identical to that of typical vertebrate mt genome. Mitochondrial genome sequences of 17 species from 12 families were used to reconstruct phylogenetic relationships within the order Pempheriformes. The phylogenetic trees were constructed with three methods (neighbor joining [NJ], maximum likelihood [ML], and Bayesian method) using 12 protein coding genes, but not ND6. In all phylogenetic trees, Pempheriformes were clustered into three strongly supported clades. Two Acropomatidae species (Synagrops japonicus in clade-Ⅰ and Doederleinia berycoides in clade-Ⅲ) were polyphyletic; S. japonicus was close to Lateolabracidae and was the sister of Glaucosomatidae + (Pempheridae/(Percophidae+Creediidae)), and D. berycoides was sister to Howellidae + Epigonidae. All phylogenetic trees supported a sister relationship between Creediidae and Percophidae in clade-Ⅰ. Glaucosomatidae formed a sister clade with Pempheridae. The relationships within clade-Ⅱ, which was composed of four families (Pentacerotidae, Polyprionidae, Banjosidae, and Bathyclupeidae), slightly differed between NJ/ML and BI tree topologies. In clade-Ⅲ, the relationships among Howellidae, Epigonidae, and Acropomatidae were strongly supported.
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Affiliation(s)
- Dae-Ju Oh
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Jong-Chul Lee
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Young-Min Ham
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
| | - Yong-Hwan Jung
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Republic of Korea
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18
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Rincon-Sandoval M, Duarte-Ribeiro E, Davis AM, Santaquiteria A, Hughes LC, Baldwin CC, Soto-Torres L, Acero P A, Walker HJ, Carpenter KE, Sheaves M, Ortí G, Arcila D, Betancur-R R. Evolutionary determinism and convergence associated with water-column transitions in marine fishes. Proc Natl Acad Sci U S A 2020; 117:33396-33403. [PMID: 33328271 PMCID: PMC7777220 DOI: 10.1073/pnas.2006511117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic-pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.
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Affiliation(s)
- Melissa Rincon-Sandoval
- Department of Biology, The University of Oklahoma, Norman, OK 73019
- Universidad Nacional de Colombia sede Caribe, Centro de Estudios en Ciencias del Mar (CECIMAR), Santa Marta, Magdalena, Colombia
| | | | - Aaron M Davis
- Centre for Tropical Water and Aquatic Ecosystem Research, School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia
| | | | - Lily C Hughes
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Luisángely Soto-Torres
- Department of Biology, Universidad de Puerto Rico-Rio Piedras, San Juan Puerto Rico, 00931
| | - Arturo Acero P
- Universidad Nacional de Colombia sede Caribe, Centro de Estudios en Ciencias del Mar (CECIMAR), Santa Marta, Magdalena, Colombia
| | - H J Walker
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0244
| | | | - Marcus Sheaves
- Marine Data Technology Hub, James Cook University, Townsville, QLD 4811, Australia
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, Norman, OK 73019
- Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, Norman, OK
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19
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van der Merwe PDW, Cotterill FPD, Kandziora M, Watters BR, Nagy B, Genade T, Flügel TJ, Svendsen DS, Bellstedt DU. Genomic fingerprints of palaeogeographic history: The tempo and mode of rift tectonics across tropical Africa has shaped the diversification of the killifish genus Nothobranchius (Teleostei: Cyprinodontiformes). Mol Phylogenet Evol 2020; 158:106988. [PMID: 33059071 DOI: 10.1016/j.ympev.2020.106988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/16/2020] [Accepted: 10/07/2020] [Indexed: 01/04/2023]
Abstract
This paper reports a phylogeny of the African killifishes (Genus Nothobranchius, Order Cyprinodontiformes) informed by five genetic markers (three nuclear, two mitochondrial) of 80 taxa (seven undescribed and 73 of the 92 recognized species). These short-lived annual fishes occupy seasonally wet habitats in central and eastern Africa, and their distribution coincides largely with the East African Rift System (EARS). The fossil dates of sister clades used to constrain a chronometric tree of all sampled Nothobranchius recovered the origin of the genus at ~13.27 Mya. It was followed by the radiations of six principal clades through the Neogene. An ancestral area estimation tested competing biogeographical hypotheses to constrain the ancestral origin of the genus to the Nilo-Sudan Ecoregion, which seeded a mid-Miocene dispersal event into the Coastal ecoregion, followed closely (~10 Mya) by dispersals southward across the Mozambique coastal plain into the Limpopo Ecoregion. Extending westwards across the Tanzanian plateau, a pulse of radiations through the Pliocene were associated with dispersals and fragmentation of wetlands across the Kalahari and Uganda Ecoregions. We interpret this congruence of drainage rearrangements with dispersals and cladogenic events of Nothobranchius to reflect congruent responses to recurrent uplift and rifting. The coevolution of these freshwater fishes and wetlands is attributed to ultimate control by tectonics, as the EARS extended southwards during the Neogene. Geobiological consilience of the combined evidence supports a tectonic hypothesis for the evolution of Nothobranchius.
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Affiliation(s)
| | | | - Martha Kandziora
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Brian R Watters
- 6141 Parkwood Drive, Nanaimo, British Columbia V9T6A2, Canada
| | - Béla Nagy
- 30, Rue du Mont Ussy, 77300 Fontainebleau, France
| | - Tyrone Genade
- Biomedical Sciences, East Tennessee State University, USA
| | - Tyrel J Flügel
- Department of Geography and Environmental Studies, Stellenbosch University, South Africa
| | - David S Svendsen
- Department of Geography and Environmental Studies, Stellenbosch University, South Africa
| | - Dirk U Bellstedt
- Department of Biochemistry, Stellenbosch University, South Africa.
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20
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Song HY, Jung YH, Choi YJ, Kim B, Nguyen TV, Lee DS. Characterization of the complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus (Spariformes, Nemipteridae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3130-3131. [PMID: 33458084 PMCID: PMC7783152 DOI: 10.1080/23802359.2020.1778576] [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: 10/27/2022]
Abstract
The complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus, which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,882 bp in size and encoded of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Nemipterus furcosus has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that N. furcosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for addressing taxonomic issues.
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Affiliation(s)
- Ha Yeun Song
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Yun-Hwan Jung
- International Center for Marine Biodiversity, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Young Ji Choi
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Bora Kim
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Tu Van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Dae-Sung Lee
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
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21
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Song HY, Jung YH, Choi YJ, Kim B, Nguyen TV, Lee DS. Characterization of the complete mitochondrial genome of the Butterfly whiptail, Pentapodus setosus (Spariformes, Nemipteridae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2898-2899. [PMID: 33457993 PMCID: PMC7782546 DOI: 10.1080/23802359.2020.1791022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complete mitochondrial genome of Pentapodus setosus which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,836 bp in length with 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that P. setosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for resolving the taxonomic issues.
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Affiliation(s)
- Ha Yeun Song
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Yun-Hwan Jung
- International Center for Marine Biodiversity, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Young Ji Choi
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Bora Kim
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Tu Van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Chi Minh city, Vietnam
| | - Dae-Sung Lee
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
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22
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On the causes of geographically heterogeneous parallel evolution in sticklebacks. Nat Ecol Evol 2020; 4:1105-1115. [DOI: 10.1038/s41559-020-1222-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/14/2020] [Indexed: 12/22/2022]
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23
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Girard MG, Davis MP, Smith WL. The Phylogeny of Carangiform Fishes: Morphological and Genomic Investigations of a New Fish Clade. COPEIA 2020. [DOI: 10.1643/ci-19-320] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Matthew G. Girard
- Biodiversity Institute, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, Kansas 66045; (MGG) . Send reprint requests to MGG
| | - Matthew P. Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota 56301
| | - W. Leo Smith
- Biodiversity Institute, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, Kansas 66045; (MGG) . Send reprint requests to MGG
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24
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Presti P, Johnson GD, Datovo A. Facial and gill musculature of polynemid fishes, with notes on their possible relationships with sciaenids (Percomorphacea: Perciformes). J Morphol 2020; 281:662-675. [PMID: 32356928 DOI: 10.1002/jmor.21134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 11/11/2022]
Abstract
The Polynemidae is a family of primarily marine fishes with eight genera and 42 extant species. Many aspects of their morphology are largely unknown, with few reports about their osteology and barely any information on their myology. This paper describes and illustrates in detail all facial and branchial muscles of representative species of polynemids. Our analysis demonstrates the existence of several remarkable and previously unknown specializations in the polynemid musculature. The aponeurotic and completely independent origin of the pars promalaris of the adductor mandibulae is apparently unique among percomorphs. The differentiation of this section into lateral and medial subsections; the total separation of the promalaris from the retromalaris; the differentiation of the pars primordialis of the levator arcus palatini into external and internal subsections are also uncommon features of polynemids that are shared by sciaenids, thus supporting the hypothesis of a closer relationship between these families.
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Affiliation(s)
- Paulo Presti
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - G David Johnson
- Division of Fishes, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Aléssio Datovo
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
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25
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Southey BR, Rodriguez-Zas SL, Rhodes JS, Sweedler JV. Characterization of the prohormone complement in Amphiprion and related fish species integrating genome and transcriptome assemblies. PLoS One 2020; 15:e0228562. [PMID: 32163422 PMCID: PMC7067429 DOI: 10.1371/journal.pone.0228562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 01/19/2020] [Indexed: 12/31/2022] Open
Abstract
The Amphiprion (anemonefish or clownfish) family of teleost fish, which is not a common model species, exhibits multiple unique characteristics, including social control of body size and protandrous sex change. The social changes in sex and body size are modulated by neuropeptide signaling pathways. These neuropeptides are formed from complex processing from larger prohormone proteins; understanding the neuropeptide complement requires information on complete prohormones sequences. Genome and transcriptome information within and across 22 teleost fish species, including 11 Amphiprion species, were assembled and integrated to achieve the first comprehensive survey of their prohormone genes. This information enabled the identification of 175 prohormone isoforms from 159 prohormone proteins across all species. This included identification of 9 CART prepropeptide genes and the loss of insulin-like 5B and tachykinin precursor 1B genes in Pomacentridae species. Transcriptome assemblies generally detected most prohormone genes but provided fewer prohormone genes than genome assemblies due to the lack of expression of prohormone genes or specific isoforms and tissue sampled. Comparisons between duplicate genes indicated that subfunctionalization, degradation, and neofunctionalization may be occurring between all copies. Characterization of the prohormone complement lays the foundation for future peptidomic investigation of the molecular basis of social physiology and behavior in the teleost fish.
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Affiliation(s)
- Bruce R. Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Sandra L. Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Justin S. Rhodes
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Psychology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States of America
| | - Jonathan V. Sweedler
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States of America
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26
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Ishikawa A, Kabeya N, Ikeya K, Kakioka R, Cech JN, Osada N, Leal MC, Inoue J, Kume M, Toyoda A, Tezuka A, Nagano AJ, Yamasaki YY, Suzuki Y, Kokita T, Takahashi H, Lucek K, Marques D, Takehana Y, Naruse K, Mori S, Monroig O, Ladd N, Schubert CJ, Matthews B, Peichel CL, Seehausen O, Yoshizaki G, Kitano J. A key metabolic gene for recurrent freshwater colonization and radiation in fishes. Science 2019; 364:886-889. [PMID: 31147520 DOI: 10.1126/science.aau5656] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
Abstract
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Koki Ikeya
- Gifu World Freshwater Aquarium, Gifu, Japan
| | - Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jennifer N Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Naoki Osada
- Graduate School of Bioengineering and Bioinformatics, Hokkaido University, Sapporo, Japan
| | - Miguel C Leal
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Manabu Kume
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | | | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Yuto Suzuki
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Hiroshi Takahashi
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Yamaguchi, Japan
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Yusuke Takehana
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu Kyoritsu University, Ogaki, Gifu, Japan
| | - Oscar Monroig
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón, Spain
| | - Nemiah Ladd
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Earth Sciences, ETH-Zurich, Zurich Switzerland
| | - Carsten J Schubert
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Aquatic Ecology, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan. .,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
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Natsidis P, Tsakogiannis A, Pavlidis P, Tsigenopoulos CS, Manousaki T. Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. Commun Biol 2019; 2:400. [PMID: 31701028 PMCID: PMC6825128 DOI: 10.1038/s42003-019-0654-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/08/2019] [Indexed: 12/29/2022] Open
Abstract
Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.
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Affiliation(s)
- Paschalis Natsidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
- School of Medicine, University of Crete, Heraklion, Greece
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology, Heraklion, Greece
| | - Costas S. Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
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28
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Nguinkal JA, Brunner RM, Verleih M, Rebl A, de Los Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch ( Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes (Basel) 2019; 10:E708. [PMID: 31540274 PMCID: PMC6770990 DOI: 10.3390/genes10090708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 01/14/2023] Open
Abstract
The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
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Affiliation(s)
- Julien Alban Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Ronald Marco Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Frieder Hadlich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marcus Stüeken
- State Research Center of Agriculture and Fisheries M-V, 17194 Hohen Wangelin, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
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29
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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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30
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Guo B, Fang B, Shikano T, Momigliano P, Wang C, Kravchenko A, Merilä J. A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus
Pungitius. Mol Ecol 2019; 28:4046-4064. [DOI: 10.1111/mec.15204] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 07/04/2019] [Accepted: 08/01/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Baocheng Guo
- The Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Bohao Fang
- Ecological Genetics Research Unit Research Programme in Organismal and Evolutionary Biology Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Takahito Shikano
- Ecological Genetics Research Unit Research Programme in Organismal and Evolutionary Biology Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Paolo Momigliano
- Ecological Genetics Research Unit Research Programme in Organismal and Evolutionary Biology Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Cui Wang
- Ecological Genetics Research Unit Research Programme in Organismal and Evolutionary Biology Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Alexandra Kravchenko
- Laboratory of Ichthyology Institute of Marine Biology Far East Branch of Russian Academy of Sciences Vladivostok Russia
| | - Juha Merilä
- Ecological Genetics Research Unit Research Programme in Organismal and Evolutionary Biology Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
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31
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Cantalice KM, Martínez-Melo A, Romero-Mayén VA. The paleoichthyofauna housed in the Colección Nacional de Paleontología of Universidad Nacional Autónoma de México. ZOOSYST EVOL 2019. [DOI: 10.3897/zse.95.35435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fishes are a paraphyletic group composed by craniates except for the four-limbed clade Tetrapoda. This group was the only vertebrate representative until the Devonian but now comprises almost half of the vertebrate species, dominating nearly all aquatic environments. The fossil record is the key to understand the ancient paleobiodiversity and the patterns that lead the modern fish fauna, and paleontological collections play a fundamental role in providing accommodation, maintenance, and access to the specimens and their respective metadata. Here we present a systematic checklist of fossil fishes housed in the type collection of the Colección Nacional de Paleontología which is located at the Instituto de Geología of Universidad Nacional Autónoma de México. Currently housed in the type collection are 14 chondrichthyan specimens, belonging to two superorders, five orders, seven families, 10 genera, and five nominal species, and 361 osteichthyan specimens, belonging to eight orders, nine families, nine genera, and 26 nominal species. These fossils come from 32 localities and 15 geological units, which range temporally from the Jurassic to the Pleistocene. The paleoichthyofauna housed in the type collection of the Colección Nacional de Paleontología is remarkable for its singularity and reveals new insights about the origin and diversification of many groups of fishes. The recovery and curation of this fossil material indicates that knowledge of Mexican fossil fish diversity and its role in understanding lower vertebrate evolution are just emerging and reaffirms the importance of the biological and paleontological collections to the future biodiversity research.
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32
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Ulloa-Rodríguez P, Contreras P, Dumorné K, Figueroa E, Risopatrón J, Valdebenito I, Farías JG. Sperm morphology and ultrastructure of Patagonian blenny (Eleginops maclovinus). Tissue Cell 2019; 57:66-69. [PMID: 30947965 DOI: 10.1016/j.tice.2019.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
In this study, the morphology and ultrastructure of Eleginops maclovinus spermatozoa were characterized through scanning and electron microscopy. Findings revealed that E. maclovinus spermatozoa can be differentiated into three major parts: a spherical head without acrosome (typical for externally fertilizing teleost), a midpiece containing 2-5 spherical mitochondria, and a long flagellum. The mean length of the spermatozoa was 40.08 ± 2.30 μm, with flagella accounting for 38.38 ± 2.08 μm. The head was 1.31 ± 0.17 μm long, and 1.63 ± 0.01 μm wide. The midpiece was 0.39 ± 0.05 μm in length and 0.95 ± 0.12 μm in width. It was located below the nucleus and contained 2 to 5 spherical mitochondria. The mitochondria were separated from the axoneme by a cytoplasmic canal. There was no evidence of the flagellum membrane forming sidefins, and the axoneme was composed of the typical 9 + 2 microtubular doublet structure enclosed by cell membrane. The present study reveals that E. maclovinus sperm can be categorized as a primitive type. This study is the first to provide comprehensive details on the ultrastructure of spermatozoa in E. maclovinus.
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Affiliation(s)
- Patricio Ulloa-Rodríguez
- Department of Chemistry Engineering, La Frontera University, Temuco, Chile; Center of Biotechnology in Reproduction (CEBIOR-BIOREN), La Frontera University, Temuco, Chile.
| | - Pablo Contreras
- Center of Biotechnology in Reproduction (CEBIOR-BIOREN), La Frontera University, Temuco, Chile; School of Aquaculture, Catholic University of Temuco, Temuco, Chile.
| | - Kelly Dumorné
- Department of Chemistry Engineering, La Frontera University, Temuco, Chile; Center of Biotechnology in Reproduction (CEBIOR-BIOREN), La Frontera University, Temuco, Chile.
| | - Elías Figueroa
- School of Aquaculture, Catholic University of Temuco, Temuco, Chile; Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.
| | - Jennie Risopatrón
- Center of Biotechnology in Reproduction (CEBIOR-BIOREN), La Frontera University, Temuco, Chile.
| | - Iván Valdebenito
- School of Aquaculture, Catholic University of Temuco, Temuco, Chile.
| | - Jorge G Farías
- Department of Chemistry Engineering, La Frontera University, Temuco, Chile; Center of Biotechnology in Reproduction (CEBIOR-BIOREN), La Frontera University, Temuco, Chile.
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Marcionetti A, Rossier V, Roux N, Salis P, Laudet V, Salamin N. Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones. Genome Biol Evol 2019; 11:869-882. [PMID: 30830203 PMCID: PMC6430985 DOI: 10.1093/gbe/evz042] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2019] [Indexed: 02/06/2023] Open
Abstract
Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones. This mutualism is particularly interesting as it likely acted as the key innovation that triggered clownfish adaptive radiation. Indeed, after the acquisition of the mutualism, clownfishes diversified into multiple ecological niches linked with host and habitat use. However, despite the importance of this mutualism, the genetic mechanisms allowing clownfishes to interact with sea anemones are still unclear. Here, we used a comparative genomics and molecular evolutionary analyses to investigate the genetic basis of clownfish mutualism with sea anemones. We assembled and annotated the genome of nine clownfish species and one closely related outgroup. Orthologous genes inferred between these species and additional publicly available teleost genomes resulted in almost 16,000 genes that were tested for positively selected substitutions potentially involved in the adaptation of clownfishes to live in sea anemones. We identified 17 genes with a signal of positive selection at the origin of clownfish radiation. Two of them (Versican core protein and Protein O-GlcNAse) show particularly interesting functions associated with N-acetylated sugars, which are known to be involved in sea anemone discharge of toxins. This study provides the first insights into the genetic mechanisms of clownfish mutualism with sea anemones. Indeed, we identified the first candidate genes likely to be associated with clownfish protection form sea anemones, and thus the evolution of their mutualism. Additionally, the genomic resources acquired represent a valuable resource for further investigation of the genomic basis of clownfish adaptive radiation.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
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34
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Verma CR, Kumkar P, Raghavan R, Katwate U, Paingankar MS, Dahanukar N. Glass in the water: Molecular phylogenetics and evolution of Indian glassy perchlets (Teleostei: Ambassidae). J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chandani R. Verma
- Department of Zoology; Modern College of Arts, Science and Commerce; Pune India
| | - Pradeep Kumkar
- Department of Zoology; Modern College of Arts, Science and Commerce; Pune India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management; Kerala University of Fisheries and Ocean Studies (KUFOS); Kochi India
| | - Unmesh Katwate
- Bombay Natural History Society (BNHS); Mumbai India
- School of Ocean Science and Technology; Kerala University of Fisheries and Ocean Studies (KUFOS); Kochi India
| | | | - Neelesh Dahanukar
- Indian Institute of Science Education and Research (IISER); Pune India
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35
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Arratia G, Quezada-Romegialli C. The South American and Australian percichthyids and perciliids. What is new about them? NEOTROPICAL ICHTHYOLOGY 2019. [DOI: 10.1590/1982-0224-20180102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT A study including morphological characters and mitogenomics of South American and Australian fishes previously assigned to Percichthyidae was conducted. Results generated from these different data sets reveal major disagreements concerning the content and interpretation of the so-called percichthyids. A phylogenetic analysis based on 54 morphological characters suggests the existence of two major clades: (1) Percichthyidae, including the South American Percichthys and the Australian taxa Macquaria australasica, Macquaria (= Plectroplites), and Maccullochella; (2) Perciliidae with the South American genus Percilia at the base plus more advanced Australian genera Nannoperca, Nannatherina, Bostockia, and Gadopsis. In contrast, molecular and mitogenomic evidence suggests only one clade (Percichthyidae), with the exclusion of species of Macquaria (= Percalates). Additionally, the results reveal the existence of various taxonomic problems, such as the current interpretation of only one species of Percichthys in Argentina, an interpretation that is not supported by the present study; the existence of cryptic species of Percilia as well as of Gadopsis, Nannoperca, and Macquaria that will increase the diversity of the genera; and the need for an extensive revision of species previously assigned to Percalates versus Macquaria. Disagreements point to the need to develop further research on the so-called percichthyids and perciliids.
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36
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Ghedotti MJ, Gruber JN, Barton RW, Davis MP, Smith WL. Morphology and evolution of bioluminescent organs in the glowbellies (Percomorpha: Acropomatidae) with comments on the taxonomy and phylogeny of Acropomatiformes. J Morphol 2018; 279:1640-1653. [DOI: 10.1002/jmor.20894] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/09/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Ryan W. Barton
- Department of Biology; Regis University; Denver Colorado
| | - Matthew P. Davis
- Department of Biological Sciences; St. Cloud State University; St. Cloud Minnesota
| | - W. Leo Smith
- Department of Ecology and Evolutionary Biology and Biodiversity Institute; University of Kansas; Lawrence Kansas
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37
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Campbell MA, Sado T, Shinzato C, Koyanagi R, Okamoto M, Miya M. Multilocus phylogenetic analysis of the first molecular data from the rare and monotypic Amarsipidae places the family within the Pelagia and highlights limitations of existing data sets in resolving pelagian interrelationships. Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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38
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Abstract
The Cretaceous-Palaeogene (K-Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K-Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic. Recent multilocus studies have provided the first resolved phylogenetic backbone for acanthomorphs and suggested novel relationships among major lineages. However, these new relationships and associated timescales have not been interrogated using phylogenomic approaches. Here, we use targeted enrichment of >1,000 ultraconserved elements in conjunction with a divergence time analysis to resolve relationships among 120 major acanthomorph lineages and provide a new timescale for acanthomorph radiation. Our results include a well-supported topology that strongly resolves relationships along the acanthomorph backbone and the recovery of several new relationships within six major percomorph subclades. Divergence time analyses also reveal that crown ages for five of these subclades, and for the bulk of the species diversity in the sixth, coincide with the K-Pg boundary, with divergences between anatomically and ecologically distinctive suprafamilial clades concentrated in the first 10 million years of the Cenozoic.
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Davis AM, Betancur-R R. Widespread ecomorphological convergence in multiple fish families spanning the marine-freshwater interface. Proc Biol Sci 2018; 284:rspb.2017.0565. [PMID: 28515206 DOI: 10.1098/rspb.2017.0565] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/19/2017] [Indexed: 11/12/2022] Open
Abstract
The theoretical definition and quantification of convergence is an increasingly topical focus in evolutionary research, with particular growing interest on study scales spanning deep phylogenetic divergences and broad geographical areas. While much progress has recently been made in understanding the role of convergence in driving terrestrial (e.g. anole lizards) and aquatic (e.g. cichlids) radiations, little is known about its macroevolutionary effects across environmental gradients. This study uses a suite of recently developed comparative approaches integrating diverse aspects of morphology, dietary data, habitat affiliation and phylogeny to assess convergence across several well-known tropical-temperate fish families in the percomorph suborder Terapontoidei, a clade with considerable phenotypic and ecological diversity radiating in both marine and freshwater environments. We demonstrate significant widespread convergence across many lineages occupying equivalent trophic niches, particularly feeding habits such as herbivory and biting of attached prey off hard substrates. These include several examples of convergent morphotypes evolving independently in marine and freshwater clades, separated by deep evolutionary divergences (tens of millions of years). The Terapontoidei present a new example of the macroevolutionary dynamics of morphological and ecological coevolution in relation to habitat and trophic preferences, at a greater phylogenetic and habitat scale than most well-studied adaptive radiations.
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Affiliation(s)
- Aaron M Davis
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), and School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia .,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 159, Washington, DC 20013-7012, USA
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 159, Washington, DC 20013-7012, USA.,Department of Biology, University of Puerto Rico, Río Piedras, PO Box 23360, San Juan, Puerto Rico 00931, USA
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Damerau M, Freese M, Hanel R. Multi-gene phylogeny of jacks and pompanos (Carangidae), including placement of monotypic vadigo Campogramma glaycos. JOURNAL OF FISH BIOLOGY 2018; 92:190-202. [PMID: 29193148 DOI: 10.1111/jfb.13509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
In this study, the phylogenetic trees of jacks and pompanos (Carangidae), an ecologically and morphologically diverse, globally distributed fish family, are inferred from a complete, concatenated data set of two mitochondrial (cytochrome c oxidase I, cytochrome b) loci and one nuclear (myosin heavy chain 6) locus. Maximum likelihood and Bayesian inferences are largely congruent and show a clear separation of Carangidae into the four subfamilies: Scomberoidinae, Trachinotinae, Naucratinae and Caranginae. The inclusion of the carangid sister lineages Coryphaenidae (dolphinfishes) and Rachycentridae (cobia), however, render Carangidae paraphyletic. The phylogenetic trees also show with high statistical support that the monotypic vadigo Campogramma glaycos is the sister to all other species within the Naucratinae.
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Affiliation(s)
- M Damerau
- Johann Heinrich von Thünen Institute, Thünen Institute of Fisheries Ecology, Palmaille 9, 22767, Hamburg, Germany
| | - M Freese
- Johann Heinrich von Thünen Institute, Thünen Institute of Fisheries Ecology, Palmaille 9, 22767, Hamburg, Germany
| | - R Hanel
- Johann Heinrich von Thünen Institute, Thünen Institute of Fisheries Ecology, Palmaille 9, 22767, Hamburg, Germany
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41
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Ahn H, Lee C, Nam BH, Kim EB, Caetano-Anolles K, Kim H. Selective pressure on the protein-coding genes of the pufferfish is correlated with phenotypic traits. Mar Genomics 2017; 37:182-186. [PMID: 29273445 DOI: 10.1016/j.margen.2017.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/04/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
Abstract
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database. In order to detect selective pressure on protein-coding sequences, we performed dN/dS estimation using codeml within the PAML software package. We selected one to one orthologous genes among seven fish species (Gasterosteus aculeatus, Oryzias latipes, Poecilia formosa, Takifugu rubripes, Tetraodon nigroviridis, and Xiphophorus maculatus). Results of dN/dS analysis on orthologous genes indicate that pufferfish showed high non-synonymous substitution rate for positively selected genes, and the evolutionary rate was faster during the diversification of two pufferfishes after divergence. Additionally, a candidate mechanism for regulation of neuro-toxicity of tetrodotoxin was identified from functional annotation of positively selected genes. These results support positive selection on protein-coding genes of the pufferfish with the acquisition of specific phenotypic traits.
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Affiliation(s)
- Hyeonju Ahn
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research & Development Institute, Busan 619-705, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Kelsey Caetano-Anolles
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea.
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Anoplodiscus Sonsino, 1890 (Monogenea: Anoplodiscidae): a new Australian species, and the first African record from South African hosts. Syst Parasitol 2017; 94:891-906. [PMID: 28864960 DOI: 10.1007/s11230-017-9750-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
Abstract
Species of Anoplodiscus Sonsino, 1890 were previously only known from host members of Sparidae. A new species, Anoplodiscus hutsonae n. sp. is proposed for museum specimens originally collected from species of Scolopsis Cuvier (Nemipteridae) off Heron Island and Lizard Island, Australia. Additionally, Anoplodiscus tai Ogawa, 1994 is synonymised with Anoplodiscus cirrusspiralis Roubal, Armitage & Rohde, 1983 due to a lack of support for differential characters, and Anoplodiscus richiardii is considered a species inquirenda. Anoplodiscus cirrusspiralis causes visible lesions on the skin and fins of its host, and may also contribute to poor food conversion rates in sparid aquaculture. Anoplodiscus cirrusspiralis has been recorded from cultured sparids in Australia, Japan, South Africa, and South Korea, and was implicated as a disease agent in fish from the former two countries. However, the discovery of A. cirrusspiralis on Chrysoblephus gibbiceps (Valenciennes), Ch. laticeps (Valenciennes) and Cymatoceps nasutus (Castelnau) in South Africa, ?Pagrus major (Temminck & Schlegel) in South Korea, and P. auratus (Forster) in Australia, New Zealand and Japan suggests that this species may have a wide distribution and low host-specificity within the Sparidae. In South Africa, A. cirrusspiralis was first encountered on a morbid C. nasutus and Ch. gibbiceps from two public aquaria in 2009 (Two Oceans Aquarium, Cape Town and uShaka Sea World, Durban, respectively). Additional material was collected from C. laticeps kept at an abalone farm in Hermanus that originated from Struisbaai on the South African south coast. Anoplodiscus cirrusspiralis is redescribed from the South African specimens. This is the first record of a member of Anoplodiscidae Tagliani, 1912 from Africa.
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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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Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Mol Phylogenet Evol 2017; 113:33-48. [PMID: 28487262 DOI: 10.1016/j.ympev.2017.05.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/23/2022]
Abstract
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.
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Hung KW, Russell BC, Chen WJ. Molecular systematics of threadfin breams and relatives (Teleostei, Nemipteridae). ZOOL SCR 2017. [DOI: 10.1111/zsc.12237] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kuo-Wei Hung
- Institute of Oceanography; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Barry C. Russell
- Museum & Art Gallery of the Northern Territory; PO Box 4646 Darwin NT 0801 Australia
| | - Wei-Jen Chen
- Institute of Oceanography; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
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Dornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Mol Phylogenet Evol 2017; 110:27-38. [PMID: 28254474 DOI: 10.1016/j.ympev.2017.02.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 02/22/2017] [Accepted: 02/25/2017] [Indexed: 11/17/2022]
Abstract
Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA.
| | - Jeffrey P Townsend
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Biostatistics, Yale University, New Haven, CT 06510, USA
| | - Willa Brooks
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Elizabeth Spriggs
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Ron I Eytan
- Marine Biology Department, Texas A&M University at Galveston, Galveston, TX 77554, USA
| | - Jon A Moore
- Florida Atlantic University, Wilkes Honors College, Jupiter, FL 33458, USA; Florida Atlantic University, Harbor Branch Oceanographic Institution, Fort Pierce, FL 34946, USA
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California, Davis, CA 95616, USA
| | - Alan Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol 2016; 17:258. [PMID: 27993155 PMCID: PMC5168715 DOI: 10.1186/s13059-016-1126-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. Results We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. Conclusions The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1126-6) contains supplementary material, which is available to authorized users.
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Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol Biol 2016; 16:224. [PMID: 27769164 PMCID: PMC5073739 DOI: 10.1186/s12862-016-0786-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/30/2016] [Indexed: 11/26/2022] Open
Abstract
Background Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes. Results We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years. Conclusions The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0786-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard C Harrington
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK. .,Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA.
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77553, USA
| | - W Leo Smith
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK.,Museum of Paleontology and Department of Earth and Environmental Science, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA
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Costa WJEM. Inferring Evolution of Habitat Usage and Body Size in Endangered, Seasonal Cynopoeciline Killifishes from the South American Atlantic Forest through an Integrative Approach (Cyprinodontiformes: Rivulidae). PLoS One 2016; 11:e0159315. [PMID: 27428070 PMCID: PMC4948875 DOI: 10.1371/journal.pone.0159315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/30/2016] [Indexed: 11/23/2022] Open
Abstract
Cynopoecilines comprise a diversified clade of small killifishes occurring in the Atlantic Forest, one of the most endangered biodiversity hotspots in the world. They are found in temporary pools of savannah-like and dense forest habitats, and most of them are highly threatened with extinction if not already extinct. The greatest gap in our knowledge of cynopoecilines stems from the absence of an integrative approach incorporating molecular phylogenetic data of species still found in their habitats with phylogenetic data taken from the rare and possibly extinct species without accessible molecular information. An integrative analysis combining 115 morphological characters with a multigene dataset of 2,108 bp comprising three nuclear loci (GLYT1, ENC1, Rho), provided a robust phylogeny of cynopoeciline killifishes, which was herein used to attain an accurate phylogenetic placement of nearly extinct species. The analysis indicates that the most recent common ancestor of the Cynopoecilini lived in open vegetation habitats of the Atlantic Forest of eastern Brazil and was a miniature species, reaching between 25 and 28 mm of standard length. The rare cases of cynopoecilines specialized in inhabiting pools within dense forests are interpreted as derived from four independent evolutionary events. Shifts in habitat usage and biogeographic patterns are tentatively associated to Cenozoic paleogeographic events, but the evolutionary history of cynopoecilines may be partially lost by a combination of poor past sampling and recent habitat decline. A sharp evolutionary shift directed to increased body size in a clade encompassing the genera Campellolebias and Cynopoecilus may be related to a parallel acquisition of an internally-fertilizing reproductive strategy, unique among aplocheiloid killifishes. This study reinforces the importance of adding morphological information to molecular databases as a tool to understand the biological complexity of organisms under intense pressure from loss of habitat.
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Affiliation(s)
- Wilson J. E. M. Costa
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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50
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Smith WL, Stern JH, Girard MG, Davis MP. Evolution of Venomous Cartilaginous and Ray-Finned Fishes. Integr Comp Biol 2016; 56:950-961. [DOI: 10.1093/icb/icw070] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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