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Abstract
The auditory systems of birds and mammals use timing information from each ear to detect interaural time difference (ITD). To determine whether the Jeffress-type algorithms that underlie sensitivity to ITD in birds are an evolutionarily stable strategy, we recorded from the auditory nuclei of crocodilians, who are the sister group to the birds. In alligators, precisely timed spikes in the first-order nucleus magnocellularis (NM) encode the timing of sounds, and NM neurons project to neurons in the nucleus laminaris (NL) that detect interaural time differences. In vivo recordings from NL neurons show that the arrival time of phase-locked spikes differs between the ipsilateral and contralateral inputs. When this disparity is nullified by their best ITD, the neurons respond maximally. Thus NL neurons act as coincidence detectors. A biologically detailed model of NL with alligator parameters discriminated ITDs up to 1 kHz. The range of best ITDs represented in NL was much larger than in birds, however, and extended from 0 to 1000 micros contralateral, with a median ITD of 450 micros. Thus, crocodilians and birds employ similar algorithms for ITD detection, although crocodilians have larger heads.
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102
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Miles LG, Isberg SR, Glenn TC, Lance SL, Dalzell P, Thomson PC, Moran C. A genetic linkage map for the saltwater crocodile (Crocodylus porosus). BMC Genomics 2009; 10:339. [PMID: 19640266 PMCID: PMC2907706 DOI: 10.1186/1471-2164-10-339] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 07/29/2009] [Indexed: 11/29/2022] Open
Abstract
Background Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL), and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary. Results A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus) was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM) respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1). Conclusion We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD). However, at this point the reason for this disparity in saltwater crocodiles remains unclear. This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition, since many of the markers placed on this genetic map have been evaluated in up to 18 other extant species of crocodilian, this map will be of intrinsic value to comparative mapping efforts aimed at understanding genome content and organization among crocodilians, as well as the molecular evolution of reptilian and other amniote genomes. As researchers continue to work towards elucidation of the crocodilian genome, this first generation map lays the groundwork for more detailed mapping investigations, as well as providing a valuable scaffold for future genome sequence assembly.
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Affiliation(s)
- Lee G Miles
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia.
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103
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Chapus C, Edwards SV. Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird. BMC Genomics 2009; 10 Suppl 2:S8. [PMID: 19607659 PMCID: PMC2966332 DOI: 10.1186/1471-2164-10-s2-s8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. RESULTS From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. CONCLUSION Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.
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Affiliation(s)
- Charles Chapus
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Fine structural observation on the oogenesis and vitellogenesis of the Chinese soft-shelled turtle ( Pelodiseus sinensis). ZYGOTE 2009; 18:109-20. [PMID: 19586560 DOI: 10.1017/s0967199409990116] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Fine structure observations were performed by means of electron microscopy on oogenesis and vitellogenesis and the special functions of follicular cells in the Chinese soft-shelled turtle (Pelodiseus sinensis). Histological examination of the ovary showed a well developed lacunae system containing fine granules, fibres or gelatiniform materials with one or two germinal beds dispersed on the dorsal surface of the ovarian cortex. The process of oogenesis comprised 10 consecutive phases according to the morphology of the yolk platelets, follicular cells and zona pellucida (ZP). Electron microscopy of vitellogenesis revealed some of the mitochondria gradually being transformed into yolk granules. In the advanced stage of vitellogenesis, large amounts of rough endoplasmic reticula, Golgiosomes and other cell organelles that are involved in synthesis and secretion were observed in follicular cells. The ZP was formed by microvilli, thus increasing the absorptive surface of the oocyte and facilitating transport of nutrients from the follicular epithelium to the ooplasm. This study demonstrated that the ovaries of members of the Testudinidae share more features with Archosaurs than with Squamates, indicating that these features were phylogenetically conserved in the Archosauria. The present observations suggest that the accumulation of yolk materials was controlled by the intrinsic and extrinsic pathways as well as by the activity of follicular cells. These results might also support a sibling relationship of the Testudinidae with the Archosauria and not with all extant reptiles.
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POKORNÁ MARTINA, KRATOCHVÍL LUKÁŠ. Phylogeny of sex-determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap? Zool J Linn Soc 2009. [DOI: 10.1111/j.1096-3642.2008.00481.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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107
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Li SF, Xu JW, Yang QL, Wang CH, Chen Q, Chapman DC, Lu G. A comparison of complete mitochondrial genomes of silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis: implications for their taxonomic relationship and phylogeny. JOURNAL OF FISH BIOLOGY 2009; 74:1787-1803. [PMID: 20735671 DOI: 10.1111/j.1095-8649.2009.02258.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Based upon morphological characters, Silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis (or Aristichthys nobilis) have been classified into either the same genus or two distinct genera. Consequently, the taxonomic relationship of the two species at the generic level remains equivocal. This issue is addressed by sequencing complete mitochondrial genomes of H. molitrix and H. nobilis, comparing their mitogenome organization, structure and sequence similarity, and conducting a comprehensive phylogenetic analysis of cyprinid species. As with other cyprinid fishes, the mitogenomes of the two species were structurally conserved, containing 37 genes including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA (tRNAs) genes and a putative control region (D-loop). Sequence similarity between the two mitogenomes varied in different genes or regions, being highest in the tRNA genes (98.8%), lowest in the control region (89.4%) and intermediate in the protein-coding genes (94.2%). Analyses of the sequence comparison and phylogeny using concatenated protein sequences support the view that the two species belong to the genus Hypophthalmichthys. Further studies using nuclear markers and involving more closely related species, and the systematic combination of traditional biology and molecular biology are needed in order to confirm this conclusion.
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Affiliation(s)
- S F Li
- Key Laboratory of Aquatic Genetic Resources and Utilization, Ministry of Agriculture, Shanghai Ocean University, Shanghai 200090, China.
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Werneburg I, Sánchez-Villagra MR. Timing of organogenesis support basal position of turtles in the amniote tree of life. BMC Evol Biol 2009; 9:82. [PMID: 19389226 PMCID: PMC2679012 DOI: 10.1186/1471-2148-9-82] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 04/23/2009] [Indexed: 11/30/2022] Open
Abstract
Background The phylogenetic position of turtles is the most disputed aspect in the reconstruction of the land vertebrate tree of life. This controversy has arisen after many different kinds and revisions of investigations of molecular and morphological data. Three main hypotheses of living sister-groups of turtles have resulted from them: all reptiles, crocodiles + birds or squamates + tuatara. Although embryology has played a major role in morphological studies of vertebrate phylogeny, data on developmental timing have never been examined to explore and test the alternative phylogenetic hypotheses. We conducted a comprehensive study of published and new embryological data comprising 15 turtle and eight tetrapod species belonging to other taxa, integrating for the first time data on the side-necked turtle clade. Results The timing of events in organogenesis of diverse character complexes in all body regions is not uniform across amniotes and can be analysed using a parsimony-based method. Changes in the relative timing of particular events diagnose many clades of amniotes and include a phylogenetic signal. A basal position of turtles to the living saurian clades is clearly supported by timing of organogenesis data. Conclusion The clear signal of a basal position of turtles provided by heterochronic data implies significant convergence in either molecular, adult morphological or developmental timing characters, as only one of the alternative solutions to the phylogenetic conundrum can be right. The development of a standard reference series of embryological events in amniotes as presented here should enable future improvements and expansion of sampling and thus the examination of other hypotheses about phylogeny and patterns of the evolution of land vertebrate development.
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Affiliation(s)
- Ingmar Werneburg
- Paläontologisches Institut und Museum der Universität Zürich, Zürich, Switzerland.
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109
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Temporal germ cell development strategy during spermatogenesis within the testis of the Ground Skink, Scincella lateralis (Sauria: Scincidae). Theriogenology 2009; 72:54-61. [PMID: 19344944 DOI: 10.1016/j.theriogenology.2009.01.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 01/20/2009] [Accepted: 01/18/2009] [Indexed: 11/24/2022]
Abstract
Ground Skink (Scincella lateralis) testes were examined histologically to determine the testicular organization and germ cell development strategy employed during spermatogenesis. Testicular tissues were collected from 19 ground skinks from Aiken County, South Carolina during the months of March-June, August, and October. The testes consisted of seminiferous tubules lined with germinal epithelia in which germ cells matured in close association with Sertoli cells. As germ cells matured, they migrated away from the basal lamina of the epithelia towards the lumina of the seminiferous tubules. The testes were spermatogenically active during the months of March, April, May, June, and October (largest seminiferous tubule diameters and epithelial heights), but entered a quiescent period in August (smallest seminiferous tubule diameter and epithelial height) where only spermatogonia type A and B and early spermatocytes were present in low numbers within the seminiferous epithelium. Although the testicular organization was similar to other amniotes, a temporal germ cell development strategy was employed during spermatogenesis within Ground Skinks, similar to that of anamniotes. Thus, this skink's germ cell development strategy, which also has been recently reported in all other major reptilian clades, may represent an evolutionary intermediate in terms of testicular organization between anamniotes and birds and mammals.
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110
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Davit-Béal T, Tucker AS, Sire JY. Loss of teeth and enamel in tetrapods: fossil record, genetic data and morphological adaptations. J Anat 2009; 214:477-501. [PMID: 19422426 PMCID: PMC2736120 DOI: 10.1111/j.1469-7580.2009.01060.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2009] [Indexed: 12/29/2022] Open
Abstract
Since their recruitment in the oral cavity, approximately 450 million years ago, teeth have been subjected to strong selective constraints due to the crucial role that they play in species survival. It is therefore quite surprising that the ability to develop functional teeth has subsequently been lost several times, independently, in various lineages. In this review, we concentrate our attention on tetrapods, the only vertebrate lineage in which several clades lack functional teeth from birth to adulthood. Indeed, in other lineages, teeth can be absent in adults but be functionally present in larvae and juveniles, can be absent in the oral cavity but exist in the pharyngeal region, or can develop on the upper jaw but be absent on the lower jaw. Here, we analyse the current data on toothless (edentate) tetrapod taxa, including information available on enamel-less species. Firstly, we provide an analysis of the dispersed and fragmentary morphological data published on the various living taxa concerned (and their extinct relatives) with the aim of tracing the origin of tooth or enamel loss, i.e. toads in Lissamphibia, turtles and birds in Sauropsida, and baleen whales, pangolins, anteaters, sloths, armadillos and aardvark in Mammalia. Secondly, we present current hypotheses on the genetic basis of tooth loss in the chicken and thirdly, we try to answer the question of how these taxa have survived tooth loss given the crucial importance of this tool. The loss of teeth (or only enamel) in all of these taxa was not lethal because it was always preceded in evolution by the pre-adaptation of a secondary tool (beak, baleens, elongated adhesive tongues or hypselodonty) useful for improving efficiency in food uptake. The positive selection of such secondary tools would have led to relaxed functional constraints on teeth and would have later compensated for the loss of teeth. These hypotheses raise numerous questions that will hopefully be answered in the near future.
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Affiliation(s)
- Tiphaine Davit-Béal
- Université Pierre & Marie CurieUMR 7138 ‘Systématique, Adaptation, Evolution’, Paris, France
| | - Abigail S Tucker
- Craniofacial Development and Orthodontics, King's College London, Guy's HospitalLondon, UK
| | - Jean-Yves Sire
- Université Pierre & Marie CurieUMR 7138 ‘Systématique, Adaptation, Evolution’, Paris, France
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111
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Lyson T, Gilbert SF. Turtles all the way down: loggerheads at the root of the chelonian tree. Evol Dev 2009; 11:133-5. [DOI: 10.1111/j.1525-142x.2009.00325.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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112
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While GM, Uller T, Wapstra E. Family conflict and the evolution of sociality in reptiles. Behav Ecol 2009. [DOI: 10.1093/beheco/arp015] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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113
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Poloczanska ES, Limpus CJ, Hays GC. Chapter 2. Vulnerability of marine turtles to climate change. ADVANCES IN MARINE BIOLOGY 2009; 56:151-211. [PMID: 19895975 DOI: 10.1016/s0065-2881(09)56002-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Marine turtles are generally viewed as vulnerable to climate change because of the role that temperature plays in the sex determination of embryos, their long life history, long age-to-maturity and their highly migratory nature. Extant species of marine turtles probably arose during the mid-late Jurassic period (180-150 Mya) so have survived past shifts in climate, including glacial periods and warm events and therefore have some capacity for adaptation. The present-day rates of increase of atmospheric greenhouse gas concentrations, and associated temperature changes, are very rapid; the capacity of marine turtles to adapt to this rapid change may be compromised by their relatively long generation times. We consider the evidence and likely consequences of present-day trends of climate change on marine turtles. Impacts are likely to be complex and may be positive as well as negative. For example, rising sea levels and increased storm intensity will negatively impact turtle nesting beaches; however, extreme storms can also lead to coastal accretion. Alteration of wind patterns and ocean currents will have implications for juveniles and adults in the open ocean. Warming temperatures are likely to impact directly all turtle life stages, such as the sex determination of embryos in the nest and growth rates. Warming of 2 degrees C could potentially result in a large shift in sex ratios towards females at many rookeries, although some populations may be resilient to warming if female biases remain within levels where population success is not impaired. Indirectly, climate change is likely to impact turtles through changes in food availability. The highly migratory nature of turtles and their ability to move considerable distances in short periods of time should increase their resilience to climate change. However, any such resilience of marine turtles to climate change is likely to be severely compromised by other anthropogenic influences. Development of coastlines may threaten nesting beaches and reproductive success, and pollution and eutrophication is threatening important coastal foraging habitats for turtles worldwide. Exploitation and bycatch in other fisheries has seriously reduced marine turtle populations. The synergistic effects of other human-induced stressors may seriously reduce the capacity of some turtle populations to adapt to the current rates of climate change. Conservation recommendations to increase the capacity of marine turtle populations to adapt to climate change include increasing population resilience, for example by the use of turtle exclusion devices in fisheries, protection of nesting beaches from the viewpoints of both conservation and coastal management, and increased international conservation efforts to protect turtles in regions where there is high unregulated or illegal fisheries (including turtle harvesting). Increasing research efforts on the critical knowledge gaps of processes influencing population numbers, such as identifying ocean foraging hotspots or the processes that underlie the initiation of nesting migrations and selection of breeding areas, will inform adaptive management in a changing climate.
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Affiliation(s)
- Elvira S Poloczanska
- Climate Adaptation Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Queensland 4163, Australia
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115
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Nomura T, Hattori M, Osumi N. Reelin, radial fibers and cortical evolution: Insights from comparative analysis of the mammalian and avian telencephalon. Dev Growth Differ 2008; 51:287-97. [DOI: 10.1111/j.1440-169x.2008.01073.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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116
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OROZCO-TERWENGEL PABLO, NAGY ZOLTÁNT, VIEITES DAVIDR, VENCES MIGUEL, LOUIS JR EDWARD. Phylogeography and phylogenetic relationships of Malagasy tree and ground boas. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01083.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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117
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Herbst LH, Lenz J, Van Doorslaer K, Chen Z, Stacy BA, Wellehan JFX, Manire CA, Burk RD. Genomic characterization of two novel reptilian papillomaviruses, Chelonia mydas papillomavirus 1 and Caretta caretta papillomavirus 1. Virology 2008; 383:131-5. [PMID: 18973915 DOI: 10.1016/j.virol.2008.09.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 08/29/2008] [Accepted: 09/08/2008] [Indexed: 10/21/2022]
Abstract
In this paper we describe the characterization of the genomes of two sea turtle papillomaviruses, Chelonia mydas PV (CmPV-1) and Caretta caretta PV (CcPV-1). The isolation and sequencing of the first non-avian reptilian PVs extend the evolutionary history of PVs to include all amniotes. PVs have now been described in mammals, birds and non-avian reptiles. The chelonian PVs form a distinct clade most closely related to the avian PVs. Unlike the avian PVs, both chelonian PVs have canonical E6 and E7 ORFs, indicating that these genes were present in the common ancestor to mammalian and non-mammalian amniote PVs. Rates of evolution among the non-mammalian PVs were generally slower than those estimated for mammalian PVs, perhaps due to lower metabolic rates among the ectothermic reptiles.
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Affiliation(s)
- Lawrence H Herbst
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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118
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Abstract
The N-terminal region of human HOXA13 has seven discrete polyalanine tracts. Our previous analysis of these tracts in multiple major vertebrate clades suggested that three are mammal-specific. We now report the N-terminal HOXA13 repetitive tract structures in the monotreme Tachyglossus aculeatus (echidna). Contrary to our expectations, echidna HOXA13 possesses a unique set of polyalanine tracts and an unprecedented polyglycine tract. The data support the conclusion that the emergence of expanded polyalanine tracts in proteins occurred very early in the stem lineage that gave rise to mammals, between 162 and 315 Ma.
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Affiliation(s)
- Jessica A Lehoczky
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
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119
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Amniote phylogenomics: testing evolutionary hypotheses with BAC library scanning and targeted clone analysis of large-scale DNA sequences from reptiles. Methods Mol Biol 2008; 422:91-117. [PMID: 18629663 DOI: 10.1007/978-1-59745-581-7_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Phylogenomics research integrating established principles of systematic biology and taking advantage of the wealth of DNA sequences being generated by genome science holds promise for answering long-standing evolutionary questions with orders of magnitude more primary data than in the past. Although it is unrealistic to expect whole-genome initiatives to proceed rapidly for commercially unimportant species such as reptiles, practical approaches utilizing genomic libraries of large-insert clones pave the way for a phylogenomics of species that are nevertheless essential for testing evolutionary hypotheses within a phylogenetic framework. This chapter reviews the case for adopting genome-enabled approaches to evolutionary studies and outlines a program for using bacterial artificial chromosome (BAC) libraries or plasmid libraries as a basis for completing "genome scans" of reptiles. We have used BACs to close a critical gap in the genome database for Reptilia, the sister group of mammals, and present the methodological approaches taken to achieve this as a guideline for designing similar comparative studies. In addition, we provide a detailed step-by-step protocol for BAC-library screening and shotgun sequencing of specific clones containing target genes of evolutionary interest. Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species.
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120
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Albert EM, San Mauro D, García-París M, Rüber L, Zardoya R. Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data. Gene 2008; 441:12-21. [PMID: 18639394 DOI: 10.1016/j.gene.2008.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 05/12/2008] [Accepted: 05/13/2008] [Indexed: 10/22/2022]
Abstract
The complete nucleotide sequences of the mitochondrial (mt) genomes of three species of squamate lizards: Blanus cinereus (Amphisbaenidae), Anguis fragilis (Anguidae), and Tarentola mauritanica (Geckkonidae) were determined anew. The deduced amino acid sequences of all 13 mt protein-coding genes were combined into a single data set and phylogenetic relationships among main squamate lineages were analyzed under maximum likelihood (ML) and Bayesian Inference (BI). Within Squamata, the monophyly of Iguanidae, Anguimorpha, Amphisbaenia, Gekkota, Serpentes, and Acrodonta received high statistical support with both methods. It is particularly striking that this is the first molecular analysis that recovers the monophyly of Scincomorpha (including Scincidae, Xantusiidae, Cordylidae, and Lacertidae), although it is only supported in the Bayesian analysis, and it is sensitive to changes in the outgroup (see below). Phylogenetic relationships among the main squamate lineages could not be resolved with ML but received strong support with BI (above 95%). The newly reconstructed phylogeny of squamates does not support the Iguania-Scleroglossa split. Acrodonta and Serpentes form a clade, which is the sister group of the remaining squamate lineages. Within these, Gekkota were the first branching out, followed by Amphisbaenia, and a clade including Anguimorpha as sister group of Scincomorpha + Iguanidae. The recovered topology differed substantially from previously reported hypotheses on squamate relationships, and the relative effect of using different outgroups, genes, and taxon samplings were explored. The sister group relationship of Serpentes + Acrodonta, and their relative basal position within Squamata could be due to a long-branch attraction artifact. Phylogenetic relationships among Scincomorpha, Amphisbaenia, and Anguimorpha were found to be rather unresolved. Future improving of squamate phylogenetic relationships would rely on finding snake and acrodont species with slower mt evolutionary rates, ensuring thorough taxon coverage of squamate diversity, and incorporating more nuclear genes with appropriate evolutionary rates.
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Affiliation(s)
- Eva M Albert
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006 Madrid, Spain
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Heiss E, Plenk H, Weisgram J. Microanatomy of the Palatal Mucosa of the Semiaquatic Malayan Box Turtle,Cuora amboinensis, and Functional Implications. Anat Rec (Hoboken) 2008; 291:876-85. [DOI: 10.1002/ar.20695] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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122
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Butcher MT, Blob RW. Mechanics of limb bone loading during terrestrial locomotion in river cooter turtles (Pseudemys concinna). ACTA ACUST UNITED AC 2008; 211:1187-202. [PMID: 18375843 DOI: 10.1242/jeb.012989] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Studies of limb bone loading during terrestrial locomotion have focused primarily on birds and mammals. However, data from a broader functional and phylogenetic range of species are critical for understanding the evolution of limb bone function and design. Turtles are an interesting lineage in this context. Although their slow walking speeds and robust limb bones might lead to low locomotor forces and limb bone stresses similar to other non-avian reptiles, their highly sprawled posture could produce high bending loads, leading to high limb bone stresses similar to those of avian and mammalian species, as well as high torsion. To test between these possibilities, we evaluated stresses experienced by the femur of river cooter turtles (Pseudemys concinna) during terrestrial walking by synchronizing measurements of three-dimensional joint kinematics and ground reaction forces (GRFs) during isolated hindlimb footfalls. Further, we evaluated femoral safety factors for this species by comparing our locomotor stress calculations with the results of mechanical property tests. The net GRF magnitude at peak tensile bone stress averaged 0.35 BW (body weight) and was directed nearly vertically for the middle 40-65% of the contact interval, essentially orthogonal to the femur. Peak bending stresses experienced by the femur were low (tensile: 24.9+/-9.0 MPa; compressive: -31.1+/-9.1 MPa) and comparable to those in other reptiles, yet peak shear stresses were higher than those in other reptiles, averaging 13.7+/-4.2 MPa. Such high torsion is present despite cooters lacking a large tail, a feature that has been hypothesized to contribute to torsion in other reptiles in which the tail is dragged along the ground. Comparison of femoral stresses to measurements of limb bone mechanical properties in cooters indicates safety factors to yield of 13.9 in bending and 6.3 in torsion, considerably higher than values typical for birds and mammals, and closer to the elevated values calculated for other reptile species. Thus, not only do turtle limb bones seem considerably ;over-designed' for resisting the loads that they encounter, but comparisons of bone loading across tetrapod lineages are consistent with the hypothesis that low limb bone loads, elevated torsion and high safety factors may be primitive features of limb bone design.
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Affiliation(s)
- Michael T Butcher
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
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Abstract
Reptiles are a karyologically heterogeneous group, where some orders and suborders exhibit characteristics similar to those of anamniotes and others share similarities with homeotherms. The class also shows different evolutionary trends, for instance in genome and chromosome size and composition. The turtle DNA base composition is similar to that of mammals, whereas that of lizards and snakes is more similar to that of anamniotes. The major karyological differences between turtles and squamates are the size and composition of the genome and the rate at which chromosomes change. Turtles have larger and more variable genome sizes, and a greater amount of middle repetitive DNA that differs even among related species. In lizards and snakes size of the genome are smaller, single-copy DNA is constant within each suborder, and differences in repetitive DNA involve fractions that become increasingly heterogeneous with widening phylogenetic distance. With regard to variation in karyotype morphology, turtles and crocodiles show low variability in chromosome number, morphology, and G-banding pattern. Greater variability is found among squamates, which have a similar degree of karyotypic change-as do some mammals, such as carnivores and bats-and in which there are also differences among congeneric species. An interesting relationship has been highlighted in the entire class Reptilia between rates of change in chromosomes, number of living species, and rate of extinction. However, different situations obtain in turtles and crocodiles on the one hand, and squamates on the other. In the former, the rate of change in chromosomes is lower and the various evolutionary steps do not seem to have entailed marked chromosomal variation, whereas squamates have a higher rate of change in chromosomes clearly related to the number of living species, and chromosomal variation seems to have played an important role in the evolution of several taxa. The different evolutionary trends in chromosomes observed between turtles and crocodiles on the one hand and squamates on the other might depend on their different patterns of G-banding.
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Affiliation(s)
- Ettore Olmo
- Istituto di Biologia e Genetica, Università Politecnica delle Marche and Istituto Nazionale di Biosistemi e Biostrutture, Via Brecce Bianche, 60131 Ancona, Italy
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KRILOFF A, GERMAIN D, CANOVILLE A, VINCENT P, SACHE M, LAURIN M. Evolution of bone microanatomy of the tetrapod tibia and its use in palaeobiological inference. J Evol Biol 2008; 21:807-26. [DOI: 10.1111/j.1420-9101.2008.01512.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Trajanovska S, Donald JA. Molecular cloning of natriuretic peptides from the heart of reptiles: loss of ANP in diapsid reptiles and birds. Gen Comp Endocrinol 2008; 156:339-46. [PMID: 18295764 DOI: 10.1016/j.ygcen.2008.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 10/08/2007] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
Abstract
Atrial natriuretic peptide (ANP) and B-type NP (BNP) are hormones involved in homeostatic control of body fluid and cardiovascular regulation. Both ANP and BNP have been cloned from the heart of mammals, amphibians, and teleost fishes, while an additional cardiac peptide, ventricular NP, has been found in selected species of teleost fish. However, in chicken, BNP is the primary cardiac peptide identified thus far. In contrast, the types of NP/s present in the reptilian heart are unknown, representing a considerable gap in our understanding of NP evolution. In the present study, we cloned and sequenced a BNP cDNA from the atria of representative species of reptile, including crocodile, lizard, snake, and tortoise. In addition, we cloned BNP from the pigeon atria. The reptilian and pigeon BNP cDNAs had ATTTA repeats in the 3' untranslated region, as observed in all vertebrate BNP mRNAs. A high sequence homology was evident when comparing reptile and pigeon preproBNP with the previously identified chicken preproBNP. In particular, the predicted mature BNP-29 was identical between crocodile, tortoise, and chicken, with pigeon having a single amino acid substitution; lizard and snake BNP had seven and nine substitutions, respectively. Furthermore, an ANP cDNA could only be cloned from the tortoise atria. Since ANP was not isolated from the heart of any non-chelonian reptile and appears to be absent in birds, we propose that the ANP gene has been lost after branching of the turtles in the amniote line. This data provides new avenues for research on NP function in reptiles.
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Affiliation(s)
- Sofie Trajanovska
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
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129
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SELIGMANN HERVÉ, MORAVEC JIŘÍ, WERNER YEHUDAHL. Morphological, functional and evolutionary aspects of tail autotomy and regeneration in the ‘living fossil’Sphenodon (Reptilia: Rhynchocephalia). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.00975.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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130
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RAWLINGS LESLEYH, RABOSKY DANIELL, DONNELLAN STEPHENC, HUTCHINSON MARKN. Python phylogenetics: inference from morphology and mitochondrial DNA. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2007.00904.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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131
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Affiliation(s)
- F Brischoux
- Centre d'Etudes Biologiques de Chizé- CNRS, Villiers en Bois, FranceUniversité François Rabelais, 3 rue des Tanneurs, Tours, Cedex 1, FranceBiological Sciences A08, University of Sydney, Sydney, NSW, Australia
| | - X Bonnet
- Centre d'Etudes Biologiques de Chizé- CNRS, Villiers en Bois, FranceUniversité François Rabelais, 3 rue des Tanneurs, Tours, Cedex 1, FranceBiological Sciences A08, University of Sydney, Sydney, NSW, Australia
| | - T R Cook
- Centre d'Etudes Biologiques de Chizé- CNRS, Villiers en Bois, FranceUniversité François Rabelais, 3 rue des Tanneurs, Tours, Cedex 1, FranceBiological Sciences A08, University of Sydney, Sydney, NSW, Australia
| | - R Shine
- Centre d'Etudes Biologiques de Chizé- CNRS, Villiers en Bois, FranceUniversité François Rabelais, 3 rue des Tanneurs, Tours, Cedex 1, FranceBiological Sciences A08, University of Sydney, Sydney, NSW, Australia
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Roos J, Aggarwal RK, Janke A. Extended mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous–Tertiary boundary. Mol Phylogenet Evol 2007; 45:663-73. [PMID: 17719245 DOI: 10.1016/j.ympev.2007.06.018] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 06/07/2007] [Accepted: 06/22/2007] [Indexed: 10/23/2022]
Abstract
The mitochondrial genomes of the dwarf crocodile, Osteolaemus tetraspis, and two species of dwarf caimans, the smooth-fronted caiman, Paleosuchus trigonatus, and Cuvier's dwarf caiman, Paleosuchus palpebrosus, were sequenced and included in a mitogenomic phylogenetic study. The phylogenetic analyses, which included a total of ten crocodylian species, yielded strong support to a basal split between Crocodylidae and Alligatoridae. Osteolaemus fell within the Crocodylidae as the sister group to Crocodylus. Gavialis and Tomistoma, which joined on a common branch, constituted a sister group to Crocodylus/Osteolaemus. This suggests that extant crocodylians are organized in two families: Alligatoridae and Crocodylidae. Within the Alligatoridae there was a basal split between Alligator and a branch that contained Paleosuchus and Caiman. The analyses also provided molecular estimates of various divergences applying recently established crocodylian and outgroup fossil calibration points. Molecular estimates based on amino acid data placed the divergence between Crocodylidae and Alligatoridae at 97-103 million years ago and that between Alligator and Caiman/Paleosuchus at 65-72 million years ago. Other crocodilian divergences were placed after the Cretaceous-Tertiary boundary. Thus, according to the molecular estimates, three extant crocodylian lineages have their roots in the Cretaceous. Considering the crocodylian diversification in the Cretaceous the molecular datings suggest that the extinction of the dinosaurs was also to some extent paralleled in the crocodylian evolution. However, for whatever reason, some crocodylian lineages survived into the Tertiary.
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Affiliation(s)
- Jonas Roos
- Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Sölvegatan 29, S-223 62 Lund, Sweden
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Rodrigues SL, Maseko BC, Ihunwo AO, Fuxe K, Manger PR. Nuclear organization and morphology of serotonergic neurons in the brain of the Nile crocodile, Crocodylus niloticus. J Chem Neuroanat 2007; 35:133-45. [PMID: 17923387 DOI: 10.1016/j.jchemneu.2007.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 08/28/2007] [Accepted: 08/28/2007] [Indexed: 10/22/2022]
Abstract
The present study describes the location and nuclear organization of the serotonergic system in a representative of the order Crocodylia, the Nile crocodile (Crocodylus niloticus). We found evidence for serotonergic neurons in three regions of the brain, including the diencephalon, rostral and caudal brainstem, as previously reported in several other species of reptile. Within the diencephalon we found neurons in the periventricular organ of the hypothalamus, but not in the infundibular recess as noted in some other reptilian species. In addition we found serotonergic neurons in the pretectal nucleus, this being the first description of these neurons in any species. Within the rostral brainstem we found medial and lateral divisions of the superior raphe nucleus and a widely dispersed group of neurons in the tegmentum, the superior reticular nucleus. In the caudal brainstem we observed the inferior raphe nucleus and the inferior reticular nucleus. While much of the serotonergic system of the Nile crocodile is similar to that seen in other reptiles the entire suite of features appears to distinguish the crocodile studied from the members of the Squamate (lizards and snakes) and Testudine (turtles, tortoises and terrapins) reptiles previously studied. The observations are suggestive of order-specific patterns of nuclear organization of this system in the reptiles, reflecting potential evolutionary constraints in the mutability of the nuclear organization as seen for similar systems in mammals.
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Affiliation(s)
- Stacey-Lee Rodrigues
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg, South Africa
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Griffin DK, Robertson LBW, Tempest HG, Skinner BM. The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenet Genome Res 2007; 117:64-77. [PMID: 17675846 DOI: 10.1159/000103166] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 09/04/2006] [Indexed: 12/15/2022] Open
Abstract
Birds are characterised by feathers, flight, a small genome and a very distinctive karyotype. Despite the large numbers of chromosomes, the diploid count of 2n approximately 80 has remained remarkably constant with 63% of birds where 2n = 74-86, 24% with 2n = 66-74 and extremes of 2n = 40 and 2n = 142. Of these, the most studied is the chicken (2n = 78), and molecular cytogenetic probes generated from this species have been used to further understand the evolution of the avian genome. The ancestral karyotype is, it appears, very similar to that of the chicken, with chicken chromosomes 1, 2, 3, 4q, 5, 6, 7, 8, 9, 4p and Z representing the ancestral avian chromosomes 1-10 + Z; chromosome 4 being the most ancient. Avian evolution occurred primarily in three stages: the divergence of the group represented by extant ratites (emu, ostrich etc.) from the rest; divergence of the Galloanserae (chicken, turkey, duck, goose etc.)--the most studied group; and divergence of the 'land' and 'water' higher birds. Other than sex chromosome differentiation in the first divergence there are no specific changes associated with any of these evolutionary milestones although certain families and orders have undergone multiple fusions (and some fissions), which has reduced their chromosome number; the Falconiformes are the best described. Most changes, overall, seem to involve chromosomes 1, 2, 4, 10 and Z where the Z changes are intrachromosomal; there are also some recurring (convergent) events. Of these, the most puzzling involves chromosomes 4 and 10, which appear to have undergone multiple fissions and/or fusions throughout evolution - three possible hypotheses are presented to explain the findings. We conclude by speculating as to the reasons for the strange behaviour of these chromosomes as well as the role of telomeres and nuclear organisation in avian evolution.
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Affiliation(s)
- D K Griffin
- University of Kent, Department of Biosciences, Canterbury, UK.
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135
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Hugall AF, Foster R, Lee MSY. Calibration Choice, Rate Smoothing, and the Pattern of Tetrapod Diversification According to the Long Nuclear Gene RAG-1. Syst Biol 2007; 56:543-63. [PMID: 17654361 DOI: 10.1080/10635150701477825] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A phylogeny of tetrapods is inferred from nearly complete sequences of the nuclear RAG-1 gene sampled across 88 taxa encompassing all major clades, analyzed via parsimony and Bayesian methods. The phylogeny provides support for Lissamphibia, Theria, Lepidosauria, a turtle-archosaur clade, as well as most traditionally accepted groupings. This tree allows simultaneous molecular clock dating for all tetrapod groups using a set of well-corroborated calibrations. Relaxed clock (PLRS) methods, using the amniote = 315 Mya (million years ago) calibration or a set of consistent calibrations, recovers reasonable divergence dates for most groups. However, the analysis systematically underestimates divergence dates within archosaurs. The bird-crocodile split, robustly documented in the fossil record as being around approximately 245 Mya, is estimated at only approximately 190 Mya, and dates for other divergences within archosaurs are similarly underestimated. Archosaurs, and particulary turtles have slow apparent rates possibly confounding rate modeling, and inclusion of calibrations within archosaurs (despite their high deviances) not only improves divergence estimates within archosaurs, but also across other groups. Notably, the monotreme-therian split ( approximately 210 Mya) matches the fossil record; the squamate radiation ( approximately 190 Mya) is younger than suggested by some recent molecular studies and inconsistent with identification of approximately 220 and approximately 165 Myo (million-year-old) fossils as acrodont iguanians and approximately 95 Myo fossils colubroid snakes; the bird-lizard (reptile) split is considerably older than fossil estimates (< or = 285 Mya); and Sphenodon is a remarkable phylogenetic relic, being the sole survivor of a lineage more than a quarter of a billion years old. Comparison with other molecular clock studies of tetrapod divergences suggests that the common practice of enforcing most calibrations as minima, with a single liberal maximal constraint, will systematically overestimate divergence dates. Similarly, saturation of mitochondrial DNA sequences, and the resultant greater compression of basal branches means that using only external deep calibrations will also lead to inflated age estimates within the focal ingroup.
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Affiliation(s)
- Andrew F Hugall
- School of Earth and Environmental Sciences, University of Adelaide, SA, Australia.
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Shoureshi P, Baron A, Szynskie L, Dores RM. Analyzing the evolution of beta-endorphin post-translational processing events: studies on reptiles. Gen Comp Endocrinol 2007; 153:148-54. [PMID: 17353011 DOI: 10.1016/j.ygcen.2007.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2006] [Revised: 01/01/2007] [Accepted: 01/10/2007] [Indexed: 10/23/2022]
Abstract
In many cartilaginous fishes, most ray-finned fishes, lungfishes, and amphibians, the post-translational processing of POMC includes the monobasic cleavage of beta-endorphin to yield an opioid that is eight to ten amino acids in length. The amino acid motif within the beta-endorphin sequence required for a monobasic cleavage event is -E-R-(S/G)-Q-. Mammals and birds lack this motif and as a result beta-endorphin(1-8) is a not an end-product in either group. Since both mammals and birds were derived from ancestors with reptilian origins, an analysis of beta-endorphin sequences from extant groups of reptiles should provide insights into the manner in which beta-endorphin post-translational processing mechanisms have evolved in amniotes. To this end a POMC cDNA was cloned from the pituitary of the turtle, Chrysemys scripta. The beta-endorphin sequence in this species was compared to other reptile beta-endorphin sequences (i.e., Chinese soft shell turtle and gecko) and to known bird and mammal sequences. This analysis indicated that either the loss of the arginine residue at the cleavage site (the two turtle species, chick, and human) or a substitution at the glutamine position in the consensus sequence (gecko and ostrich) would account for the loss of the monobasic cleavage reaction in that species. Since amphibians are capable of performing the beta-endorphin monobasic reaction, it would appear that the amino acid substitutions that eliminated this post-translational process event in reptilian-related tetrapods must have occurred in the ancestral amniotes.
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Affiliation(s)
- Pezhman Shoureshi
- University of Denver, Department of Biological Sciences, 2190 E. Iliff, Olin Hall 102, Denver, CO 80210, USA
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Roberts E, Shoureshi P, Kozak K, Szynskie L, Baron A, Lecaude S, Dores RM. Tracking the evolution of the proenkephalin gene in tetrapods. Gen Comp Endocrinol 2007; 153:189-97. [PMID: 17449037 DOI: 10.1016/j.ygcen.2007.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 02/21/2007] [Indexed: 11/29/2022]
Abstract
In gnathostomes there is remarkable consistency in the organization of the proenkephalin gene. This opioid precursor encodes seven opioid (YGGF) sequences: five pentapeptide sequences, a met-enkephalin-7 sequence and a met-enkephalin-8 sequence. Yet, within vertebrate lineages there can be distinct sets of pentapeptide opioids (YGGFM or YGGFL). In the Sarcopterygii, the sixth opioid position in lungfishes and anuran amphibian proenkephalin genes encodes a met-enkephalin (YGGFM) sequence. However, in mammalian proenkephalin there is a leu-enkephalin (YGGFL) sequence at this position. This study was done to test the hypothesis that the presence of the leu-enkephalin sequence in mammals is a feature common to amniote vertebrates, but not present in anamniote vertebrates. To resolve this issue, proenkephalin cDNAs were cloned from the urodele amphibians, Amphiuma means and Necturus maculosus, and two amniote vertebrates, the turtle, Chrysemys scripta, and the brown snake, Storeria dekayi. As predicted, a met-enkephalin sequence is present at the sixth opioid position in urodele amphibians; whereas, a leu-enkephalin sequence is present at this opioid site in the reptile proenkephalin sequences. These data are consistent with the conclusion that the transition from a met-enkephalin sequence to a leu-enkephalin sequence at the sixth opioid position in tetrapod proenkephalins occurred in the ancestral proto-reptiles. Phylogenetic analyses, using the Maximum Parsimony and Neighbor-Joining algorithms, of the amphibian proenkephalin sequences supported the position that anuran and urodele amphibians are a monophyletic assemblage. The same analysis of reptile-related proenkephalin sequences, including the deduced amino acid sequence of a partially characterized alligator proenkephalin cDNA, could not conclusively resolve the phylogeny of the major reptilian orders.
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Affiliation(s)
- Erin Roberts
- Department of Biological Sciences, University of Denver, 2190 E. Iliff, Olin Hall 102, Denver, CO 80210, USA
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138
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Nishida-Umehara C, Tsuda Y, Ishijima J, Ando J, Fujiwara A, Matsuda Y, Griffin DK. The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds. Chromosome Res 2007; 15:721-34. [PMID: 17605112 DOI: 10.1007/s10577-007-1157-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2007] [Revised: 04/28/2007] [Accepted: 04/28/2007] [Indexed: 11/25/2022]
Abstract
Palaeognathous birds (Struthioniformes and Tinamiformes) have morphologically conserved karyotypes and less differentiated ZW sex chromosomes. To delineate interspecific chromosome orthologies in palaeognathous birds we conducted comparative chromosome painting with chicken (Gallus gallus, GGA) chromosome 1-9 and Z chromosome paints (GGA1-9 and GGAZ) for emu, double-wattled cassowary, ostrich, greater rhea, lesser rhea and elegant crested tinamou. All six species showed the same painting patterns: each probe was hybridized to a single pair of chromosomes with the exception that the GGA4 was hybridized to the fourth largest chromosome and a single pair of microchromosomes. The GGAZ was also hybridized to the entire region of the W chromosome, indicating that extensive homology remains between the Z and W chromosomes on the molecular level. Comparative FISH mapping of four Z- and/or W-linked markers, the ACO1/IREBP, ZOV3 and CHD1 genes and the EE0.6 sequence, revealed the presence of a small deletion in the proximal region of the long arm of the W chromosome in greater rhea and lesser rhea. These results suggest that the karyotypes and sex chromosomes of palaeognathous birds are highly conserved not only morphologically, but also at the molecular level; moreover, palaeognathous birds appear to retain the ancestral lineage of avian karyotypes.
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Affiliation(s)
- Chizuko Nishida-Umehara
- Laboratory of Animal Cytogenetics, Division of Genome Dynamics, Creative Research Initiative Sousei, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, 060-0810, Japan
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139
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Mallatt J, Winchell CJ. Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol Phylogenet Evol 2007; 43:1005-22. [PMID: 17276090 DOI: 10.1016/j.ympev.2006.11.023] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 10/27/2006] [Accepted: 11/22/2006] [Indexed: 01/08/2023]
Abstract
This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the approximately 45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and 'vertebrates plus cephalochordates'; and (2) lungfishes are the closest living relatives of tetrapods.
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Affiliation(s)
- Jon Mallatt
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Ciuraszkiewicz J, Biczycki M, Maluta A, Martin S, Watorek W, Olczak M. Reptilian transferrins: evolution of disulphide bridges and conservation of iron-binding center. Gene 2007; 396:28-38. [PMID: 17466466 DOI: 10.1016/j.gene.2007.02.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 02/13/2007] [Accepted: 02/19/2007] [Indexed: 11/24/2022]
Abstract
Transferrins, found in invertebrates and vertebrates, form a physiologically important family of proteins playing a major role in iron acquisition and transport, defense against microbial pathogens, growth and differentiation. These proteins are bilobal in structure and each lobe is composed of two domains divided by a cleft harboring an iron atom. Vertebrate transferrins comprise of serotransferrins, lactoferrins and ovotransferrins. In mammals serotransferrins transport iron in physiological fluids and deliver it to cells, while lactoferrins scavenge iron, limiting its availability to invading microbes. In oviparous vertebrates there is only one transferrin gene, expressed either in the liver to be delivered to physiological fluids as serotransferrin, or in the oviduct with a final localization in egg white as ovotransferrin. Being products of one gene sero- and ovotransferrin are identical at the amino-acid sequence level but with different, cell specific glycosylation patterns. Our knowledge of the mechanisms of transferrin iron binding and release is based on sequence and structural data obtained for human serotransferrin and hen and duck ovotransferrins. No sequence information about other ovotransferrins was available until our recent publication of turkey, ostrich, and red-eared turtle (TtrF) ovotransferrin mRNA sequences [Ciuraszkiewicz, J., Olczak, M., Watorek, W., 2006. Isolation, cloning and sequencing of transferrins from red-eared turtle, African ostrich and turkey. Comp. Biochem. Physiol. 143 B, 301-310]. In the present paper, ten new reptilian mRNA transferrin sequences obtained from the Nile crocodile (NtrF), bearded dragon (BtrF), Cuban brown anole (AtrF), veiled and Mediterranean chameleons (VtrF and KtrF), sand lizard (StrF), leopard gecko (LtrF), Burmese python (PtrF), African house snake (HtrF), and grass snake (GtrF) are presented and analyzed. Nile crocodile and red-eared turtle transferrins have a disulphide bridge pattern identical to known bird homologues. A partially different disulphide bridge pattern was found in the Squamata (snakes and lizards). The possibility of a unique interdomain disulphide bridge was predicted for LtrF. Differences were found in iron-binding centers from those of previously known transferrins. Substitutions were found in the iron-chelating residues of StrF and TtrF and in the synergistic anion-binding residues of NtrF. In snakes, the transferrin (PtrF, HtrF and GtrF) N-lobe "dilysine trigger" occurring in all other known transferrins was not found, which indicates a different mechanism of iron release.
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Affiliation(s)
- Justyna Ciuraszkiewicz
- Laboratory of Biochemistry, Faculty of Biotechnology, Wrocław University, Tamka 2, 50-137 Wrocław, Poland
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141
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Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne PJ, Edwards SV. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci U S A 2007; 104:2767-72. [PMID: 17307883 PMCID: PMC1815256 DOI: 10.1073/pnas.0606204104] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Indexed: 11/18/2022] Open
Abstract
We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of approximately 65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174).
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Affiliation(s)
- Andrew M Shedlock
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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142
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Kondo Y, Morimoto T, Nishio T, Aslanova UF, Nishino M, Farajov EI, Sugawara N, Kumagai N, Ohsaga A, Maruyama Y, Takahashi S. Phylogenetic, ontogenetic, and pathological aspects of the urine-concentrating mechanism. Clin Exp Nephrol 2006; 10:165-74. [PMID: 17009073 DOI: 10.1007/s10157-006-0429-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 08/09/2006] [Indexed: 12/21/2022]
Abstract
The urine-concentrating mechanism is one of the most fundamental functions of avian and mammalian kidneys. This particular function of the kidneys developed as a system to accumulate NaCl in birds and as a system to accumulate NaCl and urea in mammals. Based on phylogenetic evidence, the mammalian urine-concentrating mechanism may have evolved as a modification of the renal medulla's NaCl accumulating system that is observed in birds. This qualitative conversion of the urine-concentrating mechanism in the mammalian inner medulla of the kidneys may occur during the neonatal period. Human kidneys have several suboptimal features caused by the neonatal conversion of the urine-concentrating mechanism. The urine-concentrating mechanism is composed of various functional molecules, including water channels, solute transporters, and vasopressin receptors. Abnormalities in water channels aquaporin (AQP)1 and AQP2, as well as in the vasopressin receptor V2R, are known to cause nephrogenic diabetes insipidus. An analysis of the pathological mechanism involved in nephrogenic diabetes insipidus suggests that molecular chaperones may improve the intracellular trafficking of AQP2 and V2R, and, in the near future, such chaperones may become a new clinical tool for treating nephrogenic diabetes insipidus.
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Affiliation(s)
- Yoshiaki Kondo
- Department of Medical Informatics, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan.
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143
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Abstract
It is unlikely that taxonomically diverse phylogenetic studies will be completed rapidly in the near future for nonmodel organisms on a whole-genome basis. However, one approach to advancing the field of "phylogenomics" is to estimate the structure of poorly known genomes by mining libraries of clones from suites of taxa, rather than from single species. The present analysis adopts this approach by taking advantage of megabase-scale end-sequence scanning of reptilian genomic clones to characterize diversity of CR1-like LINEs, the dominant family of transposable elements (TEs) in the sister group of mammals. As such, it helps close an important gap in the literature on the molecular systematics and evolution of retroelements in nonavian reptiles. Results from aligning more than 14 Mb of sequence from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta), Bahamian green anole (Anolis smaragdinus), Tuatara (Sphenodon punctatus), Emu (Dromaius novaehollandiae), and Zebra Finch (Taeniopygia guttata) against a comprehensive library approximately 3000 TE-encoding peptides reflect an increasing abundance of LINE and non-long-terminal-repeat (non-LTR) retrotransposon repeat types with the age of common ancestry among exemplar reptilian clades. The hypothesis that repeat diversity is correlated with basal metabolic rate was tested using comparative methods and a significant nonlinear relationship was indicated. This analysis suggests that the age of divergence between an exemplary clade and its sister group as well as metabolic correlates should be considered in addition to genome size in explaining patterns of retroelement diversity. The first phylogenetic analysis of the largely unexplored chicken repeat 1 (CR1) 3' reverse transcriptase (RT) conserved domains 8 and 9 in nonavian reptiles reveals a pattern of multiple lineages with variable branch lengths, suggesting presence of both old and young elements and the existence of several distinct well-supported clades not apparent from previous characterization of CR1 subfamily structure in birds and the turtle. This mode of CR1 evolution contrasts with historical patterns of LINE 1 diversification in mammals and hints toward the existence of a rich but still largely unexplored diversity of nonavian retroelements of importance to advancing both comparative vertebrate genomics and amniote systematics.
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Affiliation(s)
- Andrew M Shedlock
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA.
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144
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Wang Z, Miyake T, Edwards SV, Amemiya CT. Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, and Application to the DMRT Gene Family. J Hered 2006; 97:541-8. [PMID: 17135461 DOI: 10.1093/jhered/esl040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The tuatara (Sphenodon punctatus) is of "extraordinary biological interest" as the most distinctive surviving reptilian lineage (Rhyncocephalia) in the world. To provide a genomic resource for an understanding of genome evolution in reptiles, and as part of a larger project to produce genomic resources for various reptiles (evogen.jgi.doe.gov/second_levels/BACs/our_libraries.html), a large-insert bacterial artificial chromosome (BAC) library from a male tuatara was constructed. The library consists of 215 424 individual clones whose average insert size was empirically determined to be 145 kb, yielding a genomic coverage of approximately 6.3x. A BAC-end sequencing analysis of 121 420 bp of sequence revealed a genomic GC content of 46.8%, among the highest observed thus far for vertebrates, and identified several short interspersed repetitive elements (mammalian interspersed repeat-type repeats) and long interspersed repetitive elements, including chicken repeat 1 element. Finally, as a quality control measure the arrayed library was screened with probes corresponding to 2 conserved noncoding regions of the candidate sex-determining gene DMRT1 and the DM domain of the related DMRT2 gene. A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics.
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Affiliation(s)
- Zhenshan Wang
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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145
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Brainerd EL, Owerkowicz T. Functional morphology and evolution of aspiration breathing in tetrapods. Respir Physiol Neurobiol 2006; 154:73-88. [PMID: 16861059 DOI: 10.1016/j.resp.2006.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 06/08/2006] [Accepted: 06/12/2006] [Indexed: 11/28/2022]
Abstract
In the evolution of aspiration breathing, the responsibility for lung ventilation gradually shifted from the hyobranchial to the axial musculoskeletal system, with axial muscles taking over exhalation first, at the base of Tetrapoda, and then inhalation as well at the base of Amniota. This shift from hyobranchial to axial breathing freed the tongue and head to adapt to more diverse feeding styles, but generated a mechanical conflict between costal ventilation and high-speed locomotion. Some "lizards" (non-serpentine squamates) have been shown to circumvent this speed-dependent axial constraint with accessory gular pumping during locomotion, and here we present a new survey of gular pumping behavior in the tuatara and 40 lizard species. We observed gular pumping behavior in 32 of the 40 lizards and in the tuatara, indicating that the ability to inflate the lungs by gular pumping is a shared-derived character for Lepidosauria. Gular pump breathing in lepidosaurs may be homologous with buccal pumping in amphibians, but non-ventilatory buccal oscillation and gular flutter have persisted throughout amniote evolution and gular pumping may have evolved independently by modification of buccal oscillation. In addition to gular pumping in some lizards, three other innovations have evolved repeatedly in the major amniote clades to circumvent the speed-dependent axial constraint: accessory inspiratory muscles (mammals, crocodylians and turtles), changing locomotor posture (mammals and birds) and respiratory-locomotor phase coupling to reduce the mechanical conflict between aspiration breathing and locomotion (mammals and birds).
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Affiliation(s)
- Elizabeth L Brainerd
- Department of Ecology and Evolutionary Biology, Box G-B210, Brown University, Providence, RI 02912, USA.
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146
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Lazzari M, Franceschini V. Glial cytoarchitecture in the central nervous system of the soft-shell turtle, Trionyx sinensis, revealed by intermediate filament immunohistochemistry. ACTA ACUST UNITED AC 2006; 211:497-506. [PMID: 16763812 DOI: 10.1007/s00429-006-0101-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2006] [Indexed: 02/03/2023]
Abstract
The distribution of the intermediate filament molecular markers, glial fibrillary acidic protein (GFAP) and vimentin, has been studied in the central nervous system (CNS) of the soft-shell turtle (Trionyx sinensis) with immunoperoxidase histochemistry. GFAP immunohistochemistry pointed out the presence of different astroglial cell types. The brain pattern consists of ependymal radial glia whose cell bodies are located in the ependymal layer throughout the brain ventricular system. In the spinal cord, the ependyma is immunonegative, whereas positive radial astrocyte cell bodies are displaced from the ependyma into the periependymal position. Star-shaped astrocytes are observed only in the posterior intumescence of the spinal cord. The different regions of the CNS show a different intensity in GFAP immunostaining even in the same cellular type. Vimentin-immunoreactive structures are absent in the brain and spinal cord. The present study reports an heterogeneous feature of the astroglial pattern in the spinal cord compared to the brain which shows an ancestral condition.
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Affiliation(s)
- Maurizio Lazzari
- Department of Biology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
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147
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Webster MT, Axelsson E, Ellegren H. Strong Regional Biases in Nucleotide Substitution in the Chicken Genome. Mol Biol Evol 2006; 23:1203-16. [PMID: 16551647 DOI: 10.1093/molbev/msk008] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interspersed repeats have emerged as a valuable tool for studying neutral patterns of molecular evolution. Here we analyze variation in the rate and pattern of nucleotide substitution across all autosomes in the chicken genome by comparing the present-day CR1 repeat sequences with their ancestral copies and reconstructing nucleotide substitutions with a maximum likelihood model. The results shed light on the origin and evolution of large-scale heterogeneity in GC content found in the genomes of birds and mammals--the isochore structure. In contrast to mammals, where GC content is becoming homogenized, heterogeneity in GC content is being reinforced in the chicken genome. This is also supported by patterns of substitution inferred from alignments of introns in chicken, turkey, and quail. Analysis of individual substitution frequencies is consistent with the biased gene conversion (BGC) model of isochore evolution, and it is likely that patterns of evolution in the chicken genome closely resemble those in the ancestral amniote genome, when it is inferred that isochores originated. Microchromosomes and distal regions of macrochromosomes are found to have elevated substitution rates and a more GC-biased pattern of nucleotide substitution. This can largely be accounted for by a strong correlation between GC content and the rate and pattern of substitution. The results suggest that an interaction between increased mutability at CpG motifs and fixation biases due to BGC could explain increased levels of divergence in GC-rich regions.
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Affiliation(s)
- Matthew T Webster
- Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
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148
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Kuraku S, Ishijima J, Nishida-Umehara C, Agata K, Kuratani S, Matsuda Y. cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Res 2006; 14:187-202. [PMID: 16544192 DOI: 10.1007/s10577-006-1035-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 01/10/2006] [Indexed: 10/24/2022]
Abstract
Mammalian and avian genomes comprise several classes of chromosomal segments that vary dramatically in GC-content. Especially in chicken, microchromosomes exhibit a higher GC-content and a higher gene density than macrochromosomes. To understand the evolutionary history of the intra-genome GC heterogeneity in amniotes, it is necessary to examine the equivalence of this GC heterogeneity at the nucleotide level between these animals including reptiles, from which birds diverged. We isolated cDNAs for 39 protein-coding genes from the Chinese soft-shelled turtle, Pelodiscus sinensis, and performed chromosome mapping of 31 genes. The GC-content of exonic third positions (GC3) of P. sinensis genes showed a heterogeneous distribution, and exhibited a significant positive correlation with that of chicken and human orthologs, indicating that the last common ancestor of extant amniotes had already established a GC-compartmentalized genomic structure. Furthermore, chromosome mapping in P. sinensis revealed that microchromosomes tend to contain more GC-rich genes than GC-poor genes, as in chicken. These results illustrate two modes of genome evolution in amniotes: mammals elaborated the genomic configuration in which GC-rich and GC-poor regions coexist in individual chromosomes, whereas sauropsids (reptiles and birds) refined the chromosomal size-dependent GC compartmentalization in which GC-rich genomic fractions tend to be confined to microchromosomes.
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Affiliation(s)
- Shigehiro Kuraku
- Laboratory for Evolutionary Morphology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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149
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FROST DARRELR, GRANT TARAN, FAIVOVICH JULIÁN, BAIN RAOULH, HAAS ALEXANDER, HADDAD CÉLIOF, DE SÁ RAFAELO, CHANNING ALAN, WILKINSON MARK, DONNELLAN STEPHENC, RAXWORTHY CHRISTOPHERJ, CAMPBELL JONATHANA, BLOTTO BORISL, MOLER PAUL, DREWES ROBERTC, NUSSBAUM RONALDA, LYNCH JOHND, GREEN DAVIDM, WHEELER WARDC. THE AMPHIBIAN TREE OF LIFE. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2006. [DOI: 10.1206/0003-0090(2006)297[0001:tatol]2.0.co;2] [Citation(s) in RCA: 1225] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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150
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Iwasaki T, Sato KI, Yoshino KI, Itakura S, Kosuge K, Tokmakov AA, Owada K, Yonezawa K, Fukami Y. Phylogeny of Vertebrate Src Tyrosine Kinases Revealed by the Epitope Region of mAb327. ACTA ACUST UNITED AC 2006; 139:347-54. [PMID: 16567399 DOI: 10.1093/jb/mvj059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mass fingerprinting and MS/MS analysis demonstrated that Xyk, a 57-kDa Src family tyrosine kinase that is activated within minutes of Xenopus egg fertilization, comprises a mixture of two Src proteins, Src1 and Src2. However, the Xenopus Src protein, denoted as xSrc, is hardly detectable with mAb327, a universal Src-specific antibody, whose target sequence has not yet been determined. We show that a point amino acid substitution in the Src homology 3 domain of xSrc is critical for improvement of the low efficiency of its recognition by mAb327. Namely, a point-mutated xSrc, in which Arg-121 was replaced by His that is conserved among mAb327-reactive Src in mammals and chicken, showed increased recognition by mAb327. On the other hand, a mutant chicken Src, in which the His-122 residue is replaced by Arg, showed decreased recognition by mAb327. Genomic sequencing analysis also demonstrated that reptile Src proteins are of either the R-type (snake) or H-type (caiman, turtle, and tortoise). These studies revealed, for the first time, a critical amino acid in the Src SH3 domain for mAb327 recognition, and suggest a novel scheme for the molecular evolution of Src, in which the H-type Src(s) are monophyletic and derived from the R-type Src.
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Affiliation(s)
- Tetsushi Iwasaki
- Research Center for Environmental Genomics, Kobe University, Nada, Kobe 657-8501.
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