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Balachandra S, Sarkar S, Amodeo AA. The Nuclear-to-Cytoplasmic Ratio: Coupling DNA Content to Cell Size, Cell Cycle, and Biosynthetic Capacity. Annu Rev Genet 2022; 56:165-185. [PMID: 35977407 PMCID: PMC10165727 DOI: 10.1146/annurev-genet-080320-030537] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Though cell size varies between different cells and across species, the nuclear-to-cytoplasmic (N/C) ratio is largely maintained across species and within cell types. A cell maintains a relatively constant N/C ratio by coupling DNA content, nuclear size, and cell size. We explore how cells couple cell division and growth to DNA content. In some cases, cells use DNA as a molecular yardstick to control the availability of cell cycle regulators. In other cases, DNA sets a limit for biosynthetic capacity. Developmentally programmed variations in the N/C ratio for a given cell type suggest that a specific N/C ratio is required to respond to given physiological demands. Recent observations connecting decreased N/C ratios with cellular senescence indicate that maintaining the proper N/C ratio is essential for proper cellular functioning. Together, these findings suggest a causative, not simply correlative, role for the N/C ratio in regulating cell growth and cell cycle progression.
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Affiliation(s)
- Shruthi Balachandra
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Dartmouth College, Hanover, New Hampshire, USA;
| | - Amanda A Amodeo
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
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2
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Gerhardt HC, Tucker MA, von Twickel A, Walkowiak W. Anuran Vocal Communication: Effects of Genome Size, Cell Number and Cell Size. BRAIN, BEHAVIOR AND EVOLUTION 2021; 96:137-146. [PMID: 34788770 DOI: 10.1159/000520913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 11/06/2021] [Indexed: 11/19/2022]
Abstract
Significant variation in genome size occurs among anuran amphibians and can affect cell size and number. In the gray treefrog complex in North America increases in cell size in autotriploids of the diploid (Hyla chrysoscelis) altered the temporal structure of mate-attracting vocalizations and auditory selectivity for these properties. Here we show that the tetraploid species (Hyla versicolor) also has significantly fewer brain neurons than H. chrysoscelis. With regard to cell size in tissues involved in vocal communication, spinal motor neurons were larger in tetraploids than in diploids and comparable to differences in erythrocyte size; smaller increases were found in one of the three auditory centers in the torus semicircularis. Future studies should address questions about how environmental conditions during development affect cell numbers and size and the causal relationships between these cellular changes and the vocal communication system.
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Affiliation(s)
- H Carl Gerhardt
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Mitch A Tucker
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
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3
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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4
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Miller KE, Brownlee C, Heald R. The power of amphibians to elucidate mechanisms of size control and scaling. Exp Cell Res 2020; 392:112036. [PMID: 32343955 PMCID: PMC7246146 DOI: 10.1016/j.yexcr.2020.112036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 01/26/2023]
Abstract
Size is a fundamental feature of biology that affects physiology at all levels, from the organism to organs and tissues to cells and subcellular structures. How size is determined at these different levels, and how biological structures scale to fit together and function properly are important open questions. Historically, amphibian systems have been extremely valuable to describe scaling phenomena, as they occupy some of the extremes in biological size and are amenable to manipulations that alter genome and cell size. More recently, the application of biochemical, biophysical, and embryological techniques to amphibians has provided insight into the molecular mechanisms underlying scaling of subcellular structures to cell size, as well as how perturbation of normal size scaling impacts other aspects of cell and organism physiology.
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Affiliation(s)
- Kelly E Miller
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA
| | - Christopher Brownlee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794-8651, USA.
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, CA, 94720, Berkeley, USA.
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5
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Womack MC, Metz MJ, Hoke KL. Larger Genomes Linked to Slower Development and Loss of Late-Developing Traits. Am Nat 2019; 194:854-864. [PMID: 31738099 DOI: 10.1086/705897] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Genome size varies widely among organisms and is known to affect vertebrate development, morphology, and physiology. In amphibians, genome size is hypothesized to contribute to loss of late-forming structures, although this hypothesis has mainly been discussed in salamanders. Here we estimated genome size for 22 anuran species and combined this novel data set with existing genome size data for an additional 234 anuran species to determine whether larger genome size is associated with loss of a late-forming anuran sensory structure, the tympanic middle ear. We established that genome size is negatively correlated with development rate across 90 anuran species and found that genome size evolution is correlated with evolutionary loss of the middle ear bone (columella) among 241 species (224 eared and 17 earless). We further tested whether the development of the tympanic middle ear could be constrained by large cell sizes and small body sizes during key stages of tympanic middle ear development (metamorphosis). Together, our evidence suggests that larger genomes, slower development rate, and smaller body sizes at metamorphosis may contribute to the loss of the anuran tympanic middle ear. We conclude that increases in anuran genome size, although less drastic than those in salamanders, may affect development of late-forming traits.
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6
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Dawley EM. Comparative Morphology of Plethodontid Olfactory and Vomeronasal Organs: How Snouts Are Packed. HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-15-00008.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ellen M. Dawley
- Department of Biology, Ursinus College, Collegeville, PA 19426, USA
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7
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Mohlhenrich ER, Mueller RL. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 2016; 70:2865-2878. [DOI: 10.1111/evo.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/25/2022]
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8
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Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E. Transposons, Genome Size, and Evolutionary Insights in Animals. Cytogenet Genome Res 2016; 147:217-39. [PMID: 26967166 DOI: 10.1159/000444429] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
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Affiliation(s)
- Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Universitx00E0; Politecnica delle Marche, Ancona, Italy
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9
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Roth G, Walkowiak W. The Influence of Genome and Cell Size on Brain Morphology in Amphibians. Cold Spring Harb Perspect Biol 2015; 7:a019075. [PMID: 26261281 DOI: 10.1101/cshperspect.a019075] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In amphibians, nerve cell size is highly correlated with genome size, and increases in genome and cell size cause a retardation of the rate of development of nervous (as well as nonnervous) tissue leading to secondary simplification. This yields an inverse relationship between genome and cell size on the one hand and morphological complexity of the tectum mesencephali as the main visual center, the size of the torus semicircularis as the main auditory center, the size of the amphibian papilla as an important peripheral auditory structure, and the size of the cerebellum as a major sensorimotor center. Nervous structures developing later (e.g., torus and cerebellum) are more affected by secondary simplification than those that develop earlier (e.g., the tectum). This effect is more prominent in salamanders and caecilians than in frogs owing to larger genome and cells sizes in the former two taxa. We hypothesize that because of intragenomic evolutionary processes, important differences in brain morphology can arise independently of specific environmental selection.
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Affiliation(s)
- Gerhard Roth
- University of Bremen, Brain Research Institute, D-283345 Bremen, Germany
| | - Wolfgang Walkowiak
- University of Cologne, Biocenter, Institute for Zoology, D-50674 Köln, Germany
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10
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Mueller RL. Genome Biology and the Evolution of Cell-Size Diversity. Cold Spring Harb Perspect Biol 2015; 7:cshperspect.a019125. [PMID: 26254312 DOI: 10.1101/cshperspect.a019125] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cell size is highly variable among different species across the Tree of Life. For decades, biologists have generated hypotheses to explain this variation, in many cases, drawing on the correlations that exist among cell size, genome size, nucleus size, and various physiological and developmental parameters. In recent years, our understanding of the molecular processes that generate variation in genome size over evolutionary time, as well as the processes that maintain homeostasis in cell size over ontogenetic time, has increased dramatically. The goal of this article is to highlight how information from these fields can be integrated to generate new hypotheses to explain cell-size diversity.
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11
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Abstract
Regeneration is studied in a few model species of salamanders, but the ten families of salamanders show considerable variation, and this has implications for our understanding of salamander biology. The most recent classification of the families identifies the cryptobranchoidea as the basal group which diverged in the early Jurassic. Variation in the sizes of genomes is particularly obvious, and reflects a major contribution from transposable elements which is already present in the basal group.Limb development has been a focus for evodevo studies, in part because of the variable property of pre-axial dominance which distinguishes salamanders from other tetrapods. This is thought to reflect the selective pressures that operate on a free-living aquatic larva, and might also be relevant for the evolution of limb regeneration. Recent fossil evidence suggests that both pre-axial dominance and limb regeneration were present 300 million years ago in larval temnospondyl amphibians that lived in mountain lakes. A satisfying account of regeneration in salamanders may need to address all these different aspects in the future.
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12
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Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol Evol 2011; 4:168-83. [PMID: 22200636 PMCID: PMC3318908 DOI: 10.1093/gbe/evr139] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2011] [Indexed: 01/20/2023] Open
Abstract
Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.
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Affiliation(s)
- Cheng Sun
- Department of Biology, Colorado State University
| | - Donald B. Shepard
- Department of Biology, Colorado State University
- Current address: Department of Fisheries, Wildlife and Conservation Biology; University of Minnesota
| | | | | | - Kathryn Hall
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
| | - Todd A. Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
| | | | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
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13
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Dufresne F, Jeffery N. A guided tour of large genome size in animals: what we know and where we are heading. Chromosome Res 2011; 19:925-38. [DOI: 10.1007/s10577-011-9248-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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15
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Sessions SK, Stöck M, Vieites DR, Quarles R, Min MS, Wake DB. Cytogenetic analysis of the Asian plethodontid salamander, Karsenia koreana: evidence for karyotypic conservation, chromosome repatterning, and genome size evolution. Chromosome Res 2008; 16:563-74. [PMID: 18431682 DOI: 10.1007/s10577-008-1197-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 12/14/2007] [Accepted: 12/14/2007] [Indexed: 11/30/2022]
Abstract
A cytogenetic analysis, including the karyotype, C-bands, silver-stained nucleolus organizer regions and genome size, was performed on the recently discovered species, Karsenia koreana, the first plethodontid salamander from Asia. The karyotype consists of 14 pairs of bi-armed chromosomes, with no evidence of heteromorphic sex chromosomes. C-banding reveals a concentration of heterochromatin at the centromeres as well as at interstitial locations. The smallest chromosome (pair number 14) has symmetrical interstitial C-bands in each arm, resembling chromosome no. 14 of North American species of its sister group taxon, supergenus Hydromantes. Acomparative analysis of C-band heterochromatin and silver-stained nucleolus organizer regions of Karsenia and other plethodontid genera reveals that chromosomal evolution may have featured chromosome 'repatterning' within the context of conserved chromosome number and shape in this clade. Genome size is correlated with geographic distribution in plethodontids and appears to have important phenotypic correlates as well. The genome size of Karsenia is relatively large, and resembles that of the geographically closest plethodontids from western North America, especially species of the genus Hydromantes. The biological significance of these cytogenetic characteristics of plethodontid salamanders is discussed within an evolutionary context.
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16
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Mueller RL, Gregory TR, Gregory SM, Hsieh A, Boore JL. Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders. ZOOLOGY 2008; 111:218-30. [PMID: 18328681 DOI: 10.1016/j.zool.2007.07.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 06/28/2007] [Accepted: 07/11/2007] [Indexed: 11/29/2022]
Abstract
Within the salamander family Plethodontidae, five different clades have evolved high levels of enucleated red blood cells, which are extremely unusual among non-mammalian vertebrates. In each of these five clades, the salamanders have large genomes and miniaturized or attenuated body forms. Such a correlation suggests that the loss of nuclei in red blood cells may be related, in part, to the interaction between large genome size and small body size, which has been shown to have profound morphological consequences for the nervous and visual systems in plethodontids. Previous work has demonstrated that variation in both the level of enucleated cells and the size of the nuclear genome exists among species of the monophyletic plethodontid genus Batrachoseps. Here, we report extensive intraspecific variation in levels of enucleated red blood cells in 15 species and provide measurements of red blood cell size, nucleus size, and genome size for 13 species of Batrachoseps. We present a new phylogenetic hypothesis for the genus based on 6150bp of mitochondrial DNA sequence data from nine exemplar taxa and use it to examine the relationship between genome size and enucleated red blood cell morphology in a phylogenetic framework. Our analyses demonstrate positive direct correlations between genome size, nucleus size, and both nucleated and enucleated cell sizes within Batrachoseps, although only the relationship between genome size and nucleus size is significant when phylogenetically independent contrasts are used. In light of our results and broader studies of comparative hematology, we propose that high levels of enucleated, variably sized red blood cells in Batrachoseps may have evolved in response to rheological problems associated with the circulation of large red blood cells containing large, bulky nuclei in an attenuate organism.
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Affiliation(s)
- Rachel Lockridge Mueller
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Bldg., University of California, Berkeley, CA 94720-3160, USA.
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17
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Litvinchuk SN, Rosanov JM, Borkin LJ. Correlations of geographic distribution and temperature of embryonic development with the nuclear DNA content in the Salamandridae (Urodela, Amphibia). Genome 2007; 50:333-42. [PMID: 17546091 DOI: 10.1139/g07-010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used flow cytometry to measure the nuclear DNA content in erythrocytes of 27 salamandrid species. Across these species, diploid genome size varied more than 2 fold (51.3–104.4 pg). According to genome size and geographic distribution, 3 groups of newt species were recognized: West Palearctics with smaller amounts of nuclear DNA; Nearctic, with intermediate values; and East Asiatic, with higher genome sizes. Viviparous West Palearctic salamanders differed from most of the oviparous West Palearctic newts in possessing larger genome sizes. The nuclear DNA content strongly correlates with species range limits. At the same temperature, embryos of salamandrid species with larger genome sizes have a markedly longer developmental time than those with smaller genomes. We present an analysis of the relationships between the amount of nuclear DNA and water temperature at the breeding sites.
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Affiliation(s)
- Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia.
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18
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GREGORY TRYAN. Coincidence, coevolution, or causation? DNA content, cellsize, and the C-value enigma. Biol Rev Camb Philos Soc 2007. [DOI: 10.1111/j.1469-185x.2000.tb00059.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Hardie DC, Hebert PDN. The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes. Genome 2003; 46:683-706. [PMID: 12897876 DOI: 10.1139/g03-040] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.
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Affiliation(s)
- David C Hardie
- Department of Zoology, University of Guelph, Guelph, ON, Canada.
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20
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GREGORY TRYAN. Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approach to the C-value enigma. Biol J Linn Soc Lond 2003. [DOI: 10.1046/j.1095-8312.2003.00191.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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22
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Gregory TR. A bird's-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves. Evolution 2002; 56:121-30. [PMID: 11913657 DOI: 10.1111/j.0014-3820.2002.tb00854.x] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
For half a century, variation in genome size (C-value) has been an unresolved puzzle in evolutionary biology. While the initial "C-value paradox" was solved with the discovery of noncoding DNA, a much more complex "C-value enigma" remains. The present study focuses on one aspect of this puzzle, namely the small genome sizes of birds. Significant negative correlations are reported between resting metabolic rate and both C-value and erythrocyte size. Cell size is positively correlated with both nucleus size and C-value in birds, as in other vertebrates. These findings shed light on the constraints acting on genome size in birds and illustrate the importance of interactions among various levels of the biological hierarchy, ranging from the subchromosomal to the ecological. Following from a discussion of the mechanistic bases of the correlations reported and the processes by which birds achieved and/or maintain small genomes, a pluralistic approach to the C-value enigma is recommended.
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Affiliation(s)
- T Ryan Gregory
- Department of Zoology, University of Guelph, Ontario, Canada.
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23
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Chipman AD, Khaner O, Haas A, Tchernov E. The evolution of genome size: what can be learned from anuran development? THE JOURNAL OF EXPERIMENTAL ZOOLOGY 2001; 291:365-74. [PMID: 11754015 DOI: 10.1002/jez.1135] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Differences in nuclear DNA content in vertebrates have been shown to be correlated with cell size, cell division rate, and embryonic developmental rate. We compare seven species of anuran amphibians with a three-fold range of genome sizes. Parameters examined include the number and density of cells in a number of embryonic structures, and the change in cell number in the CNS during development. We show that genome size is correlated with cell proliferation rate and with developmental rate at different stages of embryonic development, but that the correlation between genome size and cell size is only evident at later stages. We discuss the evolution of genome size in amphibians. Our discussion takes into account data that reportedly support two conflicting hypotheses: the "skeletal DNA" hypothesis, which claims a selective role for differences in genome size, and the "junk DNA" hypothesis, which claims that differences in genome size are a random result of the accumulation of noncoding DNA sequences. We show that these supposedly conflicting hypotheses can be integrated into a more complex and inclusive model for the evolution of genome size.
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Affiliation(s)
- A D Chipman
- The Department for Cell and Animal Biology, The Hebrew University, Jerusalem 91904, Israel.
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24
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Abstract
We used flow cytometry to measure genome size in 15 species from seven families and subfamilies of tetraodontiform fishes. Previous studies have found that smooth pufferfishes (Tetraodontidae) have the smallest genome of any vertebrate measured to date (0.7-1.0 picograms diploid). We found that spiny pufferfishes (Diodontidae, sister group to the smooth puffers) possess a genome that is about two times larger (1.6-1.8 pg). Mola mola, a member of the sister group to Diodontidae and Tetraodontidae, also has a relatively large genome (1.7 pg). Parsimony analysis of this pattern indicates that the plesiomorphic condition for Molidae (Diodontidae, Tetraodontidae) is a genome size of 1.6-1.8 pg, and that tiny genome size is a derived character unique to smooth puffers. However, an alternative explanation is that the ancestor of Tetraodontidae acquired a heritable tendency toward decreasing genome size, such as a new or modified deletion mechanism, and genome size in all of the tetraodontid lineages has been decreasing in parallel since the split from Diodontidae. Small genome size (1.1-1.3 pg) also appears to have evolved independently in some members of Balistoidea (triggerfishes and filefishes) within Tetraodontiformes.
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Affiliation(s)
- E L Brainerd
- Department of Biology, University of Massachusetts, Amherst 01003-9297, USA.
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Gregory TR. The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates. Blood Cells Mol Dis 2001; 27:830-43. [PMID: 11783946 DOI: 10.1006/bcmd.2001.0457] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vertebrate genome sizes vary roughly 350-fold and correlate with a variety of cellular and organismal parameters. Most notable among these is the relationship between genome size ("C-value") and red blood cell (RBC) size, which can be identified within and among each of the five vertebrate classes. This relationship, in turn, leads to important associations between genome size and features such as metabolic rate (at least in homeotherms). The present article describes the correlation between genome size and RBC size in vertebrates and discusses some of the cytological, physiological, and evolutionary implications of this relationship.
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Affiliation(s)
- T R Gregory
- Department of Zoology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Gregory TR, Hebert PD, Kolasa J. Evolutionary implications of the relationship between genome size and body size in flatworms and copepods. Heredity (Edinb) 2000; 84 ( Pt 2):201-8. [PMID: 10762390 DOI: 10.1046/j.1365-2540.2000.00661.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome and body sizes were measured in 38 species of turbellarian flatworms and 16 species of copepod crustaceans. Significant positive relationships existed between genome size and body size in both groups. The slopes of these regressions indicated that increases in cell volume are reinforced by increased cell numbers, or that cell volumes show positive allometric variation with genome size. Genome sizes appear to vary in a discontinuous fashion among congeneric species in both groups, indicating that such changes have occurred rapidly, and with potentially profound effects on important morphological characters.
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Affiliation(s)
- T R Gregory
- Department of Zoology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
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Jockusch EL. An evolutionary correlate of genome size change in plethodontid salamanders. Proc Biol Sci 1997. [DOI: 10.1098/rspb.1997.0085] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Elizabeth L. Jockusch
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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Pagel M, Johnstone RA. Variation across species in the size of the nuclear genome supports the junk-DNA explanation for the C-value paradox. Proc Biol Sci 1997; 249:119-24. [PMID: 1360673 DOI: 10.1098/rspb.1992.0093] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The amount of DNA in the nuclear genome (the DNA C-value) of eukaryotes varies at least 80,000-fold across species, and yet bears little or no relation to organismic complexity or to the number of protein-coding genes. This phenomenon is known as the C-value paradox. One explanation for the C-value paradox attributes the size of the nuclear genome to 'junk' (typically non-coding) genetic elements that accumulate until the costs to the organism of replicating excess DNA select against it. Across species, organisms that develop at a slower rate should tolerate more junk DNA. Alternatively, junk DNA may function as a nucleo-skeleton to maintain the volume of the nucleus at a size proportional to the volume of the cytoplasm in the cell. Across species, the DNA C-value is predicted to vary with the nuclear and cytoplasmic volumes of cells. Previous studies have not been able to distinguish between the skeletal-DNA and junk-DNA explanations for the C-value paradox. We report a study of DNA content in 24 salamander species which does. The size of the nuclear genome is correlated with developmental rate even after the effects of nuclear and cytoplasmic volume have been removed. However, genome size is not correlated with cytoplasmic volume after controlling for developmental rate. These results support the view that junk DNA accumulates in the nuclear genome until the costs of replicating it become too great, rather than that it functions as a nucleo-skeleton.
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Affiliation(s)
- M Pagel
- Harvard University, Cambridge, Massachusetts 02138
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Tiffoche C, Chesnel A, Jego P, Le Pennec JP. Isolation and characterization of a cDNA clone encoding a Pleurodeles lectin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 213:901-7. [PMID: 8504829 DOI: 10.1111/j.1432-1033.1993.tb17834.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A cDNA encoding a lectin secreted by the oviduct of Pleurodeles waltl has been isolated and sequenced. The cDNA was identified by comparing the N-terminal amino-acid sequence of the purified P. waltl lectin polypeptides with the amino-acid sequence deduced from the cDNA. The two chains of the mature protein can be encoded within a unique mRNA. Two mRNA were also found in the oviduct extracts. However, they probably result from differential polyadenylation events. The mRNA are strictly localized in the anterior part of the oviduct and increase after estradiol stimulation, two characteristics which have been previously demonstrated for the protein. P. waltl is known to possess a very high DNA content (approximately 2 x 10(10) bp) but the aforementioned results and Southern-blot experiments suggest a unique or at least a very low gene-copy number for this protein. The amino-acid sequence of the P. waltl lectin deduced from the cDNA sequence shows similarities with the C-type carbohydrate-recognition domains of animal lectins as defined by Drickamer [Drickamer, K. (1988) J. Biol. Chem. 263, 9557-9560]. Although it is regulated by estradiol, the P. waltl lectin amino-acid sequence shows a higher similarity with animal lectins involved in the defence of the organism than with those involved in reproduction and development.
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Affiliation(s)
- C Tiffoche
- Laboratoire de Génétique Moléculaire, URA Centre National de la Recherche Scientifique 256, Université de Rennes I, France
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Walker LI, Spotorno AE, Sans J. Genome size variation and its phenotypic consequences in Phyllotis rodents. Hereditas 1991; 115:99-107. [PMID: 1810909 DOI: 10.1111/j.1601-5223.1991.tb03542.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Constitutive heterochromatin and genome size were studied in Phyllotis darwini, three Phyllotis xanthopygus subspecies, and their interspecific laboratory hybrids. P. darwini, with no or only small C-bands, had the smallest genome size; P. xanthopygus rupestris and P. x. vaccarum, with large C-bands in all the chromosomes, had the largest; and P. x. xanthopygus, with heterochromatin only in a few chromosomes, showed intermediate genome size. To examine some phenotypic consequences of nuclear DNA content, we measured nuclear and cellular surfaces and volumes. Linear regression analyses showed that all these cellular characters had a highly significant direct relationship with genome size. Hybrids had always the expected intermediate parental characteristics. Previous results indicate that P. x. vaccarum should have longer mitotic cycles and lower reproductive capacity than P. darwini. Our findings suggest that the "nucleotypic DNA" hypothesis, which considers genome size as an adaptive feature in higher plants and lower vertebrates, could be extended to these mammals. The analysis of heterochromatin and nuclear DNA amounts of other phyllotine and akodontine rodents supports the idea that small C-bands and genomes are ancestral conditions, from which independent and parallel events occurred until large genomes were produced.
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Affiliation(s)
- L I Walker
- Departamento de Biología Celular y Genética, Facultad de Medicina, Universidad de Chile, Santiago
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Morris SC, Harper E. Genome Size in Conodonts (Chordata): Inferred Variations During 270 Million Years. Science 1988; 241:1230-2. [PMID: 17740786 DOI: 10.1126/science.241.4870.1230] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
DNA is too unstable to be preserved during fossilization, but it still seems possible to infer the genome content of fossils because in every group of organisms investigated cell size is proportional to quantity of DNA. Accordingly, information on macroevolutionary trends in genome size through millions of years is potentially available. This survey of inferred variation in genome content in fossils is based on measurements of epithelial cells in extinct conodonts over a period of 270 million years. Why genome size varies so widely amongst living organisms is a subject of continuing debate. Paleontology offers a distinct temporal perspective, but lack of data on conodont paleoecology make the proposed adaptive explanations for genome variation difficult to test.
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Cabric M, Appell HJ, Resic A. Fine structural changes in electrostimulated human skeletal muscle. Evidence for predominant effects on fast muscle fibres. EUROPEAN JOURNAL OF APPLIED PHYSIOLOGY AND OCCUPATIONAL PHYSIOLOGY 1988; 57:1-5. [PMID: 3342785 DOI: 10.1007/bf00691229] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Physical education students were subjected to electrical stimulation of relatively high frequency and current amplitude for 19 days. A quantitative study of several morphological parameters was performed on biopsy samples from gastrocnemius, using stereological methods at both light and electron microscopic levels. The main results were: muscle fibre size was increased; nuclear volume was also increased, suggesting that a proliferation of nuclei had occurred; this was paralleled by an increased content of nuclear DNA. The size of single myonuclei was increased, and their heterochromatin fraction was decreased, these changes being most pronounced in type II fibres. The increase in the mitochondrial fraction was also greatest in type II fibres. It is concluded that this type of electrical stimulation has predominant effects on type II fibres.
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Affiliation(s)
- M Cabric
- Department of Physiological Kinesiology, University of Split, Yugoslavia
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Tank PW, Charlton RK, Burns ER. Flow cytometric analysis of ploidy in the axolotl,Ambystoma mexicanum. ACTA ACUST UNITED AC 1987. [DOI: 10.1002/jez.1402430309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Cells with polyploid nuclei are generally larger than cells of the same organism or species with nonpolyploid nuclei. However, no such change of cell size with ploidy level is observed in those red algae which alternate isomorphic haploid with diploid generations. The results of this investigation reveal the explanation. Nuclear DNA content and other parameters were measured in cells of the filamentous red alga Griffithsia pacifica. Nuclei of the diploid generation contain twice the DNA content of those of the haploid generation. However, all cells except newly formed reproductive cells are multinucleate. The nuclei are arranged in a nearly perfect hexagonal array just beneath the cell surface. When homologous cells of the two generations are compared, although the cell size is nearly identical, each nucleus of the diploid cell is surrounded by a region of cytoplasm (a "domain") nearly twice that surrounding a haploid nucleus. Cytoplasmic domains associated with a diploid nucleus contain twice the number of plastids, and consequently twice the amount of plastid DNA, than is associated with the domain of a haploid nucleus. Thus, doubling of ploidy is reflected in doubling of the size and organelle content of the domain associated with each nucleus. However, cell size does not differ between homologous cells of the two generations, because total nuclear DNA (sum of the DNA in all nuclei in a cell) per cell does not differ. This is the solution to the cytological paradox of isomorphy.
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Hally MK, Rasch EM, Mainwaring HR, Bruce RC. Cytophotometric evidence of variation in genome size of desmognathine salamanders. HISTOCHEMISTRY 1986; 85:185-92. [PMID: 3744902 DOI: 10.1007/bf00494802] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The amount of DNA per haploid genome, the C-value, is often directly correlated with nuclear and cell volume, but inversely correlated with cell replication rate. Also, rates of cellular growth sometimes appear to be correlated with organismal developmental rates and life history patterns. Among vertebrates, salamanders exhibit the greatest variation in genome size. In the present study we have examined interspecific and intraspecific variation in blood cell DNA levels in the genus Desmognathus, which shows greater variation in life history traits than any other salamander genus. Specimens of Desmognathus quadramaculatus, D. monticola, D. ochrophaeus and D. wrighti were collected from nature at two localities in the southern Appalachian Mountains. Estimates of genome size in pg of DNA were obtained from blood smears by DNA-Feulgen cytophotometry, using erythrocyte nuclei of Xenopus laevis as an internal reference standard of 6.35 pg DNA per cell. C-values of Desmognathus are the smallest in the order Caudata. Although significant variation in DNA levels was found among the four species, the differences were small, and do not support previously proposed relationships between C-value and life-history variation.
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Kamel S, Marsden JE, Pough FH. Diploid and tetraploid grey treefrogs (Hyla chrysoscelis and Hyla versicolor) have similar metabolic rates. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. A, COMPARATIVE PHYSIOLOGY 1985; 82:217-20. [PMID: 2864204 DOI: 10.1016/0300-9629(85)90729-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We measured oxygen consumption of the diploid frog Hyla chrysoscelis and its recently evolved tetraploid cryptic species Hyla versicolor at rest and during forced locomotory exercise. We also measured whole-body lactic acid concentrations of individuals of the two species at rest and following 4 min of exercise. Contrary to predictions based on tissue-culture experiments, rates of organismal metabolism are not different in this diploid/tetraploid species pair: the diploid and tetraploid species did not differ in rates of oxygen consumption at rest or during exercise. Furthermore, whole-body lactate concentrations of frogs at rest and following forced locomotion were the same in the diploid and tetraploid species. For these species, polyploidy does not appear to be associated with lower maintenance costs at the level of the organism. However, polyploidy also does not appear to have metabolic consequences that would limit the behavioral or ecological repertoire of an anuran.
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Sherwood SW, Patton JL. Genome evolution in pocket gophers (genus Thomomys). II. Variation in cellular DNA content. Chromosoma 1982; 85:163-79. [PMID: 7117027 DOI: 10.1007/bf00294963] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cellular DNA content (2 C-value) was measured by fluorescence flow cytometry of chromomycin-A3 stained spleen cells in 2 subgenera, 5 species, and 21 subspecies of pocket gophers (genus Thomomys). The data indicate that, in Thomomys: (1) interspecific variation is extensive but, while some congeneric species differ by as much as 230%, others are identical in C-value: (2) intraspecific differentiation can be extensive with C-values differing by as much as 35%; and (3) populations of the same subspecies with apparently similar karyotypes can differ significantly in C-value. The implications of these results for hypotheses of the "adaptive" significance of C-value variation and genome evolution are discussed.
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Morescalchi A. New developments in vertebrate cytotaxonomy I. cytotaxonomy of the amphibians. Genetica 1979. [DOI: 10.1007/bf00122043] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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John B, Miklos GL. Functional aspects of satellite DNA and heterochromatin. INTERNATIONAL REVIEW OF CYTOLOGY 1979; 58:1-114. [PMID: 391760 DOI: 10.1016/s0074-7696(08)61473-4] [Citation(s) in RCA: 300] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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Olmo E, Morescalchi A. Genome and cell sizes in frogs: A comparison with salamanders. ACTA ACUST UNITED AC 1978. [DOI: 10.1007/bf01921891] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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