1
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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2
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de Oliveira TD, de Freitas TR. Investigating the evolutionary dynamics of diploid number variation in Ctenomys (Ctenomyidae, Rodentia). Genet Mol Biol 2024; 46:e20230180. [PMID: 38315881 PMCID: PMC10842476 DOI: 10.1590/1678-4685-gmb-2023-0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
Contrary to predictions from classical hybrid sterility models of chromosomal speciation, some organisms display high rates of karyotype variation. Ctenomys are the current mammals with the greatest interspecific and intraspecific chromosomal variation. A large number of species have been studied cytogenetically. The diploid numbers of chromosomes range from 2n = 10 to 2n = 70. Here, we analyzed karyotype evolution in Ctenomys using comparative phylogenetic methods. We found a strong phylogenetic signal with chromosome number. This refutes the chromosomal megaevolution model, which proposes the independent accumulation of multiple chromosomal rearrangements in each closely related species. We found that Brownian motion (BM) described the observed characteristic changes more thoroughly than the Ornstein-Uhlenbeck and Early-Burst models. This suggests that the evolution of chromosome numbers occurs by a random walk along phylogenetic clades. However, our data indicate that the BM model alone does not fully characterize the chromosomal evolution of Ctenomys.
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Affiliation(s)
- Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Thales R.O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
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3
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Evolutionary and Genomic Diversity of True Polyploidy in Tetrapods. Animals (Basel) 2023; 13:ani13061033. [PMID: 36978574 PMCID: PMC10044425 DOI: 10.3390/ani13061033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution of polyploidy to the generation of new genomic, ecological, and species diversity in tetrapods has traditionally been underestimated. Indeed, polyploidy represents an important pathway of genomic evolution, occurring in most higher-taxa tetrapods and displaying a variety of different forms, genomic configurations, and biological implications. Herein, we report and discuss the available information on the different origins and evolutionary and ecological significance of true polyploidy in tetrapods. Among the main tetrapod lineages, modern amphibians have an unparalleled diversity of polyploids and, until recently, they were considered to be the only vertebrates with closely related diploid and polyploid bisexual species or populations. In reptiles, polyploidy was thought to be restricted to squamates and associated with parthenogenesis. In birds and mammals, true polyploidy has generally been considered absent (non-tolerated). These views are being changed due to an accumulation of new data, and the impact as well as the different evolutionary and ecological implications of polyploidy in tetrapods, deserve a broader evaluation.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
| | - Fabio Maria Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
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4
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Sladky VC, Eichin F, Reiberger T, Villunger A. Polyploidy control in hepatic health and disease. J Hepatol 2021; 75:1177-1191. [PMID: 34228992 DOI: 10.1016/j.jhep.2021.06.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022]
Abstract
A balanced increase in DNA content (ploidy) is observed in some human cell types, including bone-resorbing osteoclasts, platelet-producing megakaryocytes, cardiomyocytes or hepatocytes. The impact of increased hepatocyte ploidy on normal physiology and diverse liver pathologies is still poorly understood. Recent findings suggest swift genetic adaptation to hepatotoxic stress and the protection from malignant transformation as beneficial effects. Herein, we discuss the molecular mechanisms regulating hepatocyte polyploidisation and its implication for different liver diseases and hepatocellular carcinoma. We report on centrosomes' role in limiting polyploidy by activating the p53 signalling network (via the PIDDosome multiprotein complex) and we discuss the role of this pathway in liver disease. Increased hepatocyte ploidy is a hallmark of hepatic inflammation and may play a protective role against liver cancer. Our evolving understanding of hepatocyte ploidy is discussed from the perspective of its potential clinical application for risk stratification, prognosis, and novel therapeutic strategies in liver disease and hepatocellular carcinoma.
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Affiliation(s)
- Valentina C Sladky
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Felix Eichin
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Reiberger
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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5
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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6
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Small CD, Davis JP, Crawford BD, Benfey TJ. Early, nonlethal ploidy and genome size quantification using confocal microscopy in zebrafish embryos. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:496-510. [PMID: 34254444 DOI: 10.1002/jez.b.23069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 11/07/2022]
Abstract
Ploidy transitions through whole genome duplication have shaped evolution by allowing the sub- and neo-functionalization of redundant copies of highly conserved genes to express novel traits. The nuclear:cytoplasmic (n:c) ratio is maintained in polyploid vertebrates resulting in larger cells, but body size is maintained by a concomitant reduction in cell number. Ploidy can be manipulated easily in most teleosts, and the zebrafish, already well established as a model system for biomedical research, is therefore an excellent system in which to study the effects of increased cell size and reduced cell numbers in polyploids on development and physiology. Here we describe a novel technique using confocal microscopy to measure genome size and determine ploidy non-lethally at 48 h post-fertilization (hpf) in transgenic zebrafish expressing fluorescent histones. Volumetric analysis of myofiber nuclei using open-source software can reliably distinguish diploids and triploids from a mixed-ploidy pool of embryos for subsequent experimentation. We present an example of this by comparing heart rate between confirmed diploid and triploid embryos at 54 hpf.
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Affiliation(s)
| | - James P Davis
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Bryan D Crawford
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Tillmann J Benfey
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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7
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Shenderov E, Kandasamy M, Gileadi U, Chen J, Shepherd D, Gibbs J, Prota G, Silk JD, Yewdell JW, Cerundolo V. Generation and characterization of HLA-A2 transgenic mice expressing the human TCR 1G4 specific for the HLA-A2 restricted NY-ESO-1 157-165 tumor-specific peptide. J Immunother Cancer 2021; 9:jitc-2021-002544. [PMID: 34088742 PMCID: PMC8183295 DOI: 10.1136/jitc-2021-002544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2021] [Indexed: 01/07/2023] Open
Abstract
Background NY-ESO-1 is a tumor-specific, highly immunogenic, human germ cell antigen of the MAGE-1 family that is a promising vaccine and cell therapy candidate in clinical trial development. The mouse genome does not encode an NY-ESO-1 homolog thereby not subjecting transgenic T-cells to thymic tolerance mechanisms that might impair in-vivo studies. We hypothesized that an NY-ESO-1 T cell receptor (TCR) transgenic mouse would provide the unique opportunity to study avidity of TCR response against NY-ESO-1 for tumor vaccine and cellular therapy development against this clinically relevant and physiological human antigen. Methods To study in vitro and in vivo the requirements for shaping an effective T cell response against the clinically relevant NY-ESO-1, we generated a C57BL/6 HLA-A*0201 background TCR transgenic mouse encoding the 1G4 TCR specific for the human HLA-A2 restricted, NY-ESO-1157-165 SLLMWITQC (9C), initially identified in an NY-ESO-1 positive melanoma patient. Results The HLA-A*0201 restricted TCR was positively selected on both CD4+ and CD8+ cells. Mouse 1G4 T cells were not activated by endogenous autoimmune targets or a large library of non-cognate viral antigens. In contrast, their activation by HLA-A2 NY-ESO-1157-165 complexes was evident by proliferation, CD69 upregulation, interferon-γ production, and interleukin-2 production, and could be tuned using a twofold higher affinity altered peptide ligand, NY-ESO-1157-165V. NY-ESO-1157-165V recombinant vaccination of syngeneic mice adoptively transferred with m1G4 CD8+ T cells controlled tumor growth in vivo. 1G4 transgenic mice suppressed growth of syngeneic methylcholanthrene (MCA) induced HHD tumor cells expressing the full-length human NY-ESO-1 protein but not MCA HHD tumor cells lacking NY-ESO-1. Conclusions The 1G4 TCR mouse model for the physiological human TCR against the clinically relevant antigen, NY-ESO-1, is a valuable tool with the potential to accelerate clinical development of NY-ESO-1-targeted T-cell and vaccine therapies.
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Affiliation(s)
- Eugene Shenderov
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK .,National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA
| | - Matheswaran Kandasamy
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK
| | - Uzi Gileadi
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK
| | - Jili Chen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK
| | - Dawn Shepherd
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK
| | - James Gibbs
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gennaro Prota
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK
| | - Jonathan D Silk
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK.,Next Generation Research, Adaptimmune, Abingdon, UK
| | - Jonathan W Yewdell
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, UK
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8
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Blackmon H, Justison J, Mayrose I, Goldberg EE. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 2019; 73:511-523. [PMID: 30690715 PMCID: PMC6590138 DOI: 10.1111/evo.13682] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all bibrachial or all monobrachial chromosomes than in species with a mix of both types of morphologies. We suggest that species with homogeneous karyotypes may represent cases where meiotic drive acts to stabilize the karyotype, favoring the chromosome morphologies already present in the genome. In contrast, rapid bouts of chromosome number evolution in taxa with mixed karyotypes may indicate that a switch in the polarity of female meiotic drive favors changes in chromosome number. We do not find any evidence that karyotype morphology affects rates of speciation or extinction. Furthermore, we document that switches in meiotic drive polarity are likely common and have occurred in most major clades of mammals, and that rapid remodeling of karyotypes may be more common than once thought.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Joshua Justison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
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9
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Pearson PL, Madan K. True polyploid meiosis in the human male. Genet Mol Biol 2018; 41:410-413. [PMID: 29786103 PMCID: PMC6082232 DOI: 10.1590/1678-4685-gmb-2017-0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/18/2017] [Indexed: 11/23/2022] Open
Abstract
Polyploidy does not usually occur in germinal cells of mammals and other higher
vertebrates. We describe a unique example of mosaic autotetraploidy in the
meiosis of a human male. Although the original observations were made in the
late 1960s, we did not publish them at that time, because we expected to detect
further examples that could be described together. However, this did not occur
and we have now decided to make the observations available to demonstrate that
polyploidy in mammalian male meiosis can arise at a higher frequency than
expected by random polyploidization of individual meiotic cells, by either DNA
duplication or cell fusion prior to synapsis. This is the first description of a
population of primary spermatocytes exhibiting multivalent formation at
leptotene /diakinesis in human spermatogenesis, with ring, chain, frying pan and
other types of quadrivalents, typical of autotetraploidy. As many of the
polyploid configurations showed apoptotic breakdown, it is likely that diploid
and/or aneuploid spermatozoa would have rarely or never resulted from this
mosaic autotetraploid meiosis.
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Affiliation(s)
- Peter L Pearson
- Center for Human Genome and Stem Cell Research, Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Kamlesh Madan
- Cytogenetics Laboratory, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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10
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Evans BJ, Upham NS, Golding GB, Ojeda RA, Ojeda AA. Evolution of the Largest Mammalian Genome. Genome Biol Evol 2018; 9:1711-1724. [PMID: 28854639 PMCID: PMC5569995 DOI: 10.1093/gbe/evx113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/31/2022] Open
Abstract
The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects—including during the evolution of hypersaline dietary tolerance in T. barrerae.
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Affiliation(s)
- Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Nathan S Upham
- Biology Department, McMaster University, Hamilton, Ontario, Canada.,Field Museum of Natural History, Chicago, IL.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | | | - Ricardo A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
| | - Agustina A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
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11
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Kreutz C, MacNelly S, Follo M, Wäldin A, Binninger-Lacour P, Timmer J, Bartolomé-Rodríguez MM. Hepatocyte Ploidy Is a Diversity Factor for Liver Homeostasis. Front Physiol 2017; 8:862. [PMID: 29163206 PMCID: PMC5671579 DOI: 10.3389/fphys.2017.00862] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/16/2017] [Indexed: 01/28/2023] Open
Abstract
Polyploidy, the existence of cells containing more than one pair of chromosomes, is a well-known feature of mammalian hepatocytes. Polyploid hepatocytes are found either as cells with a single polyploid nucleus or as multinucleated cells with diploid or even polyploid nuclei. In this study, we evaluate the degree of polyploidy in the murine liver by accounting both DNA content and number of nuclei per cell. We demonstrate that mouse hepatocytes with diploid nuclei have distinct metabolic characteristics compared to cells with polyploid nuclei. In addition to strong differential gene expression, comprising metabolic as well as signaling compounds, we found a strongly decreased insulin binding of nuclear polyploid cells. Our observations were associated with nuclear ploidy but not with total ploidy within a cell. We therefore suggest ploidy of the nuclei as an new diversity factor of hepatocytes and hypothesize that hepatocytes with polyploid nuclei may have distinct biological functions than mono-nuclear ones. This diversity is independent from the well-known heterogeneity related to the cells' position along the porto-central liver-axis.
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Affiliation(s)
- Clemens Kreutz
- Faculty of Mathematics and Physics, Institute of Physics, University of Freiburg, Freiburg, Germany
- Center for Systems Biology (ZBSA), University of Freiburg, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling, University of Freiburg, Freiburg, Germany
| | - Sabine MacNelly
- Clinic for Internal Medicine II/Molecular Biology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Marie Follo
- Clinic for Internal Medicine I/Lighthouse Core Facility, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Astrid Wäldin
- Clinic for Internal Medicine II/Molecular Biology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Petra Binninger-Lacour
- Clinic for Internal Medicine II/Molecular Biology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Jens Timmer
- Faculty of Mathematics and Physics, Institute of Physics, University of Freiburg, Freiburg, Germany
- Freiburg Center for Data Analysis and Modelling, University of Freiburg, Freiburg, Germany
- BIOSS, Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - María M. Bartolomé-Rodríguez
- Clinic for Internal Medicine II/Molecular Biology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
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Ginn BR. The thermodynamics of protein aggregation reactions may underpin the enhanced metabolic efficiency associated with heterosis, some balancing selection, and the evolution of ploidy levels. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 126:1-21. [PMID: 28185903 DOI: 10.1016/j.pbiomolbio.2017.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 01/24/2017] [Indexed: 01/04/2023]
Abstract
Identifying the physical basis of heterosis (or "hybrid vigor") has remained elusive despite over a hundred years of research on the subject. The three main theories of heterosis are dominance theory, overdominance theory, and epistasis theory. Kacser and Burns (1981) identified the molecular basis of dominance, which has greatly enhanced our understanding of its importance to heterosis. This paper aims to explain how overdominance, and some features of epistasis, can similarly emerge from the molecular dynamics of proteins. Possessing multiple alleles at a gene locus results in the synthesis of different allozymes at reduced concentrations. This in turn reduces the rate at which each allozyme forms soluble oligomers, which are toxic and must be degraded, because allozymes co-aggregate at low efficiencies. The model developed in this paper can explain how heterozygosity impacts the metabolic efficiency of an organism. It can also explain why the viabilities of some inbred lines seem to decline rapidly at high inbreeding coefficients (F > 0.5), which may provide a physical basis for truncation selection for heterozygosity. Finally, the model has implications for the ploidy level of organisms. It can explain why polyploids are frequently found in environments where severe physical stresses promote the formation of soluble oligomers. The model can also explain why complex organisms, which need to synthesize aggregation-prone proteins that contain intrinsically unstructured regions (IURs) and multiple domains because they facilitate complex protein interaction networks (PINs), tend to be diploid while haploidy tends to be restricted to relatively simple organisms.
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Affiliation(s)
- B R Ginn
- University of Georgia, GA 30602, United States.
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Romanenko SA, Biltueva LS, Serdyukova NA, Kulemzina AI, Beklemisheva VR, Gladkikh OL, Lemskaya NA, Interesova EA, Korentovich MA, Vorobieva NV, Graphodatsky AS, Trifonov VA. Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting. Mol Cytogenet 2015; 8:90. [PMID: 26587056 PMCID: PMC4652396 DOI: 10.1186/s13039-015-0194-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/07/2015] [Indexed: 11/21/2022] Open
Abstract
Background Acipenseriformes take a basal position among Actinopteri and demonstrate a striking ploidy variation among species. The sterlet (Acipenser ruthenus, Linnaeus, 1758; ARUT) is a diploid 120-chromosomal sturgeon distributed in Eurasian rivers from Danube to Enisey. Despite a high commercial value and a rapid population decline in the wild, many genomic characteristics of sterlet (as well as many other sturgeon species) have not been studied. Results Cell lines from different tissues of 12 sterlet specimens from Siberian populations were established following an optimized protocol. Conventional cytogenetic studies supplemented with molecular cytogenetic investigations on obtained fibroblast cell lines allowed a detailed description of sterlet karyotype and a precise localization of 18S/28S and 5S ribosomal clusters. Localization of sturgeon specific HindIII repetitive elements revealed an increased concentration in the pericentromeric region of the acrocentric ARUT14, while the total sterlet repetitive DNA fraction (C0t30) produced bright signals on subtelomeric segments of small chromosomal elements. Chromosome and region specific probes ARUT1p, 5, 6, 7, 8 as well as 14 anonymous small sized chromosomes (probes A-N) generated by microdissection were applied in chromosome painting experiments. According to hybridization patterns all painting probes were classified into two major groups: the first group (ARUT5, 6, 8 as well as microchromosome specific probes C, E, F, G, H, and I) painted only a single region each on sterlet metaphases, while probes of the second group (ARUT1p, 7 as well as microchromosome derived probes A, B, D, J, K, M, and N) marked two genomic segments each on different chromosomes. Similar results were obtained on male and female metaphases. Conclusions The sterlet genome represents a complex mosaic structure and consists of diploid and tetraploid chromosome segments. This may be regarded as a transition stage from paleotetraploid (functional diploid) to diploid genome condition. Molecular cytogenetic and genomic studies of other 120- and 240-chromosomal sturgeons are needed to reconstruct genome evolution of this vertebrate group.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Larisa S Biltueva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | | | | | - Olga L Gladkikh
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | | | - Elena A Interesova
- Novosibirsk Branch of the Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Novosibirsk, Russia ; Tomsk State University, Tomsk, Russia
| | - Marina A Korentovich
- Federal State Budgetary Scientific Institution "State Scientific-and-Production Centre for Fisheries (Gosrybcenter)", Tyumen, Russia
| | - Nadezhda V Vorobieva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia ; Novosibirsk State University, Novosibirsk, Russia
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Romanenko SA, Perelman PL, Trifonov VA, Serdyukova NA, Li T, Fu B, O’Brien PCM, Ng BL, Nie W, Liehr T, Stanyon R, Graphodatsky AS, Yang F. A First Generation Comparative Chromosome Map between Guinea Pig (Cavia porcellus) and Humans. PLoS One 2015; 10:e0127937. [PMID: 26010445 PMCID: PMC4444286 DOI: 10.1371/journal.pone.0127937] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/21/2015] [Indexed: 11/19/2022] Open
Abstract
The domesticated guinea pig, Cavia porcellus (Hystricomorpha, Rodentia), is an important laboratory species and a model for a number of human diseases. Nevertheless, genomic tools for this species are lacking; even its karyotype is poorly characterized. The guinea pig belongs to Hystricomorpha, a widespread and important group of rodents; so far the chromosomes of guinea pigs have not been compared with that of other hystricomorph species or with any other mammals. We generated full sets of chromosome-specific painting probes for the guinea pig by flow sorting and microdissection, and for the first time, mapped the chromosomal homologies between guinea pig and human by reciprocal chromosome painting. Our data demonstrate that the guinea pig karyotype has undergone extensive rearrangements: 78 synteny-conserved human autosomal segments were delimited in the guinea pig genome. The high rate of genome evolution in the guinea pig may explain why the HSA7/16 and HSA16/19 associations presumed ancestral for eutherians and the three syntenic associations (HSA1/10, 3/19, and 9/11) considered ancestral for rodents were not found in C. porcellus. The comparative chromosome map presented here is a starting point for further development of physical and genetic maps of the guinea pig as well as an aid for genome assembly assignment to specific chromosomes. Furthermore, the comparative mapping will allow a transfer of gene map data from other species. The probes developed here provide a genomic toolkit, which will make the guinea pig a key species to unravel the evolutionary biology of the Hystricomorph rodents.
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Affiliation(s)
- Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail: (SAR); (FY)
| | - Polina L. Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Tangliang Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Patricia C. M. O’Brien
- Centre for Veterinary Science, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Bee L. Ng
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy
| | - Alexander S. Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
- * E-mail: (SAR); (FY)
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Teta P, Pardiñas UFJ, Sauthier DEU, Gallardo MH. A new species of the tetraploid vizcacha ratTympanoctomys(Caviomorpha, Octodontidae) from central Patagonia, Argentina. J Mammal 2014. [DOI: 10.1644/13-mamm-a-160] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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Arkhipova IR, Rodriguez F. Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids. Cytogenet Genome Res 2013; 140:295-311. [PMID: 23899811 DOI: 10.1159/000352069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) are discrete genetic units that have the ability to change their location within chromosomal DNA, and constitute a major and rapidly evolving component of eukaryotic genomes. They can be subdivided into 2 distinct types: retrotransposons, which use an RNA intermediate for transposition, and DNA transposons, which move only as DNA. Rapid advances in genome sequencing significantly improved our understanding of TE roles in genome shaping and restructuring, and studies of transcriptomes and epigenomes shed light on the previously unknown molecular mechanisms underlying genetic and epigenetic TE controls. Knowledge of these control systems may be important for better understanding of reticulate evolution and speciation in the context of bringing different genomes together by hybridization and perturbing the established regulatory balance by ploidy changes. See also sister article focusing on plants by Bento et al. in this themed issue.
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Affiliation(s)
- I R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA. iarkhipova @ mbl.edu
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17
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Nagamachi CY, Pieczarka JC, O'Brien PCM, Pinto JA, Malcher SM, Pereira AL, Rissino JDD, Mendes-Oliveira AC, Rossi RV, Ferguson-Smith MA. FISH with whole chromosome and telomeric probes demonstrates huge karyotypic reorganization with ITS between two species of Oryzomyini (Sigmodontinae, Rodentia): Hylaeamys megacephalus probes on Cerradomys langguthi karyotype. Chromosome Res 2013; 21:107-19. [PMID: 23494775 DOI: 10.1007/s10577-013-9341-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/14/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
Rodentia comprises 42 % of living mammalian species. The taxonomic identification can be difficult, the number of species currently known probably being underestimated, since many species show only slight morphological variations. Few studies surveyed the biodiversity of species, especially in the Amazon region. Cytogenetic studies show great chromosomal variability in rodents, with diploid numbers ranging from 10 to 102, making it difficult to find chromosomal homologies by comparative G banding. Chromosome painting is useful, but only a few species of rodents have been studied by this technique. In this study, we sorted whole chromosome probes by fluorescence-activated cell sorting from two Hylaeamys megacephalus individuals, an adult female (2n = 54) and a fetus (2n = 50). We made reciprocal chromosome painting between these karyotypes and cross-species hybridization on Cerradomys langguthi (2n = 46). Both species belong to the tribe Oryzomyini (Sigmodontinae), which is restricted to South America and were collected in the Amazon region. Twenty-four chromosome-specific probes from the female and 25 from the fetus were sorted. Reciprocal chromosome painting shows that the karyotype of the fetus does not represent a new cytotype, but an unbalanced karyotype with multiple rearrangements. Cross-species hybridization of H. megacephalus probes on metaphases of C. langguthi shows that 11 chromosomes of H. megacephalus revealed conserved synteny, 10 H. megacephalus probes hybridized to two chromosomal regions and three hybridized to three regions. Associations were observed on chromosomes pairs 1-4 and 11. Fluorescence in situ hybridization with a telomeric probe revealed interstitial regions in three pairs (1, 3, and 4) of C. langguthi chromosomes. We discuss the genomic reorganization of the C. langguthi karyotype.
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Collares-Pereira M, Matos I, Morgado-Santos M, Coelho M. Natural Pathways towards Polyploidy in Animals: TheSqualius alburnoidesFish Complex as a Model System to Study Genome Size and Genome Reorganization in Polyploids. Cytogenet Genome Res 2013; 140:97-116. [DOI: 10.1159/000351729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Wertheim B, Beukeboom L, van de Zande L. Polyploidy in Animals: Effects of Gene Expression on Sex Determination, Evolution and Ecology. Cytogenet Genome Res 2013; 140:256-69. [DOI: 10.1159/000351998] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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20
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Redi CA, Capanna E. Genome size evolution: sizing mammalian genomes. Cytogenet Genome Res 2012; 137:97-112. [PMID: 22627028 DOI: 10.1159/000338820] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The study of genome size (GS) and its variation is so fascinating to the scientific community because it constitutes the link between the present-day analytical and molecular studies of the genome and the old trunk of the holistic and synthetic view of the genome. The GS of several taxa vary over a broad range and do not correlate with the complexity of the organisms (the C-value paradox). However, the biology of transposable elements has let us reach a satisfactory view of the molecular mechanisms that give rise to GS variation and novelties, providing a less perplexing view of the significance of the GS (C-enigma). The knowledge of the composition and structure of a genome is a pre-requisite for trying to understand the evolution of the main genome signature: its size. The radiation of mammals provides an approximately 180-million-year test case for theories of how GS evolves. It has been found from data-mining GS databases that GS is a useful cyto-taxonomical instrument at the level of orders/superorders, providing genomic signatures characterizing Monotremata, Marsupialia, Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. A hypothetical ancestral mammalian-like GS of 2.9-3.7 pg has been suggested. This value appears compatible with the average values calculated for the high systematic levels of the extant Monotremata (∼2.97 pg) and Marsupialia (∼4.07 pg), suggesting invasion of mobile DNA elements concurrently with the separation of the older clades of Afrotheria (∼5.5 pg) and Xenarthra (∼4.5 pg) with larger GS, leaving the Euarchontoglires (∼3.4 pg) and Laurasiatheria (∼2.8 pg) genomes with fewer transposable elements. However, the paucity of GS data (546 mammalian species sized from 5,488 living species) for species, genera, and families calls for caution. Considering that mammalian species may be vanished even before they are known, GS data are sorely needed to phenotype the effects brought about by their variation and to validate any hypotheses on GS evolution in mammals.
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Affiliation(s)
- C A Redi
- Fondazione IRCCS Policlinico San Matteo, Dipartimento di Biologia e Biotecnologie Lazzaro Spallanzani, Pavia, Italia.
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Suárez-Villota EY, Vargas RA, Marchant CL, Torres JE, Köhler N, Núñez JJ, de la Fuente R, Page J, Gallardo MH. Distribution of repetitive DNAs and the hybrid origin of the red vizcacha rat (Octodontidae). Genome 2012; 55:105-17. [PMID: 22272977 DOI: 10.1139/g11-084] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Great genome size (GS) variations described in desert-specialist octodontid rodents include diploid species ( Octomys mimax and Octodontomys gliroides ) and putative tetraploid species ( Tympanoctomys barrerae and Pipanacoctomys aureus ). Because of its high DNA content, elevated chromosome number, and gigas effect, the genome of T. barrerae is claimed to have resulted from tetraploidy. Alternatively, the origin of its GS has been attributed to the accumulation of repetitive sequences. To better characterize the extent and origin of these repetitive DNA, self-genomic in situ hybridization (self-GISH), whole-comparative genomic hybridization (W-CGH), and conventional GISH were conducted in mitotic and meiotic chromosomes. Self-GISH on T. barrerae mitotic plates together with comparative self-GISH (using its closest relatives) discriminate a pericentromeric and a telomeric DNA fraction. As most of the repetitive sequences are pericentromeric, it seems that the large GS of T. barrerae is not due to highly repeated sequences accumulated along chromosomes arms. W-CGH using red-labeled P. aureus DNA and green-labeled O. mimax DNA simultaneously on chromosomes of T. barrerae revealed a yellow-orange fluorescence over a repetitive fraction of the karyotype. However, distinctive red-only fluorescent signals were also detected at some centromeres and telomeres, indicating closer homology with the DNA sequences of P. aureus. Conventional GISH using an excess of blocking DNA from either P. aureus or O. mimax labeled only a fraction of the T. barrerae genome, indicating its double genome composition. These data point to a hybrid nature of the T. barrerae karyotype, suggesting a hybridization event in the origin of this species.
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Affiliation(s)
- E Y Suárez-Villota
- Institute of Ecology and Evolution, Universidad Austral de Chile, Valdivia, Chile
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GUIGNARD MAÏTÉ, BÜCHI LUCIE, GÉTAZ MICHAEL, BETTO-COLLIARD CAROLINE, STÖCK MATTHIAS. Genome size rather than content might affect call properties in toads of three ploidy levels (Anura: Bufonidae: Bufo viridis subgroup). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01837.x] [Citation(s) in RCA: 8] [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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Romanenko SA, Perelman PL, Trifonov VA, Graphodatsky AS. Chromosomal evolution in Rodentia. Heredity (Edinb) 2012; 108:4-16. [PMID: 22086076 PMCID: PMC3238120 DOI: 10.1038/hdy.2011.110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 11/08/2022] Open
Abstract
Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution.
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Affiliation(s)
- S A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.
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24
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Graphodatsky AS, Trifonov VA, Stanyon R. The genome diversity and karyotype evolution of mammals. Mol Cytogenet 2011; 4:22. [PMID: 21992653 PMCID: PMC3204295 DOI: 10.1186/1755-8166-4-22] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/12/2011] [Indexed: 01/30/2023] Open
Abstract
The past decade has witnessed an explosion of genome sequencing and mapping in evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat), laboratory (mice and rat) and agricultural (cattle, pig, and horse) animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.
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Mable BK, Alexandrou MA, Taylor MI. Genome duplication in amphibians and fish: an extended synthesis. J Zool (1987) 2011. [DOI: 10.1111/j.1469-7998.2011.00829.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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The implications of gene heterozygosity for protein folding and protein turnover. J Theor Biol 2010; 265:554-64. [PMID: 20493885 DOI: 10.1016/j.jtbi.2010.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Revised: 04/11/2010] [Accepted: 05/17/2010] [Indexed: 12/14/2022]
Abstract
The offspring of closely related parents often suffer from inbreeding depression, sometimes resulting in a slower growth rate for inbred offspring relative to non-inbred offspring. Previous research has shown that some of the slower growth rate of inbred organisms can be attributed to the inbred organisms' increased levels of protein turnover. This paper attempts to show that the higher levels of protein turnover among inbred organisms can be attributed to accumulations of misfolded and aggregated proteins that require degradation by the inbred organisms' protein quality control systems. The accumulation of misfolded and aggregated proteins within inbred organisms are the result of more negative free energies of folding for proteins encoded at homozygous gene loci and higher concentrations of potentially aggregating non-native protein species within the cell. The theory presented here makes several quantitative predictions that suggest a connection between protein misfolding/aggregation and polyploidy that can be tested by future research.
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Ojeda AA. Phylogeography and genetic variation in the South American rodent Tympanoctomys barrerae (Rodentia: Octodontidae). J Mammal 2010. [DOI: 10.1644/09-mamm-a-177.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Stöck M, Ustinova J, Lamatsch DK, Schartl M, Perrin N, Moritz C. A VERTEBRATE REPRODUCTIVE SYSTEM INVOLVING THREE PLOIDY LEVELS: HYBRID ORIGIN OF TRIPLOIDS IN A CONTACT ZONE OF DIPLOID AND TETRAPLOID PALEARCTIC GREEN TOADS (BUFO VIRIDIS SUBGROUP)*. Evolution 2009; 64:944-59. [DOI: 10.1111/j.1558-5646.2009.00876.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Epigenetic processes in a tetraploid mammal. Mamm Genome 2008; 19:439-47. [PMID: 18758856 DOI: 10.1007/s00335-008-9131-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 07/01/2008] [Indexed: 10/21/2022]
Abstract
Polyploidy has played a most important role in speciation and evolution of plants and animals. It is thought that low frequency of polyploidy in mammals is due to a dosage imbalance that would interfere with proper development in mammalian polyploids. The first tetraploid mammal, Tympanoctomys barrerae (Octodontidae), appears to be an exception to this rule. In this study we investigated X chromosome inactivation (XCI) and genomic imprinting in T. barrerae, two epigenetic processes usually involved in dosage control in mammalian genomes. The imprinting status of the Peg1 gene was determined by Peg1 allelic expression studies. The inactive X chromosome was identified on interphase nuclei by immunofluorescence using specific antisera raised against Met3H3K27 and macroH2A1. Quantitative PCR was used to compare the Peg1/Dmd ratio in T. barrerae and in its most closely related diploid species, Octomys mimax. Our data demonstrate that parental-specific silencing of at least one gene and normal X chromosomal dosage mechanism are conserved in the tetraploid genome. We hypothesize a concerted action of genetic and epigenetic mechanisms during the process of functional diploidization of this tetraploid genome.
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Battini L, Macip S, Fedorova E, Dikman S, Somlo S, Montagna C, Gusella GL. Loss of polycystin-1 causes centrosome amplification and genomic instability. Hum Mol Genet 2008; 17:2819-33. [PMID: 18566106 DOI: 10.1093/hmg/ddn180] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenetic disease predominantly caused by alteration or dysregulation of the PKD1 gene, which encodes polycystin-1 (PC1). The disease is characterized by the progressive expansion of bilateral fluid-filled renal cysts that ultimately lead to renal failure. Individual cysts, even within patients with germline mutations, are genetically heterogeneous, displaying diverse chromosomal abnormalities. To date, the molecular mechanisms responsible for this genetic heterogeneity remain unknown. Using a lentiviral-mediated siRNA expression model of Pkd1 hypomorphism, we show that loss of PC1 function is sufficient to produce centrosome amplification and multipolar spindle formation. These events lead to genomic instability characterized by gross polyploidism and mitotic catastrophe. Following these dramatic early changes, the cell population rapidly converges toward a stable ploidy in which centrosome amplification is significantly decreased, though cytological abnormalities such as micronucleation, chromatin bridges and aneuploidy remain common. In agreement with our in vitro findings, we provide the first in vivo evidence that significant centrosome amplification occurs in kidneys from conditional Pkd1 knockout mice at early and late time during the disease progression as well as in human ADPKD patients. These findings establish a novel function of PC1 in ADPKD pathogenesis and a genetic mechanism that may underlie the intrafamilial variability of ADPKD progression.
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Affiliation(s)
- Lorenzo Battini
- Division of Renal Medicine, Mount Sinai School of Medicine, One Gustave Levy Place, Box 1243 New York, NY 10029, USA
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Thorpe PH, González-Barrera S, Rothstein R. More is not always better: the genetic constraints of polyploidy. Trends Genet 2007; 23:263-6. [PMID: 17418443 DOI: 10.1016/j.tig.2007.03.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 02/16/2007] [Accepted: 03/29/2007] [Indexed: 10/23/2022]
Abstract
Polyploid cells are a characteristic feature of certain human tissues, and notably many cancers. In a systematic genomic screen in yeast, Storchová and co-workers identified the genetic requirements of tetraploidy. Surprisingly, they showed that only three connected pathways are essential for the viability of tetraploid yeast cells. These data provide exciting new targets that might be essential specifically in polyploid cancer cells.
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Affiliation(s)
- Peter H Thorpe
- Department of Genetics & Development, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032-2704, USA
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Molina WF, Margarido VP, Galetti Jr PM. Natural triploidy in Leporinus cf. elongatus bearing sex chromosomes. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000400010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Chen ZJ. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. ANNUAL REVIEW OF PLANT BIOLOGY 2007; 58:377-406. [PMID: 17280525 PMCID: PMC1949485 DOI: 10.1146/annurev.arplant.58.032806.103835] [Citation(s) in RCA: 586] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Polyploidy, or whole-genome duplication (WGD), is an important genomic feature for all eukaryotes, especially many plants and some animals. The common occurrence of polyploidy suggests an evolutionary advantage of having multiple sets of genetic material for adaptive evolution. However, increased gene and genome dosages in autopolyploids (duplications of a single genome) and allopolyploids (combinations of two or more divergent genomes) often cause genome instabilities, chromosome imbalances, regulatory incompatibilities, and reproductive failures. Therefore, new allopolyploids must establish a compatible relationship between alien cytoplasm and nuclei and between two divergent genomes, leading to rapid changes in genome structure, gene expression, and developmental traits such as fertility, inbreeding, apomixis, flowering time, and hybrid vigor. Although the underlying mechanisms for these changes are poorly understood, some themes are emerging. There is compelling evidence that changes in DNA sequence, cis- and trans-acting effects, chromatin modifications, RNA-mediated pathways, and regulatory networks modulate differential expression of homoeologous genes and phenotypic variation that may facilitate adaptive evolution in polyploid plants and domestication in crops.
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Affiliation(s)
- Z Jeffrey Chen
- Department of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.
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35
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Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007; 29:288-99. [PMID: 17295292 DOI: 10.1002/bies.20544] [Citation(s) in RCA: 403] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There are two intriguing paradoxes in molecular biology--the inconsistent relationship between organismal complexity and (1) cellular DNA content and (2) the number of protein-coding genes--referred to as the C-value and G-value paradoxes, respectively. The C-value paradox may be largely explained by varying ploidy. The G-value paradox is more problematic, as the extent of protein coding sequence remains relatively static over a wide range of developmental complexity. We show by analysis of sequenced genomes that the relative amount of non-protein-coding sequence increases consistently with complexity. We also show that the distribution of introns in complex organisms is non-random. Genes composed of large amounts of intronic sequence are significantly overrepresented amongst genes that are highly expressed in the nervous system, and amongst genes downregulated in embryonic stem cells and cancers. We suggest that the informational paradox in complex organisms may be explained by the expansion of cis-acting regulatory elements and genes specifying trans-acting non-protein-coding RNAs.
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Affiliation(s)
- Ryan J Taft
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
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36
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Stöck M, Moritz C, Hickerson M, Frynta D, Dujsebayeva T, Eremchenko V, Macey JR, Papenfuss TJ, Wake DB. Evolution of mitochondrial relationships and biogeography of Palearctic green toads (Bufo viridis subgroup) with insights in their genomic plasticity. Mol Phylogenet Evol 2006; 41:663-89. [PMID: 16919484 DOI: 10.1016/j.ympev.2006.05.026] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 05/19/2006] [Accepted: 05/22/2006] [Indexed: 11/23/2022]
Abstract
Taxa involving three bisexually reproducing ploidy levels make green toads a unique amphibian system. We put a cytogenetic dataset from Central Asia in a molecular framework and apply phylogenetic and demographic methods to data from the entire Palearctic range. We study the mitochondrial relationships of diploids to infer their phylogeography and the maternal ancestry of polyploids. Control regions (and tRNAs between ND1 and ND2 in representatives) characterize a deeply branched assemblage of twelve haplotype groups, diverged since the Lower Miocene. Polyploidy has evolved several times: Central Asian tetraploids (B. oblongus, B. pewzowi) have at least two maternal origins. Intriguingly, the mitochondrial ancestor of morphologically distinctive, sexually reproducing triploid taxa (B. pseudoraddei) from Karakoram and Hindukush represents a different lineage. We report another potential case of bisexual triploid toads (B. zugmayeri). Identical d-loops in diploids and tetraploids from Iran and Turkmenistan, which differ in morphology, karyotypes and calls, suggest multiple origins and retained polymorphism and/or hybridization. A similar system involves diploids, triploids and tetraploids from Kyrgyzstan and Kazakhstan where green toads exemplify vertebrate genomic plasticity. A new form from Sicily and its African sister species (B. boulengeri) allow internal calibration and divergence time estimates for major clades. The subgroup may have originated in Eurasia rather than Africa since the earliest diverged lineages (B. latastii, B. surdus) and earliest fossils occur in Asia. We delineate ranges, contact and hybrid zones. Phylogeography, including one of the first non-avian datasets from Central Asian high mountains, reflects Quaternary climate and glaciation.
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Affiliation(s)
- Matthias Stöck
- Department of Integrative Biology, Museum of Vertebrate Zoology (MVZ), University of California-Berkeley, 3101 Valley of Life Sciences Building #3160, Berkeley, CA 94720-3160, USA.
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37
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Abstract
We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson-Dobzhansky-Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these "morphologically cryptic genetic species" are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F(1)s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is "reproductively isolated species." Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen-based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum.
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Affiliation(s)
- Robert J. Baker
- Department of Biological Sciences and the Museum, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Robert D. Bradley
- Department of Biological Sciences and the Museum, Texas Tech University, Lubbock, TX 79409-3131, USA
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38
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Abstract
Polyploidy is produced by multiplication of a single genome (autopolyploid) or combination of two or more divergent genomes (allopolyploid). The available data obtained from the study of synthetic (newly created or human-made) plant allopolyploids have documented dynamic and stochastic changes in genomic organization and gene expression, including sequence elimination, inter-chromosomal exchanges, cytosine methylation, gene repression, novel activation, genetic dominance, subfunctionalization and transposon activation. The underlying mechanisms for these alterations are poorly understood. To promote a better understanding of genomic and gene expression changes in polyploidy, we briefly review origins and forms of polyploidy and summarize what has been learned from genome-wide gene expression analyses in newly synthesized auto-and allopolyploids. We show transcriptome divergence between the progenitors and in the newly formed allopolyploids. We propose models for transcriptional regulation, chromatin modification and RNA-mediated pathways in establishing locus-specific expression of orthologous and homoeologous genes during allopolyploid formation and evolution.
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Affiliation(s)
- Z Jeffrey Chen
- Molecular Cell and Developmental Biology, University of Texas, Austin, 78714, USA.
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Murphy WJ, Pearks Wilkerson AJ, Raudsepp T, Agarwala R, Schäffer AA, Stanyon R, Chowdhary BP. Novel gene acquisition on carnivore Y chromosomes. PLoS Genet 2006; 2:e43. [PMID: 16596168 PMCID: PMC1420679 DOI: 10.1371/journal.pgen.0020043] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Accepted: 02/08/2006] [Indexed: 11/19/2022] Open
Abstract
Despite its importance in harboring genes critical for spermatogenesis and male-specific functions, the Y chromosome has been largely excluded as a priority in recent mammalian genome sequencing projects. Only the human and chimpanzee Y chromosomes have been well characterized at the sequence level. This is primarily due to the presumed low overall gene content and highly repetitive nature of the Y chromosome and the ensuing difficulties using a shotgun sequence approach for assembly. Here we used direct cDNA selection to isolate and evaluate the extent of novel Y chromosome gene acquisition in the genome of the domestic cat, a species from a different mammalian superorder than human, chimpanzee, and mouse (currently being sequenced). We discovered four novel Y chromosome genes that do not have functional copies in the finished human male-specific region of the Y or on other mammalian Y chromosomes explored thus far. Two genes are derived from putative autosomal progenitors, and the other two have X chromosome homologs from different evolutionary strata. All four genes were shown to be multicopy and expressed predominantly or exclusively in testes, suggesting that their duplication and specialization for testis function were selected for because they enhance spermatogenesis. Two of these genes have testis-expressed, Y-borne copies in the dog genome as well. The absence of the four newly described genes on other characterized mammalian Y chromosomes demonstrates the gene novelty on this chromosome between mammalian orders, suggesting it harbors many lineage-specific genes that may go undetected by traditional comparative genomic approaches. Specific plans to identify the male-specific genes encoded in the Y chromosome of mammals should be a priority. Y chromosomes are typically gene poor and enriched with repetitive elements, making them difficult to sequence by standard methods. Hence, the Y chromosome gene repertoire in mammalian species other than human has not been explored until very recently. Here the authors used a directed approach to isolate Y chromosome genes of the domestic cat, an evolutionary divergent species from human and mouse. They found that the feline Y chromosome harbors its own unique set of genes that are expressed specifically in the testes, presumably where they play an important role in spermatogenesis. Paralleling the discoveries seen from the full human Y chromosome sequence, the feline Y chromosome has acquired and remodeled some genes from autosomes, while other genes have a shared ancestry with the X chromosome. However, none of the four new genes are found on the Y chromosomes of human or mouse, although two are shared with the canine Y chromosome. This work highlights the Y chromosome as a source of potential gene novelty in different species and suggests that more directed efforts at characterizing this hitherto understudied chromosome will further enrich our understanding of the types of genes found there and the roles they may play in mammalian spermatogenesis.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America.
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40
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Gallardo MH, González CA, Cebrián I. Molecular cytogenetics and allotetraploidy in the red vizcacha rat, Tympanoctomys barrerae (Rodentia, Octodontidae). Genomics 2006; 88:214-21. [PMID: 16580173 DOI: 10.1016/j.ygeno.2006.02.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 02/08/2006] [Accepted: 02/14/2006] [Indexed: 11/24/2022]
Abstract
The theoretical impossibility of polyploidy in mammals was overturned by the discovery of tetraploidy in the red vizcacha rat, Tympanoctomys barrerae (2n = 102). As a consequence of genome duplication, remarkably increased cell dimensions are observed in the spermatozoa and in different somatic cell lines of this species. Locus duplication had been previously demonstrated by in situ PCR and Southern blot analysis of single-copy genes. Here, we corroborate duplication of loci in multiple-copy (major rDNAs) and single-copy (Hoxc8) genes by fluorescence in situ hybridization. We also demonstrate that nucleolar dominance, a large-scale epigenetic silencing phenomenon characteristic of allopolyploids, explains the presence of only one Ag-NOR chromosome pair in T. barrerae. Nucleolar dominance, together with the chromosomal heteromorphism detected in the G-banding pattern and synaptonemal complexes of the species' diploid-like meiosis, consistently indicates allotetraploidy. Allotetraploidization can coherently explain the peculiarities of gene silencing, cell dimensions, and karyotypic features of T. barrerae that remain unexplained by assuming diploidy and a large genome size attained by the dispersion of repetitive sequences.
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Affiliation(s)
- M H Gallardo
- Instituto de Ecología y Evolución, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
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