1
|
Marlétaz F, Timoshevskaya N, Timoshevskiy V, Simakov O, Parey E, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith J, Rokhsar DS. The hagfish genome and the evolution of vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537254. [PMID: 37131617 PMCID: PMC10153176 DOI: 10.1101/2023.04.17.537254] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution. Here, we investigate the complex history, timing, and functional role of genome-wide duplications in vertebrates in the light of a chromosome-scale genome of the brown hagfish Eptatretus atami. Using robust chromosome-scale (paralogon-based) phylogenetic methods, we confirm the monophyly of cyclostomes, document an auto-tetraploidization (1RV) that predated the origin of crown group vertebrates ~517 Mya, and establish the timing of subsequent independent duplications in the gnathostome and cyclostome lineages. Some 1RV gene duplications can be linked to key vertebrate innovations, suggesting that this early genomewide event contributed to the emergence of pan-vertebrate features such as neural crest. The hagfish karyotype is derived by numerous fusions relative to the ancestral cyclostome arrangement preserved by lampreys. These genomic changes were accompanied by the loss of genes essential for organ systems (eyes, osteoclast) that are absent in hagfish, accounting in part for the simplification of the hagfish body plan; other gene family expansions account for hagfishes' capacity to produce slime. Finally, we characterise programmed DNA elimination in somatic cells of hagfish, identifying protein-coding and repetitive elements that are deleted during development. As in lampreys, the elimination of these genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline/pluripotency functions. Reconstruction of the early genomic history of vertebrates provides a framework for further exploration of vertebrate novelties.
Collapse
Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | | | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Present address: UK Dementia Research Institute, University College London, London, UK
| | - Masakazu Suzuki
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kaoru Kubokawa
- Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Sydney Brenner
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
- Deceased
| | - Jeramiah Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
2
|
Higuchi S, Sugahara F, Pascual-Anaya J, Takagi W, Oisi Y, Kuratani S. Inner ear development in cyclostomes and evolution of the vertebrate semicircular canals. Nature 2018; 565:347-350. [DOI: 10.1038/s41586-018-0782-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/16/2018] [Indexed: 11/09/2022]
|
3
|
Kuraku S, Feiner N, Keeley SD, Hara Y. Incorporating tree-thinking and evolutionary time scale into developmental biology. Dev Growth Differ 2016; 58:131-42. [PMID: 26818824 DOI: 10.1111/dgd.12258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 01/11/2023]
Abstract
Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.
Collapse
Affiliation(s)
- Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | | | - Sean D Keeley
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| |
Collapse
|
4
|
Zaccone D, Icardo JM, Kuciel M, Alesci A, Pergolizzi S, Satora L, Lauriano ER, Zaccone G. Polymorphous granular cells in the lung of the primitive fish, the bichirPolypterus senegalus. ACTA ZOOL-STOCKHOLM 2015. [DOI: 10.1111/azo.12145] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Zaccone
- Department of Environmental Sciences, Territorial, Food and Health Security (S.A.S.T.A.S.); University of Messina; Viale Stagno d'Alcontres 31 I-98166 Messina Italy
| | - Jose Manuel Icardo
- Department of Anatomy and Cell Biology Polígono de Cazoña; Faculty of Medicine; University of Cantabria; s/n 39011 Santander Spain
| | - Michał Kuciel
- Poison Information Centre; Jagiellonian University Medical College; Kopernika 15 31-501 Crakow Poland
| | - Alessio Alesci
- Department of Environmental Sciences, Territorial, Food and Health Security (S.A.S.T.A.S.); University of Messina; Viale Stagno d'Alcontres 31 I-98166 Messina Italy
| | - Simona Pergolizzi
- Department of Environmental Sciences, Territorial, Food and Health Security (S.A.S.T.A.S.); University of Messina; Viale Stagno d'Alcontres 31 I-98166 Messina Italy
| | - Leszek Satora
- Department of Physiology and Reproduction of Animals; University of Rzeszow; Werynia 502 36-100 Kolbuszowa Rzeszow Poland
| | - Eugenia Rita Lauriano
- Department of Environmental Sciences, Territorial, Food and Health Security (S.A.S.T.A.S.); University of Messina; Viale Stagno d'Alcontres 31 I-98166 Messina Italy
| | - Giacomo Zaccone
- Department of Environmental Sciences, Territorial, Food and Health Security (S.A.S.T.A.S.); University of Messina; Viale Stagno d'Alcontres 31 I-98166 Messina Italy
| |
Collapse
|
5
|
Fleming A, Kishida MG, Kimmel CB, Keynes RJ. Building the backbone: the development and evolution of vertebral patterning. Development 2015; 142:1733-44. [PMID: 25968309 DOI: 10.1242/dev.118950] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The segmented vertebral column comprises a repeat series of vertebrae, each consisting of two key components: the vertebral body (or centrum) and the vertebral arches. Despite being a defining feature of the vertebrates, much remains to be understood about vertebral development and evolution. Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning.
Collapse
Affiliation(s)
- Angeleen Fleming
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Marcia G Kishida
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Charles B Kimmel
- Institute of Neuroscience, 1254 University of Oregon, Eugene OR 97403-1254, USA
| | - Roger J Keynes
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| |
Collapse
|
6
|
Schutz H, Jamniczky HA, Hallgrímsson B, Garland T. Shape-shift: semicircular canal morphology responds to selective breeding for increased locomotor activity. Evolution 2014; 68:3184-98. [PMID: 25130322 DOI: 10.1111/evo.12501] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/06/2014] [Indexed: 02/05/2023]
Abstract
Variation in semicircular canal morphology correlates with locomotor agility among species of mammals. An experimental evolutionary mouse model was used to test the hypotheses that semicircular canal morphology (1) evolves in response to selective breeding for increased locomotor activity, (2) exhibits phenotypic plasticity in response to early-onset chronic exercise, and (3) is unique in individuals possessing the minimuscle phenotype. We examined responses in canal morphology to prolonged wheel access and selection in laboratory mice from four replicate lines bred for high voluntary wheel-running (HR) and four nonselected control (C) lines. Linear measurements and a suite of 3D landmarks were obtained from 3D reconstructions of μCT-scanned mouse crania (μCT is microcomputed tomography). Body mass was smaller in HR than C mice and was a significant predictor of both radius of curvature and 3D canal shape. Controlling for body mass, radius of curvature did not differ statistically between HR and C mice, but semicircular canal shape did. Neither chronic wheel access nor minimuscle affected radius of curvature or canal shape These findings suggest that semicircular canal morphology is responsive to evolutionary changes in locomotor behavior, but the pattern of response is potentially different in small- versus large-bodied species.
Collapse
Affiliation(s)
- Heidi Schutz
- Biology Department, Pacific Lutheran University, Tacoma, Washington, 98477; Department of Biology, University of California, Riverside, California, 92521.
| | | | | | | |
Collapse
|
7
|
Maklad A, Reed C, Johnson NS, Fritzsch B. Anatomy of the lamprey ear: morphological evidence for occurrence of horizontal semicircular ducts in the labyrinth of Petromyzon marinus. J Anat 2014; 224:432-46. [PMID: 24438368 DOI: 10.1111/joa.12159] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2013] [Indexed: 02/03/2023] Open
Abstract
In jawed (gnathostome) vertebrates, the inner ears have three semicircular canals arranged orthogonally in the three Cartesian planes: one horizontal (lateral) and two vertical canals. They function as detectors for angular acceleration in their respective planes. Living jawless craniates, cyclostomes (hagfish and lamprey) and their fossil records seemingly lack a lateral horizontal canal. The jawless vertebrate hagfish inner ear is described as a torus or doughnut, having one vertical canal, and the jawless vertebrate lamprey having two. These observations on the anatomy of the cyclostome (jawless vertebrate) inner ear have been unchallenged for over a century, and the question of how these jawless vertebrates perceive angular acceleration in the yaw (horizontal) planes has remained open. To provide an answer to this open question we reevaluated the anatomy of the inner ear in the lamprey, using stereoscopic dissection and scanning electron microscopy. The present study reveals a novel observation: the lamprey has two horizontal semicircular ducts in each labyrinth. Furthermore, the horizontal ducts in the lamprey, in contrast to those of jawed vertebrates, are located on the medial surface in the labyrinth rather than on the lateral surface. Our data on the lamprey horizontal duct suggest that the appearance of the horizontal canal characteristic of gnathostomes (lateral) and lampreys (medial) are mutually exclusive and indicate a parallel evolution of both systems, one in cyclostomes and one in gnathostome ancestors.
Collapse
Affiliation(s)
- Adel Maklad
- Department of Neurobiology and Anatomical Sciences, University of Mississippi Medical Center, Jackson, MS, USA
| | | | | | | |
Collapse
|
8
|
Kuraku S. Impact of asymmetric gene repertoire between cyclostomes and gnathostomes. Semin Cell Dev Biol 2013; 24:119-27. [DOI: 10.1016/j.semcdb.2012.12.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 12/25/2012] [Indexed: 12/12/2022]
|
9
|
Fujimoto S, Oisi Y, Kuraku S, Ota KG, Kuratani S. Non-parsimonious evolution of hagfish Dlx genes. BMC Evol Biol 2013; 13:15. [PMID: 23331926 PMCID: PMC3552724 DOI: 10.1186/1471-2148-13-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/11/2013] [Indexed: 11/28/2022] Open
Abstract
Background The number of members of the Dlx gene family increased during the two rounds of whole-genome duplication that occurred in the common ancestor of the vertebrates. Because the Dlx genes are involved in the development of the cranial skeleton, brain, and sensory organs, their expression patterns have been analysed in various organisms in the context of evolutionary developmental biology. Six Dlx genes have been isolated in the lampreys, a group of living jawless vertebrates (cyclostomes), and their expression patterns analysed. However, little is known about the Dlx genes in the hagfish, the other cyclostome group, mainly because the embryological analysis of this animal is difficult. Results To identify the hagfish Dlx genes and describe their expression patterns, we cloned the cDNA from embryos of the Japanese inshore hagfish Eptatretus burgeri. Our results show that the hagfish has at least six Dlx genes and one pseudogene. In a phylogenetic analysis, the hagfish Dlx genes and those of the lampreys tended to be excluded from the clade of the gnathostome Dlx genes. In several cases, the lamprey Dlx genes clustered with the clade consisting of two hagfish genes, suggesting that independent gene duplications have occurred in the hagfish lineage. Analysis of the expression of these genes showed distinctive overlapping expression patterns in the cranial mesenchymal cells and the inner ear. Conclusions Independent duplication, pseudogenization, and loss of the Dlx genes probably occurred in the hagfish lineage after its split from the other vertebrate lineages. This pattern is reminiscent of the non-parsimonious evolution of its morphological traits, including its inner ear and vertebrae, which indicate that this group is an early-branching lineage that diverged before those characters evolved.
Collapse
Affiliation(s)
- Satoko Fujimoto
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | | | | | | | | |
Collapse
|
10
|
microRNAs revive old views about jawless vertebrate divergence and evolution. Proc Natl Acad Sci U S A 2010; 107:19137-8. [PMID: 21041649 DOI: 10.1073/pnas.1014583107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
11
|
Smith JJ, Saha NR, Amemiya CT. Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes. Integr Comp Biol 2010; 50:130-7. [PMID: 21558194 PMCID: PMC3140258 DOI: 10.1093/icb/icq023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The jawless vertebrates (lamprey and hagfish) are the closest extant outgroups to all jawed vertebrates (gnathostomes) and can therefore provide critical insight into the evolution and basic biology of vertebrate genomes. As such, it is notable that the genomes of lamprey and hagfish possess a capacity for rearrangement that is beyond anything known from the gnathostomes. Like the jawed vertebrates, lamprey and hagfish undergo rearrangement of adaptive immune receptors. However, the receptors and the mechanisms for rearrangement that are utilized by jawless vertebrates clearly evolved independently of the gnathostome system. Unlike the jawed vertebrates, lamprey and hagfish also undergo extensive programmed rearrangements of the genome during embryonic development. By considering these fascinating genome biologies in the context of proposed (albeit contentious) phylogenetic relationships among lamprey, hagfish, and gnathostomes, we can begin to understand the evolutionary history of the vertebrate genome. Specifically, the deep shared ancestry and rapid divergence of lampreys, hagfish and gnathostomes is considered evidence that the two versions of programmed rearrangement present in lamprey and hagfish (embryonic and immune receptor) were present in an ancestral lineage that existed more than 400 million years ago and perhaps included the ancestor of the jawed vertebrates. Validating this premise will require better characterization of the genome sequence and mechanisms of rearrangement in lamprey and hagfish.
Collapse
Affiliation(s)
- J J Smith
- Benaroya Research Institute at Virginia Mason, 1201 9th Avenue, Seattle, WA 98101, USA.
| | | | | |
Collapse
|
12
|
Ota KG, Kuratani S. Expression pattern of two collagen type 2 alpha1 genes in the Japanese inshore hagfish (Eptatretus burgeri) with special reference to the evolution of cartilaginous tissue. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:157-65. [PMID: 19750486 DOI: 10.1002/jez.b.21322] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Collagen type 2 alpha1 (Col2A1) protein is a major component of the cartilaginous extracellular matrix (ECM) in vertebrates. Over the past two decades, the evolutionary origin of Col2A1 has been studied at the biochemical and molecular levels in extant jawless vertebrates (hagfishes and lampreys). Although these studies have contributed to our understanding of ECM protein evolution, the expression profile of the Col2A1 gene in hagfishes has not been fully described. We have performed molecular cloning and analyzed the gene expression pattern of the Col2A1 gene in the Japanese inshore hagfish (Eptatretus burgeri). We succeeded in isolating two Col2A1 genes, EbCol2A1A and EbCol2A1B, in which EbCol2A1A was expressed in the noncartilaginous connective tissues whereas EbCol2A1B was detected in some cartilaginous elements. Based on these results, we discuss the evolutionary history of Col2A1 genes in early vertebrates.
Collapse
Affiliation(s)
- Kinya G Ota
- Laboratory for Evolutionary Morphology, Center for Developmental Biology, Minatojima-minami, Chuo, Kobe, Hyogo, Japan.
| | | |
Collapse
|
13
|
Hagey LR, Møller PR, Hofmann AF, Krasowski MD. Diversity of bile salts in fish and amphibians: evolution of a complex biochemical pathway. Physiol Biochem Zool 2010; 83:308-21. [PMID: 20113173 PMCID: PMC2845723 DOI: 10.1086/649966] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Bile salts are the major end metabolites of cholesterol and are also important in lipid and protein digestion, as well as shaping of the gut microflora. Previous studies had demonstrated variation of bile salt structures across vertebrate species. We greatly extend prior surveys of bile salt variation in fish and amphibians, particularly in analysis of the biliary bile salts of Agnatha and Chondrichthyes. While there is significant structural variation of bile salts across all fish orders, bile salt profiles are generally stable within orders of fish and do not correlate with differences in diet. This large data set allowed us to infer evolutionary changes in the bile salt synthetic pathway. The hypothesized ancestral bile salt synthetic pathway, likely exemplified in extant hagfish, is simpler and much shorter than the pathway of most teleost fish and terrestrial vertebrates. Thus, the bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution. Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates.
Collapse
Affiliation(s)
- Lee R. Hagey
- Department of Medicine, University of California at San Diego, MC 0063, La Jolla, California 92093-0063
| | - Peter R. Møller
- National History Museum of Denmark, Zoological Museum, University of Copenhagen, Denmark
| | - Alan F. Hofmann
- Department of Medicine, University of California at San Diego, MC 0063, La Jolla, California 92093-0063
| | - Matthew D. Krasowski
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261
| |
Collapse
|
14
|
Near TJ. Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312:749-61. [PMID: 19402130 DOI: 10.1002/jez.b.21293] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One of the most problematic issues in vertebrate phylogenetics is the disagreement between phenotypic and molecular inferences regarding the relationships among hagfishes, lampreys, and gnathostomes. Phenotypic characters support monophyly of lampreys and gnathostomes, whereas nearly all published analyses of molecular data sets support monophyly of hagfishes and lampreys. In this study I present results of phylogenetic analyses of combined phenotypic and molecular data sets that focus on relationships among hagfishes, lampreys, and gnathostomes. Maximum parsimony analyses of 115 phenotypic characters combined with 4,638 rRNA sites and more than 10,000 amino acids each result in monophyly of lampreys and gnathostomes, demonstrating that the addition of relatively few phenotypic characters can alter phylogenetic inferences from large molecular data sets. On the other hand, Bayesian analyses of the combined data sets support monophyly of hagfish and lampreys, indicating that model-based analyses may be prone to data "swamping," where the phylogenetic signal of the larger molecular data sets overwhelm the signal present in the much smaller phenotypic data set. Nodes that relate hagfish and lampreys were recovered at a low frequency in parametric bootstrapping analyses, indicating that the timing of diversification among hagfishes, lampreys, and gnathostomes has created a difficult phylogenetic problem for molecular data. The fact that addition of relatively few phenotypic characters can alter phylogenetic inferences of cyclostome monophyly obtained from molecular data sets, and the inability of simulated data sets to recover key nodes in the craniate phylogeny provide reasons to view the strong support for cyclostome monophyly inferred from molecular data sets with a measured degree of skepticism.
Collapse
Affiliation(s)
- Thomas J Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06520, USA.
| |
Collapse
|
15
|
Hofmann AF, Hagey LR, Krasowski MD. Bile salts of vertebrates: structural variation and possible evolutionary significance. J Lipid Res 2009; 51:226-46. [PMID: 19638645 DOI: 10.1194/jlr.r000042] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biliary bile salt composition of 677 vertebrate species (103 fish, 130 reptiles, 271 birds, 173 mammals) was determined. Bile salts were of three types: C(27) bile alcohols, C(27) bile acids, or C(24) bile acids, with default hydroxylation at C-3 and C-7. C(27) bile alcohols dominated in early evolving fish and amphibians; C(27) bile acids, in reptiles and early evolving birds. C(24) bile acids were present in all vertebrate classes, often with C(27) alcohols or with C(27) acids, indicating two evolutionary pathways from C(27) bile alcohols to C(24) bile acids: a) a 'direct' pathway and b) an 'indirect' pathway with C(27) bile acids as intermediates. Hydroxylation at C-12 occurred in all orders and at C-16 in snakes and birds. Minor hydroxylation sites were C-1, C-2, C-5, C-6, and C-15. Side chain hydroxylation in C(27) bile salts occurred at C-22, C-24, C-25, and C-26, and in C(24) bile acids, at C-23 (snakes, birds, and pinnipeds). Unexpected was the presence of C(27) bile alcohols in four early evolving mammals. Bile salt composition showed significant variation between orders but not between families, genera, or species. Bile salt composition is a biochemical trait providing clues to evolutionary relationships, complementing anatomical and genetic analyses.
Collapse
Affiliation(s)
- Alan F Hofmann
- Department of Medicine, University of California, San Diego, San Diego, CA 92093-0063, USA.
| | | | | |
Collapse
|
16
|
McCauley DW, Kuratani S. Cyclostome studies in the context of vertebrate evolution. Zoolog Sci 2009; 25:953-4. [PMID: 19267629 DOI: 10.2108/zsj.25.953] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The proceedings in this volume follow from the 15(th) Center for Developmental Biology meeting on "Advances in Cyclostome Research" that we organized. The meeting was held at the CDB RIKEN Kobe Institute on 24 and 25 January 2008 with support from the CDB. Jawless vertebrates have been of interest to embryologists and comparative morphologists for more than a century. While the comparative morphology among lampreys, hagfishes, and gnathostomes has long been recognized in contributing to understanding the origin of jaws and other gnathostome traits, the availability of modern molecular methods has rekindled interest in these topics, and evolutionary developmental biology coupled with paleontology has opened new avenues into the study of gnathostome origins. Within the last decade, because of renewed interest in evolutionary developmental biology, the importance of lampreys and hagfishes to our understanding of vertebrate evolution has undergone resurgence in interest, as evidenced by the sea lamprey genome project currently underway at the National Human Genome Research Institute. As new molecular and imaging techniques become available, both paleontological and neontological questions are being readdressed and are providing new insights and speculation into vertebrate evolution. Thus, we determined the timing was optimal to bring together many of the researchers currently contributing to our understanding of the biology of agnathans. The diversity of speakers at the meeting included evolutionary developmental biologists, phylogenetics and genomics investigators, paleontologists, and endocrinology researchers, because as we move into the 21(st) century, integration among these disciplines has encouraged synergistic activities to develop. The goal of this meeting was to highlight in a single setting the most recent advances in this important basal group of vertebrates to facilitate interactions among the cyclostome community. Secondarily, we also hope that this gathering will enhance the visibility of jawless vertebrates as important models in the vertebrate "evo-devo" community. Several topics for further discussion emerged at this symposium, including: genomic data that have spurred renewed interest in gene duplications and their contribution to our understanding of cyclostome phylogeny and vertebrate evolution; the use of paleontology coupled with modern imaging techniques to clarify vertebrate phylogeny; and the evolution of the neuroendocrine and adaptive immune systems. These were among the topics that led to fruitful discussion. Here we summarize key research topics from the symposium that continue to advance as we move forward in the 21(st) century.
Collapse
Affiliation(s)
- David W McCauley
- Department of Zoology, University of Oklahoma, Norman, Oklahoma 73019, USA
| | | |
Collapse
|
17
|
Kuratani S, Ota KG. Hagfish (cyclostomata, vertebrata): Searching for the ancestral developmental plan of vertebrates. Bioessays 2008; 30:167-72. [DOI: 10.1002/bies.20701] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
18
|
Lamb TD, Collin SP, Pugh EN. Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nat Rev Neurosci 2007; 8:960-76. [PMID: 18026166 PMCID: PMC3143066 DOI: 10.1038/nrn2283] [Citation(s) in RCA: 327] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Charles Darwin appreciated the conceptual difficulty in accepting that an organ as wonderful as the vertebrate eye could have evolved through natural selection. He reasoned that if appropriate gradations could be found that were useful to the animal and were inherited, then the apparent difficulty would be overcome. Here, we review a wide range of findings that capture glimpses of the gradations that appear to have occurred during eye evolution, and provide a scenario for the unseen steps that have led to the emergence of the vertebrate eye.
Collapse
Affiliation(s)
- Trevor D Lamb
- Australian National University, Division of Neuroscience, The John Curtin School of Medical Research, Garran Road, The Australian National University, Canberra, Australian Capital Territory 2600, Australia.
| | | | | |
Collapse
|
19
|
Abstract
Hagfishes have long held a key place in discussions of early vertebrate evolution. Frustratingly, one basis for such discussions -- namely hagfish embryology -- is very incompletely known, because the embryos of these animals are notoriously difficult to obtain. Fortunately, a recent publication on a Far Eastern hagfish describes a workable procedure for obtaining embryos and then uses this precious material to show that the hagfish neural crest arises by cell delamination as in other vertebrates -- and not by epithelial outpouchings from the wall of the neural tube as previously claimed. Importantly, because hagfish embryos should now be available on a regular basis, the way is open for additional morphological and developmental genetic investigations to help evaluate existing evolutionary scenarios and perhaps suggest new ones.
Collapse
Affiliation(s)
- Nicholas D Holland
- Marine Biology Research Division, SIO, UCSD, La Jolla, CA 92093-0202, USA.
| |
Collapse
|