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D'Aniello S, Bertrand S, Escriva H. Amphioxus as a model to study the evolution of development in chordates. eLife 2023; 12:e87028. [PMID: 37721204 PMCID: PMC10506793 DOI: 10.7554/elife.87028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023] Open
Abstract
Cephalochordates and tunicates represent the only two groups of invertebrate chordates, and extant cephalochordates - commonly known as amphioxus or lancelets - are considered the best proxy for the chordate ancestor, from which they split around 520 million years ago. Amphioxus has been an important organism in the fields of zoology and embryology since the 18th century, and the morphological and genomic simplicity of cephalochordates (compared to vertebrates) makes amphioxus an attractive model for studying chordate biology at the cellular and molecular levels. Here we describe the life cycle of amphioxus, and discuss the natural histories and habitats of the different species of amphioxus. We also describe their use as laboratory animal models, and discuss the techniques that have been developed to study different aspects of amphioxus.
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Affiliation(s)
- Salvatore D'Aniello
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton DohrnNapoliItaly
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
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2
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Murugan R, Ananthan G, Arunkumar A. DNA bar coding of Aplousobranchiata and Phlebobranchiata Ascidians (Phylum:Chordata) inferred from mitochondrial cytochrome oxidase subunit I (COI) gene sequence approach in Andaman and Nicobar Islands, India: a first report. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:285-297. [PMID: 32729766 DOI: 10.1080/24701394.2020.1798417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ascidians (Phylum: Chordata) are sessile and filter-feeding marine animal, species identification of ascidians is possible by observing various morphological and anatomical features in various stages of life span. However, this method is labor intensive, time-consuming and very difficult for non-specialists particularly when dealing with field collections. Suborder Aplousobranchiata and Phlebobranchiata is the largest group of tunicates within, morphological and molecular data suggest that Didemnidae and Ascidiidae are monophyletic, but the monophyly of each genus and their phylogenetic relationships are still poorly understood. Therefore, this study was aimed to develop DNA barcodes of ascidians belonging to the orders of Aplousobranchiata and Phlebobranchiata species namely Diplosoma listerianum, Lissoclinum fragile, Didemnum psammatode, Phallusia fumigata and Phallusia ingeria collected from Andaman and Nicobar Islands were sequenced and submitted in Gen Bank. Colony structure, Scanning Electron Microscope (SEM) for spicules of colonial ascidians, larval type and zooids formation were found to be the most useful morphological characters for discriminating the species. Our BLAST results proved D. Listerianum KP842724 (98%) L. fragile KP842726 (100%) D. psammatode KP779902 (99%), P. fumigata KP779904 (99%) and P. ingeria KP842727 (100%) similarity and this is the first report of mitochondrial COI gene of these ascidians from Andaman and Nicobar Islands. We explored the usefulness of CO1 gene sequences for molecular level identification and mtDNA data in assessing a phylogenetic relationship of ascidian species.
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Affiliation(s)
- Rajaram Murugan
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, India
| | - Gnanakkan Ananthan
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, India
| | - Anandakumar Arunkumar
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, India
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3
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DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. Genome Biol Evol 2020; 12:948-964. [PMID: 32211845 PMCID: PMC7337526 DOI: 10.1093/gbe/evaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.
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Affiliation(s)
- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
| | - William N Colgan
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Lincoln Harris
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
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4
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Ortega A, Olivares-Bañuelos TN. Neurons and Glia Cells in Marine Invertebrates: An Update. Front Neurosci 2020; 14:121. [PMID: 32132895 PMCID: PMC7040184 DOI: 10.3389/fnins.2020.00121] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
The nervous system (NS) of invertebrates and vertebrates is composed of two main types of cells: neurons and glia. In both types of organisms, nerve cells have similarities in biochemistry and functionality. The neurons are in charge of the synapse, and the glial cells are in charge of important functions of neuronal and homeostatic modulation. Knowing the mechanisms by which NS cells work is important in the biomedical area for the diagnosis and treatment of neurological disorders. For this reason, cellular and animal models to study the properties and characteristics of the NS are always sought. Marine invertebrates are strategic study models for the biological sciences. The sea slug Aplysia californica and the squid Loligo pealei are two examples of marine key organisms in the neurosciences field. The principal characteristic of marine invertebrates is that they have a simpler NS that consists of few and larger cells, which are well organized and have accessible structures. As well, the close phylogenetic relationship between Chordata and Echinodermata constitutes an additional advantage to use these organisms as a model for the functionality of neuronal cells and their cellular plasticity. Currently, there is great interest in analyzing the signaling processes between neurons and glial cells, both in vertebrates and in invertebrates. However, only few types of glial cells of invertebrates, mostly insects, have been studied, and it is important to consider marine organisms' research. For this reason, the objective of the review is to present an update of the most relevant information that exists around the physiology of marine invertebrate neuronal and glial cells.
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Affiliation(s)
- Arturo Ortega
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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5
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Bessho-Uehara M, Yamamoto N, Shigenobu S, Mori H, Kuwata K, Oba Y. Kleptoprotein bioluminescence: Parapriacanthus fish obtain luciferase from ostracod prey. SCIENCE ADVANCES 2020; 6:eaax4942. [PMID: 31934625 PMCID: PMC6949039 DOI: 10.1126/sciadv.aax4942] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Through their diet, animals can obtain substances essential for imparting special characteristics, such as toxins in monarch butterflies and luminescent substances in jellyfishes. These substances are typically small molecules because they are less likely to be digested and may be hard for the consumer to biosynthesize. Here, we report that Parapriacanthus ransonneti, a bioluminescent fish, obtains not only its luciferin but also its luciferase enzyme from bioluminescent ostracod prey. The enzyme purified from the fish's light organs was identical to the luciferase of Cypridina noctiluca, a bioluminescent ostracod that they feed upon. Experiments where fish were fed with a related ostracod, Vargula hilgendorfii, demonstrated the specific uptake of the luciferase to the fish's light organs. This "kleptoprotein" system allows an organism to use novel functional proteins that are not encoded in its genome and provides an evolutionary alternative to DNA-based molecular evolution.
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Affiliation(s)
- Manabu Bessho-Uehara
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Environmental Biology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Naoyuki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Hitoshi Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Keiko Kuwata
- Graduate School of Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuichi Oba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Environmental Biology, Chubu University, Kasugai, Aichi 487-8501, Japan
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6
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Topper TP, Guo J, Clausen S, Skovsted CB, Zhang Z. A stem group echinoderm from the basal Cambrian of China and the origins of Ambulacraria. Nat Commun 2019; 10:1366. [PMID: 30911013 PMCID: PMC6433856 DOI: 10.1038/s41467-019-09059-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 02/15/2019] [Indexed: 11/21/2022] Open
Abstract
Deuterostomes are a morphologically disparate clade, encompassing the chordates (including vertebrates), the hemichordates (the vermiform enteropneusts and the colonial tube-dwelling pterobranchs) and the echinoderms (including starfish). Although deuterostomes are considered monophyletic, the inter-relationships between the three clades remain highly contentious. Here we report, Yanjiahella biscarpa, a bilaterally symmetrical, solitary metazoan from the early Cambrian (Fortunian) of China with a characteristic echinoderm-like plated theca, a muscular stalk reminiscent of the hemichordates and a pair of feeding appendages. Our phylogenetic analysis indicates that Y. biscarpa is a stem-echinoderm and not only is this species the oldest and most basal echinoderm, but it also predates all known hemichordates, and is among the earliest deuterostomes. This taxon confirms that echinoderms acquired plating before pentaradial symmetry and that their history is rooted in bilateral forms. Yanjiahella biscarpa shares morphological similarities with both enteropneusts and echinoderms, indicating that the enteropneust body plan is ancestral within hemichordates. The early evolution of the deuterostomes is not well resolved. Here, Topper and colleagues investigate the early Cambrian metazoan Yanjiahella biscarpa, concluding that it is a stem echinoderm, is among the oldest known deuterstomes, and supports an ancestral enteropneust body plan in hemichordates.
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Affiliation(s)
- Timothy P Topper
- Shaanxi Key Laboratory of Early Life and Environments, State Key Laboratory of Continental Dynamics and Department of Geology, Northwest University, 710069, Xi'an, China. .,Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 104 05, Stockholm, Sweden. .,Department of Earth Sciences, Durham University, Durham, DH1 3LE, UK.
| | - Junfeng Guo
- School of Earth Science and Resources, Key Laboratory for the study of Focused Magmatism and Giant Ore Deposits, MLR, Chang'an University, 710054, Xi'an, China
| | | | - Christian B Skovsted
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, 104 05, Stockholm, Sweden
| | - Zhifei Zhang
- Shaanxi Key Laboratory of Early Life and Environments, State Key Laboratory of Continental Dynamics and Department of Geology, Northwest University, 710069, Xi'an, China
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7
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Phylogenomics offers resolution of major tunicate relationships. Mol Phylogenet Evol 2018; 121:166-173. [DOI: 10.1016/j.ympev.2018.01.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/15/2017] [Accepted: 01/08/2018] [Indexed: 02/03/2023]
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8
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Murugan R, Ananthan G, Arunkumar A. Aplousobranchia ascidians in Andaman and Nicobar Islands: a combined morphological and molecular discrimination. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:879-884. [PMID: 28920503 DOI: 10.1080/24701394.2017.1376053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Aplousobranchia ascidians from two different families were integrated with morphological characteristics and molecular phylogenetic analysis for the first time. The present study employed morphological descriptions (colony structures, tunic, zooids, spicules stigmata and test) and a molecular approach, using a fragment of the mitochondrial cytochrome oxidase I (COI) gene of four Aplousobranchia colonial ascidians Aplidium conicum (98%), Aplidium elegans (98%), Didemnum fulgens (92%) and Trididemnum cyanophorum (94%) from Andaman and Nicobar Islands. Bar-coded sequences were extracted with BLAST format from NCBI and the heritable diversity of the submitted sequences were compared with associated ascidian species. Study revealed that the evolutionary relationship among the ascidian species exhibited the constant clades, which may help for rapid reassessment of morphological characters of the species distributed worldwide.
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Affiliation(s)
- Rajaram Murugan
- a Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences , Annamalai University , Parangipettai , India
| | - Gnanakkan Ananthan
- a Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences , Annamalai University , Parangipettai , India
| | - Anandakumar Arunkumar
- a Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences , Annamalai University , Parangipettai , India
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9
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Oxley APA, Catalano SR, Wos-Oxley ML, Westlake EL, Grammer GL, Steer MA. Using in situ hybridization to expand the daily egg production method to new fish species. Mol Ecol Resour 2017; 17:1108-1121. [PMID: 28776945 DOI: 10.1111/1755-0998.12707] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 06/22/2017] [Accepted: 07/25/2017] [Indexed: 12/29/2022]
Abstract
The capacity to reliably identify fish eggs is critical in the application of the daily egg production method (DEPM) to estimate biomass of commercially important species. This application has largely been confined to species that have easily identifiable eggs. Various molecular strategies have been used to extend the DEPM to a broader range of species, with recent approaches like in situ hybridization (ISH) that preserves the integrity of whole eggs, embryos or larvae recommended as a suitable alternative over destructive procedures like PCR. Here, we designed and validated an ISH approach for the identification of whole eggs and larvae from Snapper (Chrysophrys auratus) from environmental samples using the mitochondrial 16S rRNA gene as a target for specific horseradish peroxidase (HRP)-conjugated oligonucleotide probes. This colorimetric assay allowed the highly specific detection of positive hybridization signals from intact C. auratus larvae and eggs from mixed-species samples comprising closely related taxa. Furthermore, evaluation of whole eggs across a range of developmental stages revealed the sensitivity of the approach for discerning early stages, thereby guiding staging and the identification of otherwise indistinguishable eggs from environmental samples. This approach represents a major advance from current molecular-based strategies as it is nondestructive and allows for the simultaneous identification and staging of fish eggs (and larvae). The resultant 100% egg identification certainty we have achieved allows the DEPM to be applied to a wider array of fish species and is particularly applicable to species in areas where morphologically similar eggs are being spawned at the same time.
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Affiliation(s)
- Andrew P A Oxley
- South Australian Research and Development Institute Aquatic Sciences Centre, West Beach, SA, Australia
| | - Sarah R Catalano
- South Australian Research and Development Institute Aquatic Sciences Centre, West Beach, SA, Australia
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Honorary Research Associate, South Australian Museum, Adelaide, SA, Australia
| | - Emma L Westlake
- South Australian Research and Development Institute Aquatic Sciences Centre, West Beach, SA, Australia
| | - Gretchen L Grammer
- South Australian Research and Development Institute Aquatic Sciences Centre, West Beach, SA, Australia
| | - Mike A Steer
- South Australian Research and Development Institute Aquatic Sciences Centre, West Beach, SA, Australia
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10
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Nydam ML, Yanckello LM, Bialik SB, Giesbrecht KB, Nation GK, Peak JL. Introgression in two species of broadcast spawning marine invertebrate. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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11
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Ananthan G, Murugan R. Molecular phylogeny of four ascidian species inferred from mitochondrial Cytochrome Oxidase subunit I (COI) sequence. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:121-125. [PMID: 28025899 DOI: 10.1080/24701394.2016.1253071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Ascidians is a crucial group for the studies of deuterostome evolution and the origin of chordates, yet little molecular work has been done to determine the evolutionary relationships and largely unexplored beyond a few species. The phylogenetic analysis are presented for four different species of solitary ascidians, Ascidia virginea, Ascidiella aspersa, Clavelina oblonga and Aplidium fuscum, obtained from Great Nicobar Biosphere reserve (GNBR). Mitochondrial Cytochrome Oxidase subunit 1(COI) gene was amplified and the genetic diversity at the phylogenic level was measured. Bar-coded sequences were extracted with BLAST format from NCBI and the genetic diversity of the submitted sequences were compared with the related ascidian species. Maximum divergences measured among the four species were as follows: Ascidia virginea (96%), Ascidiella aspersa (96%), Clavelina oblonga (94%) and Aplidium fuscum (97%). This is the first report of molecular phylogeny of ascidians from Great Nicobar Biosphere Reserve, Andaman and Nicobar Islands. From this study, we found some stable clades on the evolutionary relationships among these ascidian species that may prompt a reevaluation of some morphological characters.
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Affiliation(s)
- Gnanakkan Ananthan
- a Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences , Annamalai University , Cuddalore , Tamil Nadu , India
| | - Rajaram Murugan
- a Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences , Annamalai University , Cuddalore , Tamil Nadu , India
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12
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The phylogeny, evolutionary developmental biology, and paleobiology of the Deuterostomia: 25 years of new techniques, new discoveries, and new ideas. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0270-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Lin CY, Tung CH, Yu JK, Su YH. Reproductive periodicity, spawning induction, and larval metamorphosis of the hemichordate acorn worm Ptychodera flava. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 326:47-60. [PMID: 26663879 DOI: 10.1002/jez.b.22665] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/24/2015] [Indexed: 02/05/2023]
Abstract
The indirect-developing enteropneust acorn worm Ptychodera flava has been used as a hemichordate model system for studying the developmental evolution of deuterostome body plans and the origins of chordate characteristics. However, research progress has been hindered by the limited accessibility of its embryonic materials and metamorphosing larvae. In this study, we identified an abundant population of P. flava in Penghu, Taiwan, and examined the feasibility of using this animal for developmental studies. Through histological examination, we established that the reproductive season of this population is between September and December, with a peak breeding period in October and November. In addition, we have developed new procedures that can induce P. flava spawning at any time of the day during the breeding season, with a higher successful rate than that achieved using a previously published method. Moreover, the culturing system we developed enables rearing of P. flava larvae through various planktonic stages and eventual metamorphosis into benthic juveniles, all under laboratory conditions. We anticipate that the animal resources and new technical procedures reported here will further facilitate the use of P. flava as a model organism for evolutionary and developmental biology research.
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Affiliation(s)
- Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan.,Department of Aquatic Biosciences, National Chiayi University, Chiayi, Taiwan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
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14
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Gupta RS. Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates. Mol Phylogenet Evol 2015; 94:383-91. [PMID: 26419477 DOI: 10.1016/j.ympev.2015.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 12/12/2022]
Abstract
Members of the phylum Chordata and the subphylum Vertebrata are presently distinguished solely on the basis of morphological characteristics. The relationship of the vertebrates to the two non-vertebrate chordate subphyla is also a subject of debate. Analyses of protein sequences have identified multiple conserved signature indels (CSIs) that are specific for Chordata or for Vertebrata. Five CSIs in 4 important proteins are specific for the Vertebrata, whereas two other CSIs are uniquely found in all sequenced chordate species including Ciona intestinalis and Oikapleura dioica (Tunicates) as well as Branchiostoma floridae (Cephalochordates). The shared presence of these molecular signatures by all vertebrates/chordate species, but in no other animal taxa, strongly indicates that the genetic changes represented by the identified CSIs diagnose monophyletic groups. Two other discovered CSIs are uniquely shared by different vertebrate species and by either one (Ciona intestinalis) or both tunicate (Ciona and Oikapleura) species, but they are not found in Branchiostoma or other animal species. Specific presence of these CSIs in different vertebrates and either one or both tunicate species provides strong independent evidence that the vertebrate species are more closely related to the urochordates (tunicates) than to the cephalochordates.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
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15
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Urata M. Molecular Identification of Ptychodera flava (Hemichordata: Enteropneusta): Reconsideration in Light of Nucleotide Polymorphism in the 18S Ribosomal RNA Gene. Zoolog Sci 2015; 32:307-13. [PMID: 26003987 DOI: 10.2108/zs140144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Seven nuclear and mitochondrial DNA markers were examined in 12 specimens of Ptychodera flava, a model acorn worm used in molecular biology, collected in Japan from three local populations with different modes of living. A comparison of intraspecific results did not show genetically isolated populations despite the species' enclave habitats and asexual reproduction. Moreover, both the nuclear 18S ribosomal RNA gene and mitochondrial 16S ribosomal RNA gene sequences were identical to those from Moorea in French Polynesia, nearly 10,000 kilometers away from Japan. I also provide the first definitive information regarding polymorphisms in 18S ribosomal RNA gene, the external transcribed spacer (ETS), internal transcribed spacers (ITS), and mitochondrial cytochrome c oxidase subunit 1 (mtCO1) sequence in hemichordates using newly designed primer sets, and I show both high larval vagility and certain criteria for the molecular identification of this species.
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Affiliation(s)
- Makoto Urata
- Takehara Marine Science Station, Setouchi Field Science Center, Graduate School of Biosphere Science, Hiroshima University, 5-8-1 Minato-machi, Takehara, Hiroshima 725-0024, Japan
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16
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Tung CH, Cheng YR, Lin CY, Ho JS, Kuo CH, Yu JK, Su YH. A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. THE BIOLOGICAL BULLETIN 2014; 226:69-80. [PMID: 24648208 DOI: 10.1086/bblv226n1p69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Symbiotic copepods compose one-third of the known copepod species and are associated with a wide range of animal groups. Two parasitic copepods endoparasitic in acorn worms (Hemichordata), Ive balanoglossi and Ubius hilli, collected in the Mediterranean Sea and Australian waters, respectively, were described a century ago. Here we report a new parasitic copepod species, Ive ptychoderae sp. nov., found in Ptychodera flava, a widespread acorn worm in the Indo-Pacific Ocean and an emerging organism for developmental and evolutionary studies. The female of I. ptychoderae is characterized by having a reduced maxilliped and five pairs of annular swellings along the body that are morphologically similar but distinguishable from those in the two previously described parasitic copepods in acorn worms. Phylogenetic analysis based on the 18S rDNA sequence shows that I. ptychoderae may belong to Poecilostomatoida but represent a new family, which we name Iveidae fam. nov. Ive ptychoderae is commonly found in the acorn worm population with an average prevalence of 42% during the collecting period. The infection of the parasite induces the formation of cysts and causes localized lesions of the host tissues, suggesting that it may have negative effects on its host. Interestingly, most cysts contain a single female with one or multiple male copepods, suggesting that their sex determination may be controlled by environmental conditions. The relationships between the parasitic copepods and acorn worms thus provide a platform for understanding physiological and ecological influences and coevolution between parasites and hosts.
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Affiliation(s)
- Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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Sheffield NC. The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution. ACTA ACUST UNITED AC 2013. [DOI: 10.5402/2013/391561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Many commonly used models of molecular evolution assume homogeneous nucleotide frequencies. A deviation from this assumption has been shown to cause problems for phylogenetic inference. However, some claim that only extreme heterogeneity affects phylogenetic accuracy and suggest that violations of other model assumptions, such as variable rates among sites, are more problematic. In order to explore the interaction between compositional heterogeneity and variable rates among sites, I reanalyzed 3 real heterogeneous datasets using several models. My Bayesian inference recovers accurate topologies under variable rates-among-sites models, but fails under some models that account for compositional heterogeneity. I also ran simulations and found that accounting for rates among sites improves topology accuracy in compositionally heterogeneous data. This indicates that in some cases, models accounting for among-site rate variation can improve outcomes for data that violates the assumption of compositional homogeneity.
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Affiliation(s)
- Nathan C. Sheffield
- Program in Computational Biology and Bioinformatics, Institute for Genome Sciences and Policy, Duke University, 101 Science Drive, Box 3382, Durham, NC 27708, USA
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Opatova V, Bond JE, Arnedo MA. Ancient origins of the Mediterranean trap-door spiders of the family Ctenizidae (Araneae, Mygalomorphae). Mol Phylogenet Evol 2013; 69:1135-45. [DOI: 10.1016/j.ympev.2013.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 11/15/2022]
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Cannon JT, Swalla BJ, Halanych KM. Hemichordate molecular phylogeny reveals a novel cold-water clade of harrimaniid acorn worms. THE BIOLOGICAL BULLETIN 2013; 225:194-204. [PMID: 24445445 DOI: 10.1086/bblv225n3p194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Hemichordates are instrumental to understanding early deuterostome and chordate evolution, yet diversity and relationships within the group have been understudied. Recently, there has been renewed interest in hemichordate diversity and taxonomy, although current findings suggest that much hemichordate diversity remains to be discovered. Herein, we present a molecular phylogenetic study based on nuclear 18S rDNA sequence data, which includes 35 previously unsampled taxa and represents all recognized hemichordate families. We include mitochondrial 16S rDNA data from 66 enteropneust taxa and three pterobranch Rhabdopleura species, and recover colonial pterobranchs and solitary enteropneusts as reciprocally monophyletic taxa. Our phylogenetic results also reveal a previously unknown clade of at least four species of harrimaniid enteropneusts from cold waters, including Antarctica, the North Atlantic around Iceland and Norway, and the deep sea off Oregon. These small worms (1-5 mm in length), occur from 130 to 2950 m and are not closely related to other deep-sea harrimaniids, indicating that diversity of enteropneusts within the deep sea is broader than previously described in the literature. Discovery of this clade, as well as larger torquaratorids from Antarctica, strengthens hypotheses of close associations between Antarctic and deep-sea fauna.
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Affiliation(s)
- Johanna T Cannon
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, Alabama 36849
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Shylla JA, Ghatani S, Tandon V. Utility of divergent domains of 28S ribosomal RNA in species discrimination of paramphistomes (Trematoda: Digenea: Paramphistomoidea). Parasitol Res 2013; 112:4239-53. [PMID: 24096607 DOI: 10.1007/s00436-013-3616-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/19/2013] [Indexed: 11/29/2022]
Abstract
Among the digenetic trematodes, paramphistomes are known to be the causative agent of "amphistomiasis" or the stomach fluke disease of domestic and wild animals, mainly ruminants. The use of 28S (divergent domains) and 18S rRNA for phylogenetic inference is significantly warranted for these flukes since it is as yet limited to merely the exploration of the second internal transcribed spacer (ITS2) region. The present study intended to explore the divergent domains (D1-D3) of 28S rRNA and simultaneously equate the phylogenetic information with 18S rRNA in paramphistomes. Divergence of the 28S rRNA domains was evident amongst the divergent (D) domains, where D1 domain emerged as the most variable and D2, the most robust domain, since the latter could provide a higher resolution of the species. D2 was the only domain that comprised compensatory mutations in the helices of its structural constraints; this domain is thus well suited for species distinction and may be considered a potential DNA barcode complementary to mitochondrial DNA. 28S (D1 + D2 + D3) rRNA provided a significant resolution of the taxa corroborating with the taxonomy of these flukes and thus proved to be more robust as a phylogenetic marker for lower levels than 18S rRNA. Phylogenetic inferences of paramphitomes are still scarcely explored; additional data from other taxa belonging to this family may estimate better the biodiversity of these flukes.
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Affiliation(s)
- Jollin A Shylla
- Department of Zoology, North-Eastern Hill University, Shillong, 793022, Meghalaya, India
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Osborn KJ, Gebruk AV, Rogacheva A, Holland ND. An externally brooding acorn worm (Hemichordata, Enteropneusta, Torquaratoridae) from the Russian arctic. THE BIOLOGICAL BULLETIN 2013; 225:113-123. [PMID: 24243964 DOI: 10.1086/bblv225n2p113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A single specimen of a previously undescribed acorn worm in the family Torquaratoridae was trawled from a bottom depth of about 350 m in the Kara Sea (Russian Arctic). The new species is the shallowest of the exclusively deep-sea torquaratorids found to date, possibly an example of high-latitude emergence. On the basis of ribosomal DNA sequences and morphology, the worm is described here as the holotype of Coleodesmium karaensis n. gen., n. sp. It is most similar in overall body shape to the previously described enteropneust genus Allapasus, but is uniquely characterized by a tubular component of the proboscis skeleton ensheathing the collar nerve cord. Additionally, within the proboscis, the sparseness of the musculature of C. karaensis clearly distinguishes it from the much more muscular members of Allapasus. The holotype is a female bearing about a dozen embryos on the surface of her pharyngeal region, each recessed within a shallow depression in the dorsal epidermis. The embryos, ranging from late gastrula to an early stage of coelom formation, are a little more than 1 mm in diameter and surrounded by a thin membrane. Each embryo comprises an external ectoderm of monociliated cells (not arranged in obvious ciliated bands) and an internal endo-mesoderm; the blastopore is closed. In the most advanced embryos, the anterior coelom is starting to constrict off from the archenteron. Coleodesmium karaensis is the first enteropneust (and indeed the first hemichordate) found brooding embryos on the surface of the mother's body.
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MESH Headings
- Animals
- Arctic Regions
- Chordata, Nonvertebrate/classification
- Chordata, Nonvertebrate/genetics
- Chordata, Nonvertebrate/physiology
- Chordata, Nonvertebrate/ultrastructure
- Female
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Reproduction
- Russia
- Species Specificity
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Affiliation(s)
- Karen J Osborn
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, Washington, DC 20013-7012
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Czarkwiani A, Dylus DV, Oliveri P. Expression of skeletogenic genes during arm regeneration in the brittle star Amphiura filiformis. Gene Expr Patterns 2013; 13:464-72. [PMID: 24051028 PMCID: PMC3838619 DOI: 10.1016/j.gep.2013.09.002] [Citation(s) in RCA: 42] [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: 03/22/2013] [Revised: 09/05/2013] [Accepted: 09/07/2013] [Indexed: 11/19/2022]
Abstract
Analysis of brittle star regenerating arms using differentiation markers. Identification of the early segregation of skeletal and muscle progenitor cells. Expression of skeletal and non-skeletal genes at different stages of regeneration. Combinatorial role of TF genes in early specification of skeletal cells. Same TF genes identify different skeletal structures later in regeneration.
The brittle star Amphiura filiformis, which regenerates its arms post autotomy, is emerging as a useful model for studying the molecular underpinnings of regeneration, aided by the recent availability of some molecular resources. During regeneration a blastema initially is formed distally to the amputation site, and then a rapid rebuild is obtained by adding metameric units, which will eventually differentiate and become fully functional. In this work we first characterize the developmental process of the regenerating arms using two differentiation markers for muscle and skeletal structures – Afi-trop-1 and Afi-αcoll. Both genes are not expressed in the blastema and newly added undifferentiated metameric units. Their expression at different regenerating stages shows an early segregation of muscle and skeletal cells during the regenerating process, long before the metameric units become functional. We then studied the expression of a set of genes orthologous of the sea urchin transcription factors involved in the development of skeletal and non-skeletal mesoderm: Afi-ets1/2, Afi-alx1, Afi-tbr, Afi-foxB and Afi-gataC. We found that Afi-ets1/2, Afi-alx1, Afi-foxB and Afi-gataC are all expressed at the blastemal stage. As regeneration progresses those genes are expressed in a similar small undifferentiated domain beneath the distal growth cap, while in more advanced metameric units they become restricted to different skeletal domains. Afi-foxB becomes expressed in non-skeletal structures. This suggests that they might play a combinatorial role only in the early cell specification process and that subsequently they function independently in the differentiation of different structures. Afi-tbr is not present in the adult arm tissue at any stage of regeneration. In situ hybridization results have been confirmed with a new strategy for quantitative PCR (QPCR), using a subdivision of the three stages of regeneration into proximal (differentiated) and distal (undifferentiated) arm segments.
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Affiliation(s)
- Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, UCL, Gower Street, London WC1E 6BT, UK
| | - David V. Dylus
- Research Department of Genetics, Evolution and Environment, UCL, Gower Street, London WC1E 6BT, UK
- CoMPLEX/SysBio, UCL, Gower Street, London WC1E 6BT, UK
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, UCL, Gower Street, London WC1E 6BT, UK
- Corresponding author. Address: Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London WC1E 6BT, UK. Tel.: +44 020 767 93719; fax: +44 020 7679 7193.
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Merker S, Gruhl A, Stach T. Comparative anatomy of the heart–glomerulus complex of Cephalodiscus gracilis (Pterobranchia): structure, function, and phylogenetic implications. ZOOMORPHOLOGY 2013. [DOI: 10.1007/s00435-013-0200-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Ikuta T, Chen YC, Annunziata R, Ting HC, Tung CH, Koyanagi R, Tagawa K, Humphreys T, Fujiyama A, Saiga H, Satoh N, Yu JK, Arnone MI, Su YH. Identification of an intact ParaHox cluster with temporal colinearity but altered spatial colinearity in the hemichordate Ptychodera flava. BMC Evol Biol 2013; 13:129. [PMID: 23802544 PMCID: PMC3698058 DOI: 10.1186/1471-2148-13-129] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 06/19/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND ParaHox and Hox genes are thought to have evolved from a common ancestral ProtoHox cluster or from tandem duplication prior to the divergence of cnidarians and bilaterians. Similar to Hox clusters, chordate ParaHox genes including Gsx, Xlox, and Cdx, are clustered and their expression exhibits temporal and spatial colinearity. In non-chordate animals, however, studies on the genomic organization of ParaHox genes are limited to only a few animal taxa. Hemichordates, such as the Enteropneust acorn worms, have been used to gain insights into the origins of chordate characters. In this study, we investigated the genomic organization and expression of ParaHox genes in the indirect developing hemichordate acorn worm Ptychodera flava. RESULTS We found that P. flava contains an intact ParaHox cluster with a similar arrangement to that of chordates. The temporal expression order of the P. flava ParaHox genes is the same as that of the chordate ParaHox genes. During embryogenesis, the spatial expression pattern of PfCdx in the posterior endoderm represents a conserved feature similar to the expression of its orthologs in other animals. On the other hand, PfXlox and PfGsx show a novel expression pattern in the blastopore. Nevertheless, during metamorphosis, PfXlox and PfCdx are expressed in the endoderm in a spatially staggered pattern similar to the situation in chordates. CONCLUSIONS Our study shows that P. flava ParaHox genes, despite forming an intact cluster, exhibit temporal colinearity but lose spatial colinearity during embryogenesis. During metamorphosis, partial spatial colinearity is retained in the transforming larva. These results strongly suggest that intact ParaHox gene clustering was retained in the deuterostome ancestor and is correlated with temporal colinearity.
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Affiliation(s)
- Tetsuro Ikuta
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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Peterson KJ, Su YH, Arnone MI, Swalla B, King BL. MicroRNAs support the monophyly of enteropneust hemichordates. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:368-74. [PMID: 23703796 DOI: 10.1002/jez.b.22510] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/28/2013] [Accepted: 04/06/2013] [Indexed: 01/24/2023]
Abstract
Understanding the evolutionary history of deuterostomes requires elucidating the phylogenetic interrelationships amongst the constituent taxa. Although the monophyly and interrelationships among the three principal groups-the chordates, the echinoderms, and the hemichordates-are well established, as are the internal relationships among the echinoderm and chordate taxa, the interrelationships among the principal groups of hemichordates-the harrimaniid enteropneusts, the ptychoderid enteropneusts, and the pterobranchs-remain unresolved. Depending on the study some find enteropneusts paraphyletic with pterobranchs (e.g., Cephalodiscus) more closely related to the harrimaniid enteropneusts (e.g., Saccoglossus) than either are to the ptychoderid enteropneusts (e.g., Ptychodera), whereas other studies support a monophyletic Enteropneusta. To try and resolve between these two competing hypotheses, we turned to microRNAs, small ∼22 nt non-coding RNA genes that have been shown to shed insight into particularly difficult phylogenetic questions. Using deep sequencing we characterized the small RNA repertoires of two hemichordate species, Cephalodiscus hodgsoni and Ptychodera flava, and the crinoid echinoderm Antedon mediterranea, and combined our results with the described complements of the hemichordate Saccoglossus kowalevskii, the sea urchin Strongylocentrotus purpuratus, and the starfish Patiria miniata. Our data unambiguously support the monophyly of Enteropneusts as S. kowalevskii shares 12 miRNA sequences with P. flava that are not present in the C. hodgsoni or A. mediterranea libraries, and have never been reported from another metazoan taxon. Thus, these data resolve the phylogenetic position of pterobranchs, ultimately allowing for a better understanding of body plan evolution throughout the deuterostomes.
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Affiliation(s)
- Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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Mashanov VS, Zueva OR, García-Arrarás JE. Radial glial cells play a key role in echinoderm neural regeneration. BMC Biol 2013; 11:49. [PMID: 23597108 PMCID: PMC3652774 DOI: 10.1186/1741-7007-11-49] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022] Open
Abstract
Background Unlike the mammalian central nervous system (CNS), the CNS of echinoderms is capable of fast and efficient regeneration following injury and constitutes one of the most promising model systems that can provide important insights into evolution of the cellular and molecular events involved in neural repair in deuterostomes. So far, the cellular mechanisms of neural regeneration in echinoderm remained obscure. In this study we show that radial glial cells are the main source of new cells in the regenerating radial nerve cord in these animals. Results We demonstrate that radial glial cells of the sea cucumber Holothuria glaberrima react to injury by dedifferentiation. Both glia and neurons undergo programmed cell death in the lesioned CNS, but it is the dedifferentiated glial subpopulation in the vicinity of the injury that accounts for the vast majority of cell divisions. Glial outgrowth leads to formation of a tubular scaffold at the growing tip, which is later populated by neural elements. Most importantly, radial glial cells themselves give rise to new neurons. At least some of the newly produced neurons survive for more than 4 months and express neuronal markers typical of the mature echinoderm CNS. Conclusions A hypothesis is formulated that CNS regeneration via activation of radial glial cells may represent a common capacity of the Deuterostomia, which is not invoked spontaneously in higher vertebrates, whose adult CNS does not retain radial glial cells. Potential implications for biomedical research aimed at finding the cure for human CNS injuries are discussed.
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Affiliation(s)
- Vladimir S Mashanov
- Department of Biology, University of Puerto Rico, San Juan, PR 00936-8377, USA.
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MALLATT JON, HOLLAND NICHOLAS. Pikaia gracilensWalcott: Stem Chordate, or Already Specialized in the Cambrian? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:247-71. [DOI: 10.1002/jez.b.22500] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 03/11/2013] [Indexed: 12/25/2022]
Affiliation(s)
- JON MALLATT
- School of Biological Sciences; Washington State University; Pullman; Washington
| | - NICHOLAS HOLLAND
- Scripps Institution of Oceanography; University of California; San Diego, La Jolla; California
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Gou H, Guan G, Ma M, Liu A, Liu Z, Ren Q, Li Y, Yang J, Chen Z, Yin H, Luo J. Phylogenetic analysis based on 28S rRNA of Babesia spp. in ruminants in China. EXPERIMENTAL & APPLIED ACAROLOGY 2013; 59:463-472. [PMID: 23124328 DOI: 10.1007/s10493-012-9607-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
Molecular phylogenetic analyses are mainly based on the small ribosomal RNA subunit (18S rRNA), internal transcribed spacer regions, and other molecular markers. We compared the phylogenetic relationships of Babesia spp. using large subunit ribosomal RNA, i.e., 28S rRNA, and the united 28S + 18S rRNA sequence fragments from 11 isolates of Babesia spp. collected in China. Due to sequence length and variability, the 28S rRNA gene contained more information than the 18S rRNA gene and could be used to elucidate the phlyogenetic relationships of B. motasi, B. major, and B. bovis. Thus, 28S rRNA is another candidate marker that can be used for the phylogenetic analysis of Babesia spp. However, the united fragment (28S + 18S) analysis provided better supported phylogenetic relationships than single genes for Babesia spp. in China.
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Affiliation(s)
- Huitian Gou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Grazing Animal Diseases MOA, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046 Gansu, People's Republic of China
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Tubicolous enteropneusts from the Cambrian period. Nature 2013; 495:503-6. [PMID: 23485974 DOI: 10.1038/nature12017] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 02/18/2013] [Indexed: 11/08/2022]
Abstract
Hemichordates are a marine group that, apart from one monospecific pelagic larval form, are represented by the vermiform enteropneusts and minute colonial tube-dwelling pterobranchs. Together with echinoderms, they comprise the clade Ambulacraria. Despite their restricted diversity, hemichordates provide important insights into early deuterostome evolution, notably because of their pharyngeal gill slits. Hemichordate phylogeny has long remained problematic, not least because the nature of any transitional form that might serve to link the anatomically disparate enteropneusts and pterobranchs is conjectural. Hence, inter-relationships have also remained controversial. For example, pterobranchs have sometimes been compared to ancestral echinoderms. Molecular data identify enteropneusts as paraphyletic, and harrimaniids as the sister group of pterobranchs. Recent molecular phylogenies suggest that enteropneusts are probably basal within hemichordates, contrary to previous views, but otherwise provide little guidance as to the nature of the primitive hemichordate. In addition, the hemichordate fossil record is almost entirely restricted to peridermal skeletons of pterobranchs, notably graptolites. Owing to their low preservational potentials, fossil enteropneusts are exceedingly rare, and throw no light on either hemichordate phylogeny or the proposed harrimaniid-pterobranch transition. Here we describe an enteropneust, Spartobranchus tenuis (Walcott, 1911), from the Middle Cambrian-period (Series 3, Stage 5) Burgess Shale. It is remarkably similar to the extant harrimaniids, but differs from all known enteropneusts in that it is associated with a fibrous tube that is sometimes branched. We suggest that this is the precursor of the pterobranch periderm, and supports the hypothesis that pterobranchs are miniaturized and derived from an enteropneust-like worm. It also shows that the periderm was acquired before size reduction and acquisition of feeding tentacles, and that coloniality emerged through aggregation of individuals, perhaps similar to the Cambrian rhabdopleurid Fasciculitubus. The presence of both enteropneusts and pterobranchs in Middle Cambrian strata, suggests that hemichordates originated at the onset of the Cambrian explosion.
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Perseke M, Golombek A, Schlegel M, Struck TH. The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny. Mol Phylogenet Evol 2013; 66:898-905. [DOI: 10.1016/j.ympev.2012.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 11/09/2012] [Accepted: 11/22/2012] [Indexed: 10/27/2022]
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Ludueña RF. A Hypothesis on the Origin and Evolution of Tubulin. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:41-185. [DOI: 10.1016/b978-0-12-407699-0.00002-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Worsaae K, Sterrer W, Kaul-Strehlow S, Hay-Schmidt A, Giribet G. An anatomical description of a miniaturized acorn worm (hemichordata, enteropneusta) with asexual reproduction by paratomy. PLoS One 2012; 7:e48529. [PMID: 23144898 PMCID: PMC3492459 DOI: 10.1371/journal.pone.0048529] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 09/26/2012] [Indexed: 11/26/2022] Open
Abstract
The interstitial environment of marine sandy bottoms is a nutrient-rich, sheltered habitat whilst at the same time also often a turbulent, space-limited, and ecologically challenging environment dominated by meiofauna. The interstitial fauna is one of the most diverse on earth and accommodates miniaturized representatives from many macrofaunal groups as well as several exclusively meiofaunal phyla. The colonization process of this environment, with the restrictions imposed by limited space and low Reynolds numbers, has selected for great morphological and behavioral changes as well as new life history strategies.Here we describe a new enteropneust species inhabiting the interstices among sand grains in shallow tropical waters of the West Atlantic. With a maximum body length of 0.6 mm, it is the first microscopic adult enteropneust known, a group otherwise ranging from 2 cm to 250 cm in adult size. Asexual reproduction by paratomy has been observed in this new species, a reproductive mode not previously reported among enteropneusts. Morphologically, Meioglossus psammophilus gen. et sp. nov. shows closest resemblance to an early juvenile stage of the acorn worm family Harrimaniidae, a result congruent with its phylogenetic placement based on molecular data. Its position, clearly nested within the larger macrofaunal hemichordates, suggests that this represents an extreme case of miniaturization. The evolutionary pathway to this simple or juvenile appearance, as chiefly demonstrated by its small size, dense ciliation, and single pair of gill pores, may be explained by progenesis. The finding of M. psammophilus gen. et sp. nov. underscores the notion that meiofauna may constitute a rich source of undiscovered metazoan diversity, possibly disguised as juveniles of other species.
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Affiliation(s)
- Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Röttinger E, Lowe CJ. Evolutionary crossroads in developmental biology: hemichordates. Development 2012; 139:2463-75. [PMID: 22736243 DOI: 10.1242/dev.066712] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hemichordates are a deuterostome phylum, the sister group to echinoderms, and closely related to chordates. They have thus been used to gain insights into the origins of deuterostome and chordate body plans. Developmental studies of this group have a long and distinguished history. Recent improvements in animal husbandry, functional tool development and genomic resources have resulted in novel developmental data from several species in this group. In this Primer, we introduce representative hemichordate species with contrasting modes of development and summarize recent findings that are beginning to yield important insights into deuterostome developmental mechanisms.
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Affiliation(s)
- Eric Röttinger
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii, Honolulu, HI 96734, USA
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes from 371 Animalia: Updated structure-based alignment and detailed phylogenetic analysis. Mol Phylogenet Evol 2012; 64:603-17. [DOI: 10.1016/j.ympev.2012.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022]
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Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0087-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ramulu HG, Raoult D, Pontarotti P. The rhizome of life: what about metazoa? Front Cell Infect Microbiol 2012; 2:50. [PMID: 22919641 PMCID: PMC3417402 DOI: 10.3389/fcimb.2012.00050] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/23/2012] [Indexed: 02/03/2023] Open
Abstract
The increase in huge number of genomic sequences in recent years has contributed to various genetic events such as horizontal gene transfer (HGT), gene duplication and hybridization of species. Among them HGT has played an important role in the genome evolution and was believed to occur only in Bacterial and Archaeal genomes. As a result, genomes were found to be chimeric and the evolution of life was represented in different forms such as forests, networks and species evolution was described more like a rhizome, rather than a tree. However, in the last few years, HGT has also been evidenced in other group such as metazoa (for example in root-knot nematodes, bdelloid rotifers and mammals). In addition to HGT, other genetic events such as transfer by retrotransposons and hybridization between more closely related lineages are also well established. Therefore, in the light of such genetic events, whether the evolution of metazoa exists in the form of a tree, network or rhizome is highly questionable and needs to be determined. In the current review, we will focus on the role of HGT, retrotransposons and hybridization in the metazoan evolution.
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Affiliation(s)
- Hemalatha G. Ramulu
- LATP UMR-CNRS 7353, Evolution Biologique et Modélisation, Aix-Marseille UniversitéeMarseille, France
- URMITE CNRS-IRD UMR6236-198Marseille, France
| | | | - Pierre Pontarotti
- LATP UMR-CNRS 7353, Evolution Biologique et Modélisation, Aix-Marseille UniversitéeMarseille, France
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Smith KF, Stefaniak L, Saito Y, Gemmill CEC, Cary SC, Fidler AE. Increased inter-colony fusion rates are associated with reduced COI haplotype diversity in an invasive colonial ascidian Didemnum vexillum. PLoS One 2012; 7:e30473. [PMID: 22303442 PMCID: PMC3269411 DOI: 10.1371/journal.pone.0030473] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/20/2011] [Indexed: 11/18/2022] Open
Abstract
Considerable progress in our understanding of the population genetic changes associated with biological invasions has been made over the past decade. Using selectively neutral loci, it has been established that reductions in genetic diversity, reflecting founder effects, have occurred during the establishment of some invasive populations. However, some colonial organisms may actually gain an ecological advantage from reduced genetic diversity because of the associated reduction in inter-colony conflict. Here we report population genetic analyses, along with colony fusion experiments, for a highly invasive colonial ascidian, Didemnum vexillum. Analyses based on mitochondrial cytochrome oxidase I (COI) partial coding sequences revealed two distinct D. vexillum clades. One COI clade appears to be restricted to the probable native region (i.e., north-west Pacific Ocean), while the other clade is present in widely dispersed temperate coastal waters around the world. This clade structure was supported by 18S ribosomal DNA (rDNA) sequence data, which revealed a one base-pair difference between the two clades. Recently established populations of D. vexillum in New Zealand displayed greatly reduced COI genetic diversity when compared with D. vexillum in Japan. In association with this reduction in genetic diversity was a significantly higher inter-colony fusion rate between randomly paired New Zealand D. vexillum colonies (80%, standard deviation ±18%) when compared with colonies found in Japan (27%, standard deviation ±15%). The results of this study add to growing evidence that for colonial organisms reductions in population level genetic diversity may alter colony interaction dynamics and enhance the invasive potential of newly colonizing species.
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Kawauchi GY, Sharma PP, Giribet G. Sipunculan phylogeny based on six genes, with a new classification and the descriptions of two new families. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2011.00507.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Bertrand S, Escriva H. Evolutionary crossroads in developmental biology: amphioxus. Development 2011; 138:4819-30. [DOI: 10.1242/dev.066720] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The phylogenetic position of amphioxus, together with its relatively simple and evolutionarily conserved morphology and genome structure, has led to its use as a model for studies of vertebrate evolution. In particular, the recent development of technical approaches, as well as access to the complete amphioxus genome sequence, has provided the community with tools with which to study the invertebrate-chordate to vertebrate transition. Here, we present this animal model, discussing its life cycle, the model species studied and the experimental techniques that it is amenable to. We also summarize the major findings made using amphioxus that have informed us about the evolution of vertebrate traits.
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Affiliation(s)
- Stephanie Bertrand
- CNRS UMR7232, UPMC Université Paris 06, Observatoire océanologique, F-66651 Banyuls-sur-Mer, France
| | - Hector Escriva
- CNRS UMR7232, UPMC Université Paris 06, Observatoire océanologique, F-66651 Banyuls-sur-Mer, France
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The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. BMC Evol Biol 2011; 11:134. [PMID: 21599892 PMCID: PMC3121625 DOI: 10.1186/1471-2148-11-134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 05/20/2011] [Indexed: 11/30/2022] Open
Abstract
Background The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch Rhabdopleura compacta to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution. Results The mitochondrial DNA of Rhabdopleura compacta corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in R. compacta is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of R. compacta, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in R. compacta but possess an identical mutation in the anticodon sequence of the tRNALys. Conclusion A strong reversed asymmetrical mutational constraint in the mitochondrial genome of Rhabdopleura compacta may have arisen by an inversion of the replication direction and adaptation to this bias in the protein sequences leading to an enigmatic mitochondrial genome. Although, phylogenetic analyses of protein coding sequences are hampered, features of the tRNA system of R. compacta support the monophyly of Ambulacraria. The identical reassignment of AGG to Lysine in two distinct groups may have occurred by convergent evolution in the anticodon sequence of the tRNALys.
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Affiliation(s)
- Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Petch 207, 3800 Finnerty Road, Victoria, BC, Canada V8N 3N5.
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Escobar JS, Glémin S, Galtier N. GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes. Mol Biol Evol 2011; 28:2561-75. [DOI: 10.1093/molbev/msr079] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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43
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Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. Higher-level metazoan relationships: recent progress and remaining questions. ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0044-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Stach T, Kaul S. The postanal tail of the enteropneust Saccoglossus kowalevskii is a ciliary creeping organ without distinct similarities to the chordate tail. ACTA ZOOL-STOCKHOLM 2011. [DOI: 10.1111/j.1463-6395.2010.00462.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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45
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Heimberg AM, Cowper-Sal·lari R, Sémon M, Donoghue PCJ, Peterson KJ. microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate. Proc Natl Acad Sci U S A 2010; 107:19379-83. [PMID: 20959416 PMCID: PMC2984222 DOI: 10.1073/pnas.1010350107] [Citation(s) in RCA: 194] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more primitive microRNA families, and 22 unique substitutions to the mature gene products. Reanalysis of morphological data reveals that support for cyclostome paraphyly was based largely on incorrect character coding, and a revised dataset is not decisive on the mono- vs. paraphyly of cyclostomes. Furthermore, we show fundamental conservation of microRNA expression patterns among lamprey, hagfish, and gnathostome organs, implying that the role of microRNAs within specific organs is coincident with their appearance within the genome and is conserved through time. Together, these data support the monophyly of cyclostomes and suggest that the last common ancestor of all living vertebrates was a more complex organism than conventionally accepted by comparative morphologists and developmental biologists.
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Affiliation(s)
| | | | - Marie Sémon
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; and
| | - Philip C. J. Donoghue
- Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, United Kingdom
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
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Nydam ML, Harrison RG. INTROGRESSION DESPITE SUBSTANTIAL DIVERGENCE IN A BROADCAST SPAWNING MARINE INVERTEBRATE. Evolution 2010; 65:429-42. [DOI: 10.1111/j.1558-5646.2010.01153.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lopardo L, Giribet G, Hormiga G. Morphology to the rescue: molecular data and the signal of morphological characters in combined phylogenetic analyses-a case study from mysmenid spiders (Araneae, Mysmenidae), with comments on the evolution of web architecture. Cladistics 2010; 27:278-330. [DOI: 10.1111/j.1096-0031.2010.00332.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Tsagkogeorga G, Turon X, Galtier N, Douzery EJP, Delsuc F. Accelerated evolutionary rate of housekeeping genes in tunicates. J Mol Evol 2010; 71:153-67. [PMID: 20697701 DOI: 10.1007/s00239-010-9372-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 07/16/2010] [Indexed: 01/11/2023]
Abstract
Phylogenomics has recently revealed that tunicates represent the sister-group of vertebrates in the newly defined clade Olfactores. However, phylogenomic and comparative genomic studies have also suggested that tunicates are characterized by an elevated rate of molecular evolution and a high degree of genomic divergence. Despite the recurrent interest in the group, the picture of tunicate peculiar evolutionary dynamics is still fragmentary, as it mainly lies in studies focusing on only a few model species. In order to expand the available genomic data for the group, we used the high-throughput 454 technology to sequence the partial transcriptome of a previously unsampled tunicate, Microcosmus squamiger. This allowed us to get further insights into tunicate-accelerated evolution through a comparative analysis based on pertinent phylogenetic markers, i.e., a core of 35 housekeeping genes conserved across bilaterians. Our results showed that tunicates evolved on average about two times faster than the other chordates, yet the degree of this acceleration varied extensively upon genes and upon lineages. Appendicularia and Aplousobranchia were detected as the most divergent groups which were also characterized by highly heterogeneous substitution rates across genes. Finally, an estimation of the d (N)/d (S) ratio in three pairs of closely related taxa within Olfactores did not reveal strong differences between the tunicate and vertebrate lineages suggesting that for this set of housekeeping genes, the accelerated evolution of tunicates is plausibly due to an elevated mutation rate rather than to particular selective effects.
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Affiliation(s)
- Georgia Tsagkogeorga
- Université Montpellier 2 and CNRS, Institut des Sciences de l'Evolution (UMR 5554), CC064, Place Eugène Bataillon, 34095, Montpellier Cedex 05, France
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Kano S. Genomics and Developmental Approaches to an Ascidian Adenohypophysis Primordium. Integr Comp Biol 2010; 50:35-52. [DOI: 10.1093/icb/icq050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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50
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Mol Phylogenet Evol 2010; 55:1-17. [DOI: 10.1016/j.ympev.2009.09.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 08/28/2009] [Accepted: 09/22/2009] [Indexed: 10/20/2022]
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