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Fedosov AE, Zaharias P, Lemarcis T, Modica MV, Holford M, Oliverio M, Kantor YI, Puillandre N. Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush. Syst Biol 2024; 73:521-531. [PMID: 38456663 PMCID: PMC11377187 DOI: 10.1093/sysbio/syae010] [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: 10/12/2022] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024] Open
Abstract
The molluskan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in the early stages of diversification, generating a "bush" at the base of their evolutionary tree, which has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, 3 prove problematic: First, the uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major "core Neogastropoda" grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analyzed phylogenetic signal of targeted loci in relation to potential biases, and we propose the most probable resolutions in the latter 2 recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci.
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Affiliation(s)
- Alexander E Fedosov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Paul Zaharias
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Thomas Lemarcis
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Maria Vittoria Modica
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Mandë Holford
- Department of Chemistry, Hunter College, Belfer Research Building, City University of New York, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Invertebrate Zoology, the American Museum of Natural History, New York, NY 10024, USA
- PhD Programs in Biology, Biochemistry, and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Marco Oliverio
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
- Department of Biology and Biotechnologies "Charles Darwin," Sapienza University of Rome, Viale dell'Università 32, I-00185 Rome, Italy
| | - Yuri I Kantor
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
- Department of Ecology and Morphology of Marine Invertebrates, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky prospect, 33, 119071 Moscow, Russia
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
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Lozano D, López JM, Chinarro A, Morona R, Moreno N. A detailed 3D MRI brain atlas of the African lungfish Protopterus annectens. Sci Rep 2024; 14:7999. [PMID: 38580713 PMCID: PMC10997765 DOI: 10.1038/s41598-024-58671-x] [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: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
The study of the brain by magnetic resonance imaging (MRI) in evolutionary analyses is still in its incipient stage, however, it is particularly useful as it allows us to analyze detailed anatomical images and compare brains of rare or otherwise inaccessible species, evolutionarily contextualizing possible differences, while at the same time being non-invasive. A good example is the lungfishes, sarcopterygians that are the closest living relatives of tetrapods and thus have an interesting phylogenetic position in the evolutionary conquest of the terrestrial environment. In the present study, we have developed a three-dimensional representation of the brain of the lungfish Protopterus annectens together with a rostrocaudal anatomical atlas. This methodological approach provides a clear delineation of the major brain subdivisions of this model and allows to measure both brain and ventricular volumes. Our results confirm that lungfish show neuroanatomical patterns reminiscent of those of extant basal sarcopterygians, with an evaginated telencephalon, and distinctive characters like a small optic tectum. These and additional characters uncover lungfish as a remarkable model to understand the origins of tetrapod diversity, indicating that their brain may contain significant clues to the characters of the brain of ancestral tetrapods.
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Affiliation(s)
- Daniel Lozano
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain.
| | - Jesús M López
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
| | - Adrián Chinarro
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
| | - Ruth Morona
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
| | - Nerea Moreno
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
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Kaczmarek EB, Gartner SM, Westneat MW, Brainerd EL. Air Breathing and Suction Feeding Kinematics in the West African Lungfish, Protopterus Annectens. Integr Comp Biol 2022; 62:865-877. [PMID: 35798019 DOI: 10.1093/icb/icac109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/17/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Research on the water-to-land transition tends to focus on the locomotor changes necessary for terrestriality. But the evolution from water breathing to air breathing was also a necessary precursor to the invasion of land. Air is approximately 1,000 times less dense, 50 times less viscous, and contains hundreds of times more oxygen than water. However, unlike the transition to terrestrial locomotion, breathing air does not require body weight support, so the evolution of air breathing may have necessitated smaller changes to morphology and function. We used X-ray Reconstruction of Moving Morphology to compare the cranial kinematics of aquatic buccal pumping, such as seen in suction feeding, with the aerial buccal pumping required for lung ventilation in the West African lungfish (Protopterus annectens). During buccal pumping behaviors, the cranial bones and associated soft tissues act as valves and pumps, and the sequence of their motions controls the pattern of fluid flow. Both behaviors are characterized by an anterior-to-posterior wave of expansion and an anterior-to-posterior wave of compression. We found that the pectoral girdle and cranial rib rotate consistently during air breathing and suction feeding, and that the muscle between them shortens during buccal expansion. Overall, we conclude that the major cranial bones maintain the same basic functions (i.e., acting as valves or pumps, or transmitting power) across aquatic and aerial buccal pumping. The cranial morphology that enables aquatic buccal pumping is well-suited to perform air-breathing and accommodates the physical differences between air and water.
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Affiliation(s)
- Elska B Kaczmarek
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence RI 02912
| | - Samantha M Gartner
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637
| | - Mark W Westneat
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637
| | - Elizabeth L Brainerd
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence RI 02912
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Kooijman SALM, Lika K, Augustine S, Marn N. Multidimensional scaling for animal traits in the context of dynamic energy budget theory. CONSERVATION PHYSIOLOGY 2021; 9:coab086. [PMID: 36531935 PMCID: PMC8677455 DOI: 10.1093/conphys/coab086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 12/09/2021] [Indexed: 06/15/2023]
Abstract
The method of multidimensional scaling (MDS) has long existed, but could only recently be applied to animal traits in the context of dynamic energy budget (DEB) theory. The application became possible because of the following: (i) the Add-my-Pet (AmP) collection of DEB parameters and traits (approximately 280) recently reached 3000 animal species with 45000 data sets of measurements; (ii) we found a natural distance measure for species based on their traits as a side result of our research on parameter estimation in DEB context; and (iii) we developed plotting code for visualization that allows labelling of taxonomic relationships. Traits, here defined as DEB parameters or any function of these parameters, have different dimensions, which hamper application of many popular distance measures since they (implicitly) assume that all traits have the same dimensions. The AmP collection follows the workflow that measured data determine parameters and parameters determine trait values. In this way we could fill up the species traits table completely, which we could not do by using measured values only, as data availability varies considerably between species and is typically poor. The goodness of fit of predictions for all data sets is generally excellent. This paper discusses links between the MDS method and parameter estimation and illustrates the application of MDS for the AmP collection to five taxa, three ectothermic and two endothermic, which we consider to be 'complete', in the sense that we expect that it will be difficult to find more species with data in the open literature. This application of MDS shows links between traits and taxonomy that supplements our efforts to find patterns in the co-variation of parameter values. Knowledge about metabolic performance is key to conservation biology, sustainable management and environmental risk assessment, which are seen as interlinked fields.
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Affiliation(s)
- Sebastiaan A L M Kooijman
- Department of Theoretical Biology, VU University Amsterdam, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Konstadia Lika
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Starrlight Augustine
- Akvaplan-niva AS, Fram High North Research Centre for Climate and the Environment, 9296 Tromsø, Norway
| | - Nina Marn
- Division for Environmental and Marine Research, Rudjer Bošković Institute, 10000 Zagreb, Croatia
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Zakipour Z, Alemzadeh A. Molecular evolution of Na, K-ATPase β-subunit. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Coelacanth SERINC2 Inhibits HIV-1 Infectivity and Is Counteracted by Envelope Glycoprotein from Foamy Virus. J Virol 2021; 95:e0022921. [PMID: 33883219 PMCID: PMC8316019 DOI: 10.1128/jvi.00229-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
SERINC5 restricts nef-defective HIV-1 by affecting early steps of the virus life cycle. Distantly related retroviruses with a wide host range encode virulent factors in response to challenge by SERINC5. However, the evolutionary origins of this antiretroviral activity, its prevalence among the paralogs, and its ability to target retroviruses remain understudied. In agreement with previous studies, we found that four human SERINC paralogs inhibit nef-defective HIV-1, with SERINC2 being an exception. Here, we demonstrate that this lack of activity in human SERINC2 is associated with its post-whole-genome duplication (post-WGD) divergence, as evidenced by the ability of pre-WGD orthologs from Saccharomyces cerevisiae and flies and a post-WGD-proximate SERINC2 from coelacanths to inhibit the virus. Intriguingly, Nef is unable to counter coelacanth SERINC2, indicating that such activity was directed toward other retroviruses found in coelacanths (like foamy viruses). However, foamy virus-derived vectors are intrinsically resistant to the action of SERINC2, and we show that the foamy virus envelope confers this resistance by affecting its steady-state levels. Our study highlights an ancient origin of antiretroviral activity in SERINCs and a hitherto-unknown interaction with a foamy virus. IMPORTANCESERINC5 constitutes a critical barrier to the propagation of retroviruses, as highlighted by parallel emergence of anti-SERINC5 activities among distant retroviral lineages. Therefore, understanding the origin and evolution of these host factors will provide key information about virus-host relationships that can be exploited for future drug development. Here, we show that SERINC5-mediated nef-defective HIV-1 infection inhibition is evolutionarily conserved. SERINC2 from coelacanth restricts HIV-1, and it was functionally adapted to target foamy viruses. Our findings provide insights into the evolutionary origin of antiretroviral activity in the SERINC gene family and uncover the role of SERINCs in shaping the long-term conflicts between retroviruses and their hosts.
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Recurrent sequence evolution after independent gene duplication. BMC Evol Biol 2020; 20:98. [PMID: 32770961 PMCID: PMC7414715 DOI: 10.1186/s12862-020-01660-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/17/2020] [Indexed: 11/10/2022] Open
Abstract
Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.
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Morona R, López JM, Northcutt RG, González A. Regional chemoarchitecture of the brain of lungfishes based on calbindin D-28K and calretinin immunohistochemistry. J Comp Neurol 2018. [PMID: 29520817 DOI: 10.1002/cne.24422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lungfishes are the closest living relatives of land vertebrates, and their neuroanatomical organization is particularly relevant for deducing the neural traits that have been conserved, modified, or lost with the transition from fishes to land vertebrates. The immunohistochemical localization of calbindin (CB) and calretinin (CR) provides a powerful method for discerning segregated neuronal populations, fiber tracts, and neuropils and is here applied to the brains of Neoceratodus and Protopterus, representing the two extant orders of lungfishes. The results showed abundant cells containing these proteins in pallial and subpallial telencephalic regions, with particular distinct distribution in the basal ganglia, amygdaloid complex, and septum. Similarly, the distribution of CB and CR containing cells supports the division of the hypothalamus of lungfishes into neuromeric regions, as in tetrapods. The dense concentrations of CB and CR positive cells and fibers highlight the extent of the thalamus. As in other vertebrates, the optic tectum is characterized by numerous CB positive cells and fibers and smaller numbers of CR cells. The so-called cerebellar nucleus contains abundant CB and CR cells with long ascending axons, which raises the possibility that it could be homologized to the secondary gustatory nucleus of other vertebrates. The corpus of the cerebellum is devoid of CB and CR and cells positive for both proteins are found in the cerebellar auricles and the octavolateralis nuclei. Comparison with other vertebrates reveals that lungfishes share most of their features of calcium binding protein distribution with amphibians, particularly with salamanders.
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Affiliation(s)
- Ruth Morona
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Spain
| | - Jesús M López
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Spain
| | - R Glenn Northcutt
- Laboratory of Comparative Neurobiology, Scripps Institution of Oceanography and Department of Neurosciences, School of Medicine, , University of California, San Diego, California, USA
| | - Agustín González
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Spain
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Abstract
The ductus arteriosus is typically viewed as a mammalian fetal blood vessel providing a right-to-left shunt of right ventricular outflow away from the lungs and to the systemic circuit, that must close at birth. This review provides a wider comparative examination of the ductus arteriosus in lungfish, reptiles, birds, and mammals. The ductus arteriosus evolved with the lung in the ancestors of the lungfish as a connection between the pulmonary arteries and dorsal aorta. During embryonic development, reptiles, birds, and mammals all possess either one or two paired ductus arteriosi that provide a fetal shunt of blood away from the lungs. Differences in the fetal circulatory arrangement are seen between these groups and this influences the importance of the ductus arteriosus as an embryonic shunt. The ductus arteriosus from lungfish and tetrapod vertebrates is an oxygen sensitive blood vessel, with shared conserved pathways involved in oxygen sensing. By expanding studies into more comparative models such as lungfish or developing birds a better understanding of the physiology of the ductus arteriosus can be developed.
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Affiliation(s)
- Edward M Dzialowski
- Developmental Integrative Biology Research Group, Department of Biological Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203.
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Rotwein P. Insulinlike Growth Factor 1 Gene Variation in Vertebrates. Endocrinology 2018; 159:2288-2305. [PMID: 29697760 PMCID: PMC6692883 DOI: 10.1210/en.2018-00259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022]
Abstract
IGF1-a small, single-chain, secreted peptide in mammals-is essential for normal somatic growth and is involved in a variety of other physiological and pathophysiological processes. IGF1 expression appears to be controlled by several different signaling mechanisms in mammals, with GH playing a key role by activating an inducible transcriptional pathway via the Jak2 protein kinase and the Stat5b transcription factor. Here, to understand aspects of Igf1 gene regulation over a substantially longer timeline than is discernible in mammals, Igf1 genes have been examined in 21 different nonmammalian vertebrates representing five different classes and ranging over ∼500 million years of evolutionary history. Parts of vertebrate Igf1 genes resemble components found in mammals. Conserved exons encoding the mature IGF1 protein are detected in all 21 species studied and are separated by a large intron, as seen in mammals; the single promoter contains putative regulatory elements that are similar to those functionally mapped in human IGF1 promoter 1. In contrast, GH-activated Stat5b-binding enhancers found in mammalian IGF1 loci are completely absent, there is no homolog of promoter 2 or exon 2 in any nonmammalian vertebrate, and different types of "extra" exons not present in mammals are found in birds, reptiles, and teleosts. These data collectively define properties of Igf1 genes and IGF1 proteins that were likely present in the earliest vertebrates and support the contention that common structural and regulatory features in Igf1 genes have a long evolutionary history.
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Affiliation(s)
- Peter Rotwein
- Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
- Correspondence: Peter Rotwein, MD, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, 5001 El Paso Drive, El Paso, Texas 79905. E-mail:
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Phylogeny mandalas for illustrating the Tree of Life. Mol Phylogenet Evol 2017; 117:168-178. [DOI: 10.1016/j.ympev.2016.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
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López JM, Morona R, González A. Immunohistochemical Localization of DARPP-32 in the Brain of Two Lungfishes: Further Assessment of Its Relationship with the Dopaminergic System. BRAIN, BEHAVIOR AND EVOLUTION 2017; 90:289-310. [PMID: 29161694 DOI: 10.1159/000481929] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/03/2017] [Indexed: 01/23/2023]
Abstract
The distribution of DARPP-32 (a phosphoprotein related to the dopamine D1 receptor) has been widely used as a means to clarify the brain regions with dopaminoceptive cells, primarily in representative species of tetrapods. The relationship between dopaminergic and dopaminoceptive elements is frequently analyzed using the catecholamine marker tyrosine hydroxylase (TH). In the present study, by means of combined immunohistochemistry, we have analyzed these relationships in lungfishes, the only group of sarcopterygian fishes represented by 6 extant species that are the phylogenetically closest living relatives of tetrapods. We used the Australian lungfish Neoceratodus forsteri and the African lungfish Protopterus dolloi. The DARPP-32 antibody yields a distinct and consistent pattern of neuronal staining in brain areas that, in general, coincide with areas that are densely innervated by TH-immunoreactive fibers. The striatum, thalamus, optic tectum, and torus semicircularis contain intensely DARPP-32-immunoreactive cell bodies and fibers. Cells are also located in the olfactory bulbs, amygdaloid complex, lateral septum, pallidum, preoptic area, suprachiasmatic nucleus, tuberal hypothalamic region, rostral rhombencephalic reticular formation, superior raphe nucleus, octavolateral area, solitary tract nucleus, and spinal cord. Remarkably, DARPP-32-immunoreactive fibers originating in the striatum reach the region of the dopaminergic cells in the mesencephalic tegmentum and represent a well-established striatonigral pathway in lungfishes. Double immunolabeling reveals that DARPP-32 is present in neurons that most likely receive TH input, but it is absent from the catecholaminergic neurons themselves, with the only exception of a few cells in the suprachiasmatic nucleus of Neoceratodus and the solitary tract nucleus of Protopterus. In addition, some species differences exist in the localization of DARPP-32 cells in the pallium, lateral amygdala, thalamus, prethalamus, and octavolateral area. In general, the present study demonstrates that the distribution pattern of DARPP-32, and its relationship with TH, is largely comparable to those reported for tetrapods, highlighting a shared situation among all sarcopterygians.
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Affiliation(s)
- Jesús M López
- Departamento de Biología Celular, Facultad de Biología, Universidad Complutense, Madrid, Spain
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López JM, González A. Organization of the catecholaminergic systems in the brain of lungfishes, the closest living relatives of terrestrial vertebrates. J Comp Neurol 2017. [DOI: 10.1002/cne.24266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jesús M. López
- Department of Cell Biology; Faculty of Biology, University Complutense of Madrid; Madrid Spain
| | - Agustín González
- Department of Cell Biology; Faculty of Biology, University Complutense of Madrid; Madrid Spain
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Chng YR, Ong JLY, Ching B, Chen XL, Hiong KC, Wong WP, Chew SF, Lam SH, Ip YK. Aestivation Induces Changes in the mRNA Expression Levels and Protein Abundance of Two Isoforms of Urea Transporters in the Gills of the African Lungfish, Protopterus annectens. Front Physiol 2017; 8:71. [PMID: 28261105 PMCID: PMC5311045 DOI: 10.3389/fphys.2017.00071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/26/2017] [Indexed: 11/26/2022] Open
Abstract
The African lungfish, Protopterus annectens, is ammonotelic in water despite being ureogenic. When it aestivates in mucus cocoon on land, ammonia is detoxified to urea. During the maintenance phase of aestivation, urea accumulates in the body, which is subsequently excreted upon arousal. Urea excretion involves urea transporters (UT/Ut). This study aimed to clone and sequence the ut isoforms from the gills of P. annectens, and to test the hypothesis that the mRNA and/or protein expression levels of ut/Ut isoforms could vary in the gills of P. annectens during the induction, maintenance, and arousal phases of aestivation. Two isoforms of ut, ut-a2a and ut-a2b, were obtained from the gills of P. annectens. ut-a2a consisted of 1227 bp and coded for 408 amino acids with an estimated molecular mass of 44.7 kDa, while ut-a2b consisted of 1392 bp and coded for 464 amino acids with an estimated molecular mass of 51.2 kDa. Ut-a2a and Ut-a2b of P. annectens had a closer phylogenetic relationship with Ut/UT of tetrapods than Ut of fishes. While the mRNA expression pattern of ut-a2a and ut-a2b across various tissues of P. annectens differed, the transcript levels of ut-a2a and ut-a2b in the gills were comparable, indicating that they might be equally important for branchial urea excretion during the initial arousal phase of aestivation. During the maintenance phase of aestivation, the transcript level of ut-a2a increased significantly, but the protein abundance of Ut-a2a remained unchanged in the gills of P. annectens. This could be an adaptive feature to prepare for an increase in the production of Ut-a2a upon arousal. Indeed, arousal led to a significant increase in the branchial Ut-a2a protein abundance. Although the transcript level of ut-a2b remained unchanged, there were significant increases in the protein abundance of Ut-a2b in the gills of P. annectens throughout the three phases of aestivation. The increase in the protein abundance of Ut-a2b during the maintenance phase could also be an adaptive feature to prepare for efficient urea excretion when water becomes available.
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Affiliation(s)
- You R. Chng
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Jasmine L. Y. Ong
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Biyun Ching
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Xiu L. Chen
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Kum C. Hiong
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Wai P. Wong
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Shit F. Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological UniversitySingapore, Singapore
| | - Siew H. Lam
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
- NUS Environmental Research Institute, National University of SingaporeSingapore, Singapore
| | - Yuen K. Ip
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
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15
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Ong JLY, Chng YR, Ching B, Chen XL, Hiong KC, Wong WP, Chew SF, Ip YK. Molecular characterization of myostatin from the skeletal muscle of the African lungfish, Protopterus annectens, and changes in its mRNA and protein expression levels during three phases of aestivation. J Comp Physiol B 2017; 187:575-589. [PMID: 28184997 DOI: 10.1007/s00360-017-1057-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 12/26/2016] [Accepted: 01/11/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Jasmine L Y Ong
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore, 117543, Singapore
| | - You R Chng
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore, 117543, Singapore
| | - Biyun Ching
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore, 117543, Singapore
| | - Xiu L Chen
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore, 117543, Singapore
| | - Kum C Hiong
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore, 117543, Singapore
| | - Wai P Wong
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore, 117543, Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore, 117543, Singapore.
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16
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Chng YR, Ong JLY, Ching B, Chen XL, Hiong KC, Wong WP, Chew SF, Lam SH, Ip YK. Molecular Characterization of Aquaporin 1 and Aquaporin 3 from the Gills of the African Lungfish, Protopterus annectens, and Changes in Their Branchial mRNA Expression Levels and Protein Abundance during Three Phases of Aestivation. Front Physiol 2016; 7:532. [PMID: 27891097 PMCID: PMC5102888 DOI: 10.3389/fphys.2016.00532] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/25/2016] [Indexed: 01/07/2023] Open
Abstract
African lungfishes can undergo long periods of aestivation on land during drought. During aestivation, lungfishes are confronted with desiccation and dehydration, and their gills become non-functional and covered with a thick layer of dried mucus. Aquaporins (Aqps) are a superfamily of integral membrane proteins which generally facilitate the permeation of water through plasma membranes. This study aimed to obtain the complete cDNA coding sequences of aqp1 and aqp3 from the gills of Protopterus annectens, and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation. Dendrogramic analyses of the deduced Aqp1 and Aqp3 amino acid sequences of P. annectens revealed their close relationships with those of Latimeria chalumnae and tetrapods. During the induction phase, there were significant decreases in the transcript levels of aqp1 and aqp3 in the gills of P. annectens, but the branchial Aqp1 and Aqp3 protein abundance remained unchanged. As changes in transcription might precede changes in translation, this could be regarded as an adaptive response to decrease the protein abundance of Aqp1 and Aqp3 in the subsequent maintenance phase of aestivation. As expected, the branchial transcript levels and protein abundance of aqp1/Aqp1 and aqp3/Aqp3 were significantly down-regulated during the maintenance phase, probably attributable to the shutdown of branchial functions and the cessation of volume regulation of branchial epithelial cells. Additionally, these changes could reduce the loss of water through branchial epithelial surfaces, supplementing the anti-desiccating property of the dried mucus. Upon arousal, it was essential for the lungfish to restore branchial functions. Indeed, the protein abundance of Aqp1 recovered partially, with complete recovery of mRNA expression level and protein abundance of Aqp3, in the gills of P. annectens after 3 days of arousal. These results provide insights into how P. annectens regulates branchial Aqp expression to cope with desiccation and rehydration during different phases of aestivation.
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Affiliation(s)
- You R. Chng
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Jasmine L. Y. Ong
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Biyun Ching
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Xiu L. Chen
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Kum C. Hiong
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Wai P. Wong
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
| | - Shit F. Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological UniversitySingapore, Singapore
| | - Siew H. Lam
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
- NUS Environmental Research Institute, National University of SingaporeSingapore, Singapore
| | - Yuen K. Ip
- Department of Biological Sciences, National University of SingaporeSingapore, Singapore
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17
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Irisarri I, Meyer A. The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes. Syst Biol 2016; 65:1057-1075. [PMID: 27425642 DOI: 10.1093/sysbio/syw057] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 06/08/2016] [Indexed: 01/08/2023] Open
Abstract
Identifying the closest living relative(s) of tetrapods is an important, yet still contested question in vertebrate phylogenetics. Three hypotheses are possible and ruling out alternatives has proven difficult even with large molecular data sets due to weak phylogenetic signal coupled nonphylogenetic noise resulting from relatively rapid speciation events that occurred a long time ago ([Formula: see text]400 Ma). Here, we revisit the identity of the closest living relative of land vertebrates from a phylogenomic perspective and include new genomic data for all extant lungfish genera. RNA-seq proves to be a great alternative to genomic sequencing, which currently is technically not feasible in lungfishes due to their huge (50-130 Gb) and repetitive genomes. We examined the most important sources of systematic error, namely long-branch attraction (LBA), compositional heterogeneity and distribution of missing data and applied different correction techniques. A multispecies coalescent approach is used to account for deep coalescence that might come from the short and deep internodes separating early sarcopterygian splits. Concatenation methods favored lungfishes as the closest living relatives of tetrapods with strong statistical support. Amino acid profile mixture models can unambiguously resolve this difficult internode thanks to their ability to avoid systematic error. We assessed the performance of different site-heterogeneous models and data partitioning and compared the ability of different strategies designed to overcome LBA, including taxon manipulation, reduction of among-lineage rate heterogeneity and removal of fast-evolving or compositionally heterogeneous positions. The identification of lungfish as sister group of tetrapods is robust regarding the effects of nonstationary composition and distribution of missing data. The multispecies coalescent method reconstructed strongly supported topologies that were congruent with concatenation, despite pervasive gene tree heterogeneity. We reject alternative topologies for early sarcopterygian relationships by increasing the signal-to-noise ratio in our alignments. The analytical pipeline outlined here combines probabilistic phylogenomic inference with methods for evaluating data quality, model adequacy, and assessing systematic error, and thus is likely to help resolve similarly difficult internodes in the tree of life. [Coalescence; coelacanth; compositional heterogeneity; gene tree; long-branch attraction; lungfish; missing data; model misspecification; phylogenomic; species tree; systematic error.].
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Affiliation(s)
- Iker Irisarri
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Axel Meyer
- Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
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18
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Takezaki N, Nishihara H. Resolving the Phylogenetic Position of Coelacanth: The Closest Relative Is Not Always the Most Appropriate Outgroup. Genome Biol Evol 2016; 8:1208-21. [PMID: 27026053 PMCID: PMC4860700 DOI: 10.1093/gbe/evw071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Determining the phylogenetic relationship of two extant lineages of lobe-finned fish, coelacanths and lungfishes, and tetrapods is important for understanding the origin of tetrapods. We analyzed data sets from two previous studies along with a newly collected data set, each of which had varying numbers of species and genes and varying extent of missing sites. We found that in all the data sets the sister relationship of lungfish and tetrapods was constructed with the use of cartilaginous fish as the outgroup with a high degree of statistical support. In contrast, when ray-finned fish were used as the outgroup, which is taxonomically an immediate outgroup of lobe-finned fish and tetrapods, the sister relationship of coelacanth and tetrapods was supported most strongly, although the statistical support was weaker. Even though it is generally accepted that the closest relative is an appropriate outgroup, our analysis suggested that the large divergence of the ray-finned fish as indicated by their long branch lengths and different amino acid frequencies made them less suitable as an outgroup than cartilaginous fish.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
| | - Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-Cho, Midori-Ku, Yokohama, Kanagawa, Japan
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19
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Biscotti MA, Gerdol M, Canapa A, Forconi M, Olmo E, Pallavicini A, Barucca M, Schartl M. The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land. Sci Rep 2016; 6:21571. [PMID: 26908371 PMCID: PMC4764851 DOI: 10.1038/srep21571] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 01/20/2016] [Indexed: 01/12/2023] Open
Abstract
Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.
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Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Marco Gerdol
- Dipartimento di Scienze della Vita, Università di Trieste, Via Licio Giorgeri 5, 34127, Trieste, Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Alberto Pallavicini
- Dipartimento di Scienze della Vita, Università di Trieste, Via Licio Giorgeri 5, 34127, Trieste, Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Manfred Schartl
- Department Physiological Chemistry, Biocenter, University of Würzburg, 97074 Würzburg and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97078 Würzburg, Germany
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20
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Brain - Endocast Relationship in the Australian Lungfish, Neoceratodus forsteri, Elucidated from Tomographic Data (Sarcopterygii: Dipnoi). PLoS One 2015; 10:e0141277. [PMID: 26492190 PMCID: PMC4619648 DOI: 10.1371/journal.pone.0141277] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
Although the brains of the three extant lungfish genera have been previously described, the spatial relationship between the brain and the neurocranium has never before been fully described nor quantified. Through the application of virtual microtomography (μCT) and 3D rendering software, we describe aspects of the gross anatomy of the brain and labyrinth region in the Australian lungfish, Neoceratodus forsteri and compare this to previous accounts. Unexpected characters in this specimen include short olfactory peduncles connecting the olfactory bulbs to the telencephalon, and an oblong telencephalon. Furthermore, we illustrate the endocast (the mould of the internal space of the neurocranial cavity) of Neoceratodus, also describing and quantifying the brain-endocast relationship in a lungfish for the first time. Overall, the brain of the Australian lungfish closely matches the size and shape of the endocast cavity housing it, filling more than four fifths of the total volume. The forebrain and labyrinth regions of the brain correspond very well to the endocast morphology, while the midbrain and hindbrain do not fit so closely. Our results cast light on the gross neural and endocast anatomy in lungfishes, and are likely to have particular significance for palaeoneurologists studying fossil taxa.
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21
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Austin CM, Tan MH, Croft LJ, Hammer MP, Gan HM. Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes. Genome Biol Evol 2015; 7:2885-95. [PMID: 26446539 PMCID: PMC4684697 DOI: 10.1093/gbe/evv186] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is presented consisting of 42,110 scaffolds with a total size of 708 Mb (2.85% gaps) representing 93.95% of core eukaryotic genes. Using a k-mer-based method, a genome size of 900 Mb was also estimated. We present an update on the phylogenomics of fishes based on a total of 27 species (23 fish species and 4 tetrapods) using 177 orthologous proteins (71,360 amino acid sites), which supports established relationships except that arowana is placed as the sister lineage to all teleost clades (Bayesian posterior probability 1.00, bootstrap replicate 93%), that evolved after the teleost genome duplication event rather than the eels (Elopomorpha). Evolutionary rates are highly heterogeneous across the tree with fishes represented by both slowly and rapidly evolving lineages. A total of 94 putative pigment genes were identified, providing the impetus for development of molecular markers associated with the spectacular colored phenotypes found within this species.
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Affiliation(s)
- Christopher M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Mun Hua Tan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Larry J Croft
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Malaysian Genomics Resource Centre Berhad, Boulevard Signature Office, Kuala Lumpur, Malaysia
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
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22
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Criswell KE. The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12255] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Ong JLY, Woo JM, Hiong KC, Ching B, Wong WP, Chew SF, Ip YK. Molecular characterization of betaine-homocysteine methyltransferase 1 from the liver, and effects of aestivation on its expressions and homocysteine concentrations in the liver, kidney and muscle, of the African lungfish, Protopterus annectens. Comp Biochem Physiol B Biochem Mol Biol 2015; 183:30-41. [PMID: 25575738 DOI: 10.1016/j.cbpb.2014.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 12/19/2014] [Accepted: 12/23/2014] [Indexed: 01/12/2023]
Abstract
Homocysteine accumulation has numerous deleterious effects, and betaine-homocysteine S-methyltransferase (BHMT) catalyses the synthesis of methionine from homocysteine and betaine. This study aimed to determine homocysteine concentrations, and mRNA expression levels and protein abundances of bhmt1/Bhmt1 in the liver, kidney and muscle of the African lungfish, Protopterus annectens, during the induction (6 days), maintenance (6 months) or arousal (3 days after arousal) phase of aestivation. The homocysteine concentration decreased significantly in the liver of P. annectens after 6 days or 6 months of aestivation, but it returned to the control level upon arousal. By contrast, homocysteine concentrations in the kidney and muscle remained unchanged during the three phases of aestivation. The complete coding cDNA sequence of bhmt1 from P. annectens consisted of 1236 bp, coding for 412 amino acids. The Bhmt1 from P. annectens had a close phylogenetic relationship with those from tetrapods and Callorhinchus milii. The expression of bhmt1 was detected in multiple organs/tissues of P. annectens, and this is the first report on the expression of bhmt1/Bhmt1 in animal skeletal muscle. The mRNA and protein expression levels of bhmt1/Bhmt1 were up-regulated in the liver of P. annectens during the induction and maintenance phases of aestivation, possibly to regulate the hepatic homocysteine concentration. The significant increase in hepatic Bhmt1 protein abundance during the arousal phase could be a response to increased cellular methylation for the purpose of tissue reconstruction. Unlike the liver, Bhmt1 expression in the kidney and muscle of P. annectens was regulated translationally, and its up-regulation could be crucial to prevent homocysteine accumulation.
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Affiliation(s)
- Jasmine L Y Ong
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore 117543, Republic of Singapore
| | - Jia M Woo
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore 117543, Republic of Singapore
| | - Kum C Hiong
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore 117543, Republic of Singapore
| | - Biyun Ching
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore 117543, Republic of Singapore
| | - Wai P Wong
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore 117543, Republic of Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K Ip
- Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Road, Singapore 117543, Republic of Singapore; The Tropical Marine Science Institute, National University of Singapore, Kent Ridge, Singapore 119227, Republic of Singapore.
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24
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Hiong KC, Tan XR, Boo MV, Wong WP, Chew SF, Ip YK. Aestivation induces changes in transcription and translation of coagulation factor II and fibrinogen gamma chain in the liver of the African lungfish, Protopterus annectens. J Exp Biol 2015; 218:3717-28. [DOI: 10.1242/jeb.125260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/17/2015] [Indexed: 11/20/2022]
Abstract
This study aimed to sequence and characterize two pro-coagulant genes, coagulation factor II (f2) and fibrinogen gamma chain (fgg), from the liver of the African lungfish Protopterus annectens, and to determine their hepatic mRNA expression levels during three phases of aestivation. The protein abundances of F2 and Fgg in the liver and plasma were determined by immunoblotting. Results indicated that F2 and Fgg of P. annectens were phylogenetically closer to those of amphibians than those of teleosts. Three days of aestivation resulted in an up-regulation in the hepatic fgg mRNA expression level, while 6 days of aestivation led to a significant increase (3-fold) in the protein abundance of Fgg in the plasma. Hence, there could be an increase in the blood clotting ability in P. annectens during the induction phase of aestivation. By contrast, the blood clotting ability in P. annectens might be reduced in response to decreased blood flow and increased possibility of thrombosis during the maintenance phase of aestivation, as 6 months of aestivation led to significant decreases in mRNA expression levels of f2 and fgg in the liver. There could also be a decrease in the export of F2 and Fgg from the liver to the plasma so as to avert thrombosis. Upon 3-6 days of arousal from 6 months of aestivation, the protein abundances of F2 and Fgg recovered partially in the plasma of P. annectens, and a complete recovery of the transcription and translation of f2/F2 in the liver might occur only after refeeding.
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Affiliation(s)
- Kum C. Hiong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Xiang R. Tan
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Mel V. Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Wai P. Wong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F. Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K. Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
- The Tropical Marine Science Institute, National University of Singapore, Kent Ridge, Singapore 119227, Republic of Singapore
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25
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Kaiya H, Konno N, Kangawa K, Uchiyama M, Miyazato M. Identification, tissue distribution and functional characterization of the ghrelin receptor in West African lungfish, Protopterus annectens. Gen Comp Endocrinol 2014; 209:106-17. [PMID: 25093625 DOI: 10.1016/j.ygcen.2014.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 07/16/2014] [Accepted: 07/26/2014] [Indexed: 12/29/2022]
Abstract
We identified two ghrelin receptor isoforms, the ghrelin receptor type-1a (GHS-R1a) and its alternative splice form (GHS-R1b) for West African lungfish, Protopterus annectens. Lungfish GHS-R1a and 1b comprised 361 and 281 amino acids, respectively. Lungfish GHS-R1a showed the highest identity to coelacanth GHS-R1a (80.4%). The highest expression of GHS-R1a mRNAs was seen in the brain, liver, ovary, heart, intestine, and gills. GHS-R1b mRNAs were also detected in the same tissues with GHS-R1a, but their expression level was 1/20 that of GHS-R1a. In human embryonic kidney 293 cells transiently expressing lungfish GHS-R1a, rat and bullfrog ghrelin, and two GHS-R1a agonists, GHRP-6 and hexarelin, increased intracellular Ca(2+) concentrations. The intensity of the Ca(2+) increases induced by GHS-R1a agonists was twice when compared to that induced by ghrelin, although the median effective doses (ED50) were similar, suggesting a long-lasting effect of GHS-R1a agonists with similar affinity. We also examined changes in the GHS-R gene expression during an eight-week estivation. Body weight was slightly lowered, but plasma sodium and glucose concentrations decreased; plasma urea concentration increased significantly 4weeks after the start of estivation. Overall, expression of GHS-R1a mRNA decreased, but changes in GHS-R1b mRNA expression were inconsistent with those of GHS-R1a during estivation, suggesting an involvement of GHS-R in energy homeostasis, as seen in mammals. Our results suggest that the ghrelin-GHS-R1a system is present in this lungfish although ghrelin has not yet been found. The structure of GHS-R1a is closer to that of tetrapods than Actinopterygian fish, indicating a process of evolution that follows the Crossopterygii such as coelacanth.
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Affiliation(s)
- Hiroyuki Kaiya
- Department of Biochemistry, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan.
| | - Norifumi Konno
- Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555, Japan
| | - Kenji Kangawa
- Department of Biochemistry, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
| | - Minoru Uchiyama
- Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555, Japan
| | - Mikiya Miyazato
- Department of Biochemistry, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
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26
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Brain Na+/K+-ATPase α-subunit isoforms and aestivation in the African lungfish, Protopterus annectens. J Comp Physiol B 2014; 184:571-87. [PMID: 24696295 DOI: 10.1007/s00360-014-0809-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/16/2014] [Accepted: 01/24/2014] [Indexed: 10/25/2022]
Abstract
This study aimed to clone and sequence Na (+) / K (+)-ATPase (nka) α-subunit isoforms from, and to determine their mRNA expression levels and protein abundance in the brain of the African lungfish, Protopterus annectens during the induction, maintenance and arousal phases of aestivation in air. We obtained the full cDNA sequences of nkaα1, nkaα2 and nkaα3 from the brain of P. annectens. Phylogenetic analysis of their deduced amino acid sequences revealed that they are closer to the corresponding NKA α-subunits of tetrapods than to those of fishes. The mRNA expression of these three nkaα isoforms showed differential changes in the brain of P. annectens during the three phases of aestivation. After 12 days of aestivation, there was a significant increase in the protein abundance of Nkaα1 in the brain of P. annectens. This could be an important response to maintain cellular Na(+) and K(+) concentrations and regulate cell volume during the early maintenance phase of aestivation. On the other hand, the mRNA expression of nkaα2 decreased significantly in the brain of P. annectens after 6 months of aestivation, which could be a result of a suppression of transcriptional activities to reduce energy expenditure. The down-regulation of mRNA expression of nkaα1, nkaα2 and nkaα3 and the overall protein abundance of Nka α-subunit isoforms in the brain of P. annectens after 1 day of arousal from 6 months of aestivation were novel observations, and it could be an adaptive response to restore blood pressure and/or to prevent brain oedema.
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López JM, González A. Comparative analysis of the serotonergic systems in the CNS of two lungfishes, Protopterus dolloi and Neoceratodus forsteri. Brain Struct Funct 2013; 220:385-405. [DOI: 10.1007/s00429-013-0661-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/15/2013] [Indexed: 02/02/2023]
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Zhu T, Xu PZ, Liu JP, Peng S, Mo XC, Gao LZ. Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions. Mol Phylogenet Evol 2013; 70:348-61. [PMID: 24148990 DOI: 10.1016/j.ympev.2013.10.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 08/17/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022]
Abstract
Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes. We fully reconstruct phylogenetic relationships of AA- genome species with confidence. Oryza meridionalis, native to Australia, is found to be the earliest divergent lineage around 2.93 mya, whereas O. punctata, a BB- genome species, serves as the best outgroup to distinguish their phylogenetic relationships. They separated from O. punctata approximately 9.11 mya during the Miocene epoch, and subsequently radiated to generate the entire AA- genome lineage diversity. The success in resolving the phylogeny of AA- genome species highlights the potential of phylogenomics to determine their divergence and evolutionary histories.
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Affiliation(s)
- Ting Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650204, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
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Single-male paternity in coelacanths. Nat Commun 2013; 4:2488. [PMID: 24048316 DOI: 10.1038/ncomms3488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/22/2013] [Indexed: 11/08/2022] Open
Abstract
Latimeria chalumnae, a 'living fossil,' is of great scientific interest, as it is closely related to the aquatic ancestors of land-living tetrapods. Latimeria show internal fertilization and bear live young, but their reproductive behaviour is poorly known. Here we present for the first time a paternity analysis of the only available material from gravid females and their offspring. We genotype two L. chalumnae females and their unborn brood for 14 microsatellite loci. We find that the embryos are closely related to each other and never show more than three different alleles per locus, providing evidence for a single father siring all of the offspring. We reconstruct the father's genotype but cannot identify it in the population. These data suggest that coelacanths have a monogamous mating system and that individual relatedness is not important for mate choice.
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Pallavicini A, Canapa A, Barucca M, Alfőldi J, Biscotti MA, Buonocore F, De Moro G, Di Palma F, Fausto AM, Forconi M, Gerdol M, Makapedua DM, Turner-Meier J, Olmo E, Scapigliati G. Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis. BMC Genomics 2013; 14:538. [PMID: 23927401 PMCID: PMC3750513 DOI: 10.1186/1471-2164-14-538] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 06/26/2013] [Indexed: 02/01/2023] Open
Abstract
Background Latimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species. Results The deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome. The RNA-seq analysis revealed remarkable differences in the expression profiles between the two tissues, allowing the identification of liver- and testis-specific transcripts which may play a fundamental role in important biological processes carried out by these two organs. Conclusion Given the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.
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Chalopin D, Fan S, Simakov O, Meyer A, Schartl M, Volff JN. Evolutionary active transposable elements in the genome of the coelacanth. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:322-33. [DOI: 10.1002/jez.b.22521] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/22/2013] [Accepted: 06/17/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon; Ecole Normale Supérieure de Lyon; CNRS UMR 5242; Université Lyon 1; Lyon France
| | - Shaohua Fan
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- Konstanz Research School Chemical Biology; University of Konstanz; Konstanz Germany
| | - Oleg Simakov
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- European Molecular Biology Laboratory; Heidelberg Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- Konstanz Research School Chemical Biology; University of Konstanz; Konstanz Germany
| | - Manfred Schartl
- Department Physiological Chemistry, Biocenter; University of Wuerzburg; Wuerzburg Germany
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon; Ecole Normale Supérieure de Lyon; CNRS UMR 5242; Université Lyon 1; Lyon France
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Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, Suzuki H, Okuno M, Aibara M, Ngatunga BP, Mzighani SI, Kalombo HWJ, Masengi KWA, Tuda J, Nogami S, Maeda R, Iwata M, Abe Y, Fujimura K, Okabe M, Amano T, Maeno A, Shiroishi T, Itoh T, Sugano S, Kohara Y, Fujiyama A, Okada N. Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res 2013; 23:1740-8. [PMID: 23878157 PMCID: PMC3787270 DOI: 10.1101/gr.158105.113] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coelacanths are known as “living fossils,” as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish to tetrapods. Here, we report the genome sequences of five coelacanths, including four Latimeria chalumnae individuals (three specimens from Tanzania and one from Comoros) and one L. menadoensis individual from Indonesia. These sequences cover two African breeding populations and two known extant coelacanth species. The genome is ∼2.74 Gbp and contains a high proportion (∼60%) of repetitive elements. The genetic diversity among the individuals was extremely low, suggesting a small population size and/or a slow rate of evolution. We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands. We also found that limb enhancers of bmp7 and gli3, both of which are essential for limb formation, are conserved between coelacanth and tetrapods, but not ray-finned fishes. We expect that some tetrapod-like genes may have existed early in the evolution of primitive Sarcopterygii and were later co-opted to adapt to terrestrial environments. These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals.
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Affiliation(s)
- Masato Nikaido
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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Myllykoski M, Raasakka A, Lehtimäki M, Han H, Kursula I, Kursula P. Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family. J Mol Biol 2013; 425:4307-22. [PMID: 23831225 PMCID: PMC7094350 DOI: 10.1016/j.jmb.2013.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 11/26/2022]
Abstract
2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase), a membrane-associated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the β5–α7 loop is observed. The role of the N terminus of helix α7—unique for CNPase in the 2H family—during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating that the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms. A detailed structural analysis of the CNPase catalytic cycle was carried out. Complexes with substrates, products, and analogues highlight roles for a nearby helix and loop in the reaction mechanism. The full-length CNPase adopts an elongated conformation in solution. CNPase is a unique member of the 2H family, and the results will help understand its physiological significance.
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Affiliation(s)
- Matti Myllykoski
- Department of Biochemistry, University of Oulu, FIN-90014 Oulu, Finland; Biocenter Oulu, University of Oulu, FIN-90014 Oulu, Finland
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Fritzsch B, Pan N, Jahan I, Duncan JS, Kopecky BJ, Elliott KL, Kersigo J, Yang T. Evolution and development of the tetrapod auditory system: an organ of Corti-centric perspective. Evol Dev 2013; 15:63-79. [PMID: 23331918 DOI: 10.1111/ede.12015] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The tetrapod auditory system transmits sound through the outer and middle ear to the organ of Corti or other sound pressure receivers of the inner ear where specialized hair cells translate vibrations of the basilar membrane into electrical potential changes that are conducted by the spiral ganglion neurons to the auditory nuclei. In other systems, notably the vertebrate limb, a detailed connection between the evolutionary variations in adaptive morphology and the underlying alterations in the genetic basis of development has been partially elucidated. In this review, we attempt to correlate evolutionary and partially characterized molecular data into a cohesive perspective of the evolution of the mammalian organ of Corti out of the tetrapod basilar papilla. We propose a stepwise, molecularly partially characterized transformation of the ancestral, vestibular developmental program of the vertebrate ear. This review provides a framework to decipher both discrete steps in development and the evolution of unique functional adaptations of the auditory system. The combined analysis of evolution and development establishes a powerful cross-correlation where conclusions derived from either approach become more meaningful in a larger context which is not possible through exclusively evolution or development centered perspectives. Selection may explain the survival of the fittest auditory system, but only developmental genetics can explain the arrival of the fittest auditory system. [Modified after (Wagner 2011)].
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Affiliation(s)
- Bernd Fritzsch
- Department of Biology, University of Iowa, CLAS, 143 BB, Iowa City, IA, 52242, USA. bernd‐
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Liang D, Shen XX, Zhang P. One Thousand Two Hundred Ninety Nuclear Genes from a Genome-Wide Survey Support Lungfishes as the Sister Group of Tetrapods. Mol Biol Evol 2013; 30:1803-7. [DOI: 10.1093/molbev/mst072] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Broughton RE, Betancur-R R, Li C, Arratia G, Ortí G. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLOS CURRENTS 2013; 5:ecurrents.tol.2ca8041495ffafd0c92756e75247483e. [PMID: 23788273 PMCID: PMC3682800 DOI: 10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Over half of all vertebrates are "fishes", which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.
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Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K. Localization of the primordial vomeronasal organ and its relationship to the associated gland in lungfish. J Anat 2013; 222:481-5. [PMID: 23368671 DOI: 10.1111/joa.12025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2013] [Indexed: 11/30/2022] Open
Abstract
The lungfish, the closest fish to tetrapods, has two types of sensory epithelia in the olfactory organ: the lamellar olfactory epithelium and the recess epithelium. The former resembles the olfactory epithelium of ordinary teleosts and the latter resembles the vomeronasal organ of tetrapods with respect to the G-protein expressions and the morphological properties of olfactory receptor cells. In contrast to the lamellar olfactory epithelium covering the surface of olfactory lamella, the recess epithelium, together with the glandular epithelium, lines the recesses at the base of olfactory lamellae and is separated from the surrounding tissues by nonsensory epithelium. In the present study, we examined the distribution of these recesses and the relationship between the recess epithelium and the associated gland in the nasal sac of lungfish. We found that the posterior part of the nasal sac contained more recesses than the anterior one, and the medial one contained more recesses than the lateral one. In addition, virtually all recesses consisted of both the recess epithelium and the glandular epithelium. Furthermore, the glandular epithelium was invariably situated proximal to the midline raphe of the nasal sac, and the recess epithelium distal to it. Possible roles of the recess epithelium and the glandular epithelium are discussed.
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Affiliation(s)
- Shoko Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, Morioka, Japan
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Sabbah S, Troje NF, Gray SM, Hawryshyn CW. High complexity of aquatic irradiance may have driven the evolution of four-dimensional colour vision in shallow-water fish. J Exp Biol 2013; 216:1670-82. [DOI: 10.1242/jeb.079558] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Summary
Humans use three cone photoreceptor classes for colour vision, yet many birds, reptiles and shallow-water fish are tetrachromatic and use four cone classes. Screening pigments, that narrow the spectrum of photoreceptors in birds and diurnal reptiles, render visual systems with four cone classes more efficient. To date, however, the question of tetrachromacy in shallow-water fish, that, like humans, lack screening pigments, is still unsolved. We raise the possibility that tetrachromacy in fish has evolved in response to higher spectral complexity of underwater light. We compared the dimensionality of colour vision in humans and fish by examining the spectral complexity of the colour-signal reflected from objects into their eyes. Here we show that fish require four to six cone classes to reconstruct the colour-signal of aquatic objects at the accuracy level achieved by humans viewing terrestrial objects. This is because environmental light, which alters the colour-signals, is more complex and contains more spectral fluctuations underwater than on land. We further show that fish cones are better suited than human cones to detect these spectral fluctuations, suggesting that the capability of fish cones to detect high-frequency fluctuations in the colour-signal confers an advantage. Taken together, we propose that tetrachromacy in fish has evolved to enhance the reconstruction of complex colour-signals in shallow aquatic environments. Of course, shallow-water fish might possess less than four cone classes; however, this would come with the inevitable loss in accuracy of signal reconstruction.
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Pirrello J, Prasad BCN, Zhang W, Chen K, Mila I, Zouine M, Latché A, Pech JC, Ohme-Takagi M, Regad F, Bouzayen M. Functional analysis and binding affinity of tomato ethylene response factors provide insight on the molecular bases of plant differential responses to ethylene. BMC PLANT BIOLOGY 2012; 12:190. [PMID: 23057995 PMCID: PMC3548740 DOI: 10.1186/1471-2229-12-190] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/02/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND The phytohormone ethylene is involved in a wide range of developmental processes and in mediating plant responses to biotic and abiotic stresses. Ethylene signalling acts via a linear transduction pathway leading to the activation of Ethylene Response Factor genes (ERF) which represent one of the largest gene families of plant transcription factors. How an apparently simple signalling pathway can account for the complex and widely diverse plant responses to ethylene remains yet an unanswered question. Building on the recent release of the complete tomato genome sequence, the present study aims at gaining better insight on distinctive features among ERF proteins. RESULTS A set of 28 cDNA clones encoding ERFs in the tomato (Solanum lycopersicon) were isolated and shown to fall into nine distinct subclasses characterised by specific conserved motifs most of which with unknown function. In addition of being able to regulate the transcriptional activity of GCC-box containing promoters, tomato ERFs are also shown to be active on promoters lacking this canonical ethylene-responsive-element. Moreover, the data reveal that ERF affinity to the GCC-box depends on the nucleotide environment surrounding this cis-acting element. Site-directed mutagenesis revealed that the nature of the flanking nucleotides can either enhance or reduce the binding affinity, thus conferring the binding specificity of various ERFs to target promoters.Based on their expression pattern, ERF genes can be clustered in two main clades given their preferential expression in reproductive or vegetative tissues. The regulation of several tomato ERF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signalling pathways of the two hormones. CONCLUSIONS The data reveal that regions flanking the core GCC-box sequence are part of the discrimination mechanism by which ERFs selectively bind to their target promoters. ERF tissue-specific expression combined to their responsiveness to both ethylene and auxin bring some insight on the complexity and fine regulation mechanisms involving these transcriptional mediators. All together the data support the hypothesis that ERFs are the main component enabling ethylene to regulate a wide range of physiological processes in a highly specific and coordinated manner.
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Affiliation(s)
- Julien Pirrello
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - BC Narasimha Prasad
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Wangshu Zhang
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
- Institute of Fruit Science, Zhejiang University, Hangzhou, 310029, China
| | - Kunsong Chen
- Institute of Fruit Science, Zhejiang University, Hangzhou, 310029, China
| | - Isabelle Mila
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Mohamed Zouine
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Alain Latché
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Jean Claude Pech
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Masaru Ohme-Takagi
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, Central 4, Tsukuba, 305-8562, Japan
| | - Farid Regad
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
| | - Mondher Bouzayen
- INP-ENSA Toulouse, Université de Toulouse, GBF, Avenue de l′Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France
- INRA, UMR990 Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan, F-31326, France
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Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, Horvath P, Heidenreich J, Perna NT, Barrangou R, Steele JL. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 2012; 13:533. [PMID: 23035691 PMCID: PMC3496567 DOI: 10.1186/1471-2164-13-533] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022] Open
Abstract
Background The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources. Results Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay. Conclusions Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.
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Affiliation(s)
- Jeff R Broadbent
- Department of Nutrition, Dietetics, and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA.
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Han GZ, Worobey M. An endogenous foamy-like viral element in the coelacanth genome. PLoS Pathog 2012; 8:e1002790. [PMID: 22761578 PMCID: PMC3386198 DOI: 10.1371/journal.ppat.1002790] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/22/2012] [Indexed: 11/18/2022] Open
Abstract
Little is known about the origin and long-term evolutionary mode of retroviruses. Retroviruses can integrate into their hosts' genomes, providing a molecular fossil record for studying their deep history. Here we report the discovery of an endogenous foamy virus-like element, which we designate 'coelacanth endogenous foamy-like virus' (CoeEFV), within the genome of the coelacanth (Latimeria chalumnae). Phylogenetic analyses place CoeEFV basal to all known foamy viruses, strongly suggesting an ancient ocean origin of this major retroviral lineage, which had previously been known to infect only land mammals. The discovery of CoeEFV reveals the presence of foamy-like viruses in species outside the Mammalia. We show that foamy-like viruses have likely codiverged with their vertebrate hosts for more than 407 million years and underwent an evolutionary transition from water to land with their vertebrate hosts. These findings suggest an ancient marine origin of retroviruses and have important implications in understanding foamy virus biology.
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Affiliation(s)
- Guan-Zhu Han
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (GZH); (MW)
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (GZH); (MW)
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DAVIES WAYNEIL, COLLIN SHAUNP, HUNT DAVIDM. Molecular ecology and adaptation of visual photopigments in craniates. Mol Ecol 2012; 21:3121-58. [DOI: 10.1111/j.1365-294x.2012.05617.x] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lavoué S, Miya M, Arnegard ME, Sullivan JP, Hopkins CD, Nishida M. Comparable ages for the independent origins of electrogenesis in African and South American weakly electric fishes. PLoS One 2012; 7:e36287. [PMID: 22606250 PMCID: PMC3351409 DOI: 10.1371/journal.pone.0036287] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 03/29/2012] [Indexed: 11/26/2022] Open
Abstract
One of the most remarkable examples of convergent evolution among vertebrates is illustrated by the independent origins of an active electric sense in South American and African weakly electric fishes, the Gymnotiformes and Mormyroidea, respectively. These groups independently evolved similar complex systems for object localization and communication via the generation and reception of weak electric fields. While good estimates of divergence times are critical to understanding the temporal context for the evolution and diversification of these two groups, their respective ages have been difficult to estimate due to the absence of an informative fossil record, use of strict molecular clock models in previous studies, and/or incomplete taxonomic sampling. Here, we examine the timing of the origins of the Gymnotiformes and the Mormyroidea using complete mitogenome sequences and a parametric bayesian method for divergence time reconstruction. Under two different fossil-based calibration methods, we estimated similar ages for the independent origins of the Mormyroidea and Gymnotiformes. Our absolute estimates for the origins of these groups either slightly postdate, or just predate, the final separation of Africa and South America by continental drift. The most recent common ancestor of the Mormyroidea and Gymnotiformes was found to be a non-electrogenic basal teleost living more than 85 millions years earlier. For both electric fish lineages, we also estimated similar intervals (16-19 or 22-26 million years, depending on calibration method) between the appearance of electroreception and the origin of myogenic electric organs, providing rough upper estimates for the time periods during which these complex electric organs evolved de novo from skeletal muscle precursors. The fact that the Gymnotiformes and Mormyroidea are of similar age enhances the comparative value of the weakly electric fish system for investigating pathways to evolutionary novelty, as well as the influences of key innovations in communication on the process of species radiation.
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Affiliation(s)
- Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
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Moreno N, Morona R, López JM, Domínguez L, Joven A, Bandín S, González A. Characterization of the bed nucleus of the stria terminalis in the forebrain of anuran amphibians. J Comp Neurol 2012; 520:330-63. [PMID: 21674496 DOI: 10.1002/cne.22694] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Major common features have been reported for the organization of the basal telencephalon in amniotes, and most characteristics were thought to be acquired in the transition from anamniotes to amniotes. However, gene expression, neurochemical, and hodological data obtained for the basal ganglia and septal and amygdaloid complexes in amphibians (anamniotic tetrapods) have strengthened the idea of a conserved organization in tetrapods. A poorly characterized region in the forebrain of amniotes has been the bed nucleus of the stria terminalis (BST), but numerous recent investigations have characterized it as a member of the extended amygdala. Our study analyzes the main features of the BST in anuran amphibians to establish putative homologies with amniotes. Gene expression patterns during development identified the anuran BST as a subpallial, nonstriatal territory. The BST shows Nkx2.1 and Lhx7 expression and contains an Islet1-positive cell subpopulation derived from the lateral ganglionic eminence. Immunohistochemistry for diverse peptides and neurotransmitters revealed that the distinct chemoarchitecture of the BST is strongly conserved among tetrapods. In vitro tracing techniques with dextran amines revealed important connections between the BST and the central and medial amygdala, septal territories, medial pallium, preoptic area, lateral hypothalamus, thalamus, and prethalamus. The BST receives dopaminergic projections from the ventral tegmental area and is connected with the laterodorsal tegmental nucleus and the rostral raphe in the brainstem. All these data suggest that the anuran BST shares many features with its counterpart in amniotes and belongs to a basal continuum, likely controlling similar reflexes, reponses, and behaviors in tetrapods.
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Affiliation(s)
- Nerea Moreno
- Department of Cell Biology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain.
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Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K. Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) 2012; 295:481-91. [PMID: 22271496 DOI: 10.1002/ar.22415] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 12/28/2011] [Indexed: 11/10/2022]
Abstract
Many vertebrates have two anatomically distinct olfactory organs--the olfactory epithelium and the vomeronasal organ--to detect chemicals such as general odorants and pheromones in their environment. The vomeronasal organ is not present in fish but is present in vertebrates of a higher order than amphibians. Among all extant fishes, the lungfish is considered to be genetically and phylogenetically closest to tetrapods. In this study, we examined the olfactory organs of African lungfish, Protopterus annectens, by lectin histochemistry, immunohistochemistry, and transmission electron microscopy. Two types of sensory epithelia were identified in the olfactory organ--the olfactory epithelium covering the surface of lamellae and the sensory epithelium lining the recesses both at the base of lamellae and in the wall of the nasal sac--and designated here as the lamellar olfactory epithelium and the recess epithelium, respectively. Based on analysis of G-protein expression and ultrastructure, the lamellar olfactory epithelium resembled the olfactory epithelium of ordinary teleosts and the recess epithelium resembled the vomeronasal organ of tetrapods. Furthermore, lectin histochemistry demonstrated that the axons from the recess epithelium converge and project to the ventrolateral part of the olfactory bulb, suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as "a primordium of the vomeronasal organ." This study may provide important clues to elucidate how the vomeronasal organ emerged during the evolution of vertebrates.
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Affiliation(s)
- Shoko Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
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Almeida FC, Giannini NP, DeSalle R, Simmons NB. Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): another star phylogeny? BMC Evol Biol 2011; 11:281. [PMID: 21961908 PMCID: PMC3199269 DOI: 10.1186/1471-2148-11-281] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 09/30/2011] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The family Pteropodidae comprises bats commonly known as megabats or Old World fruit bats. Molecular phylogenetic studies of pteropodids have provided considerable insight into intrafamilial relationships, but these studies have included only a fraction of the extant diversity (a maximum of 26 out of the 46 currently recognized genera) and have failed to resolve deep relationships among internal clades. Here we readdress the systematics of pteropodids by applying a strategy to try to resolve ancient relationships within Pteropodidae, while providing further insight into subgroup membership, by 1) increasing the taxonomic sample to 42 genera; 2) increasing the number of characters (to >8,000 bp) and nuclear genomic representation; 3) minimizing missing data; 4) controlling for sequence bias; and 5) using appropriate data partitioning and models of sequence evolution. RESULTS Our analyses recovered six principal clades and one additional independent lineage (consisting of a single genus) within Pteropodidae. Reciprocal monophyly of these groups was highly supported and generally congruent among the different methods and datasets used. Likewise, most relationships within these principal clades were well resolved and statistically supported. Relationships among the 7 principal groups, however, were poorly supported in all analyses. This result could not be explained by any detectable systematic bias in the data or incongruence among loci. The SOWH test confirmed that basal branches' lengths were not different from zero, which points to closely-spaced cladogenesis as the most likely explanation for the poor resolution of the deep pteropodid relationships. Simulations suggest that an increase in the amount of sequence data is likely to solve this problem. CONCLUSIONS The phylogenetic hypothesis generated here provides a robust framework for a revised cladistic classification of Pteropodidae into subfamilies and tribes and will greatly contribute to the understanding of character evolution and biogeography of pteropodids. The inability of our data to resolve the deepest relationships of the major pteropodid lineages suggests an explosive diversification soon after origin of the crown pteropodids. Several characteristics of pteropodids are consistent with this conclusion, including high species diversity, great morphological diversity, and presence of key innovations in relation to their sister group.
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Affiliation(s)
- Francisca C Almeida
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park West at 79th Street, New York, NY 10024, USA
- Universitat de Barcelona, Departament de Genètica, Diagonal 645, Barcelona, 08028, Spain
| | - Norberto P Giannini
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
- CONICET, Programa de Investigaciones de Biodiversidad Argentina, Universidad Nacional de Tucumán, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Miguel Lillo 205, Tucumán, CP 4000, Argentina
| | - Rob DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park West at 79th Street, New York, NY 10024, USA
| | - Nancy B Simmons
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
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George D, Blieck A. Rise of the earliest tetrapods: an early Devonian origin from marine environment. PLoS One 2011; 6:e22136. [PMID: 21779385 PMCID: PMC3136505 DOI: 10.1371/journal.pone.0022136] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/16/2011] [Indexed: 12/01/2022] Open
Abstract
Tetrapod fossil tracks are known from the Middle Devonian (Eifelian at ca. 397 million years ago - MYA), and their earliest bony remains from the Upper Devonian (Frasnian at 375–385 MYA). Tetrapods are now generally considered to have colonized land during the Carboniferous (i.e., after 359 MYA), which is considered to be one of the major events in the history of life. Our analysis on tetrapod evolution was performed using molecular data consisting of 13 proteins from 17 species and different paleontological data. The analysis on the molecular data was performed with the program TreeSAAP and the results were analyzed to see if they had implications on the paleontological data collected. The results have shown that tetrapods evolved from marine environments during times of higher oxygen levels. The change in environmental conditions played a major role in their evolution. According to our analysis this evolution occurred at about 397–416 MYA during the Early Devonian unlike previously thought. This idea is supported by various environmental factors such as sea levels and oxygen rate, and biotic factors such as biodiversity of arthropods and coral reefs. The molecular data also strongly supports lungfish as tetrapod's closest living relative.
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Affiliation(s)
- David George
- Department of Biotechnology, St. Peter's Engineering College, Chennai, Tamil Nadu, India.
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Characterization of new medium-chain alcohol dehydrogenases adds resolution to duplications of the class I/III and the sub-class I genes. Chem Biol Interact 2011; 191:8-13. [DOI: 10.1016/j.cbi.2011.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/01/2011] [Accepted: 02/02/2011] [Indexed: 11/22/2022]
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Shan Y, Gras R. 43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model. BMC Res Notes 2011; 4:49. [PMID: 21385375 PMCID: PMC3069939 DOI: 10.1186/1756-0500-4-49] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 03/07/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the discovery of the "living fossil" in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. FINDINGS We used the Bayesian method under the coalescence model with the latest published program (Bayesian Estimation of Species Trees, or BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear protein-coding genes with the jackknife method for taxon sub-sampling. The lungfish-coelacanth sister group was consistently reconstructed with the Bayesian method under the coalescence model in 17 out of 21 taxon sets with a Bayesian posterior probability as high as 99%. Lungfish-tetrapod was only inferred from BCLS and BACLS. Neither coelacanth-tetrapod nor lungfish-coelacanth-tetrapod was recovered out of all 21 taxon sets. CONCLUSIONS Our results provide strong evidence in favor of accepting the hypothesis that lungfishes and coelacanths form a monophyletic sister-group that is the closest living relative of tetrapods. This clade was supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.
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Affiliation(s)
- Yunfeng Shan
- School of Computer Science, University of Windsor, 401 Sunset Avenue, Windsor, ON N9B 3P4, Canada.
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