1
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Walter NG. Are non-protein coding RNAs junk or treasure?: An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non-functional or functional RNAs. Bioessays 2024; 46:e2300201. [PMID: 38351661 DOI: 10.1002/bies.202300201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 03/28/2024]
Abstract
The human genome project's lasting legacies are the emerging insights into human physiology and disease, and the ascendance of biology as the dominant science of the 21st century. Sequencing revealed that >90% of the human genome is not coding for proteins, as originally thought, but rather is overwhelmingly transcribed into non-protein coding, or non-coding, RNAs (ncRNAs). This discovery initially led to the hypothesis that most genomic DNA is "junk", a term still championed by some geneticists and evolutionary biologists. In contrast, molecular biologists and biochemists studying the vast number of transcripts produced from most of this genome "junk" often surmise that these ncRNAs have biological significance. What gives? This essay contrasts the two opposing, extant viewpoints, aiming to explain their bases, which arise from distinct reference frames of the underlying scientific disciplines. Finally, it aims to reconcile these divergent mindsets in hopes of stimulating synergy between scientific fields.
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Affiliation(s)
- Nils G Walter
- Center for RNA Biomedicine, Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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2
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Jiménez AG, Nash-Braun E, Meyers JR. White epaxial muscle aerobic and anaerobic potential and muscle fiber structure in surface and cave morphotypes of the Mexican cavefish (Astyanax mexicanus). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:861-868. [PMID: 37493010 DOI: 10.1002/jez.2736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
Proper muscle function and muscle fiber structures that match the environmental demands of organisms are imperative to their success in any ecosystem. The Mexican cavefish, Astyanax mexicanus, has two morphotypes: an obligate cave-dwelling form that lives in thermally insulated caves and an O2 poor environment, and a surface form that lives in a more thermally variable, but O2 rich river environment. As environment can determine physiological adaptations, it is of interest to compare the aerobic and anaerobic metabolic profiles of white muscle metabolism in both morphotypes of this species, as well as their muscle structures. Here, we used white muscle of both morphotypes of the Mexican cavefish to determine citrate synthase (CS) activity as a measure of aerobic potential, and lactate concentration as a measure of anaerobic potential at three different chronic acclimation temperatures (14°C, 25°C, and 31°C). By examining aerobic and anaerobic potential in both morphs, we sought to link environmental thermal flexibility to muscle metabolism. We found that the surface morphotype had higher CS activity and lower lactate concentration, suggesting an overall more efficient usage of aerobic metabolism; whereas the cave morphotype showed lower CS activity and higher lactate concentration, suggesting a stronger reliance on anaerobic pathways. We also measured white muscle histological variables that have been previously linked to whole-animal metabolism: fiber diameter, number of nuclei per mm of fiber and myonuclear domain (MND) of both morphotypes at 25°C to examine cell-level differences in muscle morphology. However, we found no differences in fiber diameter, number of nuclei per mm of fiber or MND between the two morphotypes. Thus, although the cellular morphology is similar in these species, the environmental differences in the evolution of the two morphs has led to differences in their metabolic profiles.
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Affiliation(s)
| | - Evan Nash-Braun
- Department of Biology, Colgate University, Hamilton, New York, USA
| | - Jason R Meyers
- Department of Biology, Colgate University, Hamilton, New York, USA
- Neuroscience Program, Colgate University, Hamilton, New York, USA
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3
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Zhang M, Qiu X. Genetic basis of genome size variation of wheat. Funct Integr Genomics 2023; 23:285. [PMID: 37648783 DOI: 10.1007/s10142-023-01194-x] [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: 06/15/2023] [Revised: 07/22/2023] [Accepted: 07/29/2023] [Indexed: 09/01/2023]
Abstract
Research on various species has revealed a connection between genome size variation and the physiological and ecological characteristics of the species, suggesting that it could be a crucial factor influencing a species' adaptability to different environments. Wheat, being one of the world's three primary grains, holds significance in this regard. Investigating the genome size of wheat and analyzing the genetic factors contributing to its variation could offer valuable insights for enhancing wheat agronomic traits. This project has developed a conservative site ratio calculation approach to determine the size of the wheat genome. Additionally, it employs flow cytometry and k-mer distribution analysis to validate this method. Furthermore, the researchers use re-sequencing data to investigate the impact of environmental selection pressure and transposon dynamics on the variation in the size of the wheat genome. The findings from this study demonstrate a strong relationship between the size of the wheat genome and several environmental factors. These results serve as a valuable reference for understanding the development of variation in the size of the hetero-hexaploid wheat genome. Moreover, they contribute to advancing fundamental research on the genetic mechanisms underlying wheat characteristics. Additionally, the study paves the way for exploring new research directions in wheat breeding, which holds promise for future advancements in this field.
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Affiliation(s)
- Ming Zhang
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuebing Qiu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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4
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Medeiros APM, Santos BA, Betancur-R R. Does genome size increase with water depth in marine fishes? Evolution 2022; 76:1578-1589. [PMID: 35585426 DOI: 10.1111/evo.14510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 01/22/2023]
Abstract
A growing body of research suggests that genome size in animals can be affected by ecological factors. Half a century ago, Ebeling et al. proposed that genome size increases with depth in some teleost fish groups and discussed a number of biological mechanisms that may explain this pattern (e.g., passive accumulation, adaptive acclimation). Using phylogenetic comparative approaches, we revisit this hypothesis based on genome size and ecological data from up to 708 marine fish species in combination with a set of large-scale phylogenies, including a newly inferred tree. We also conduct modeling approaches of trait evolution and implement a variety of regression analyses to assess the relationship between genome size and depth. Our reanalysis of Ebeling et al.'s dataset shows a weak association between these variables, but the overall pattern in their data is driven by a single clade. Although new analyses based on our "all-species" dataset resulted in positive correlations, providing some evidence that genome size evolves as a function of depth, only one subclade consistently yielded statistically significant correlations. By contrast, negative correlations are rare and nonsignificant. All in all, we find modest evidence for an increase in genome size along the depth axis in marine fishes. We discuss some mechanistic explanations for the observed trends.
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Affiliation(s)
- Aline P M Medeiros
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, 58051-900, Brazil.,Department of Biology, The University of Oklahoma, Norman, Oklahoma, 73019
| | - Bráulio A Santos
- Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, 58051-900, Brazil
| | - Ricardo Betancur-R
- Department of Biology, The University of Oklahoma, Norman, Oklahoma, 73019
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5
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Kornaliková M, Hampl V, Treitli SC. Investigation of the Genome Sizes and Ploidy Within the Genus
Monocercomonoides. J Eukaryot Microbiol 2022; 69:e12925. [DOI: 10.1111/jeu.12925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martina Kornaliková
- Department of Parasitology, Faculty of Science Charles University, BIOCEV Vestec Czech Republic
| | - Vladimir Hampl
- Department of Parasitology, Faculty of Science Charles University, BIOCEV Vestec Czech Republic
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6
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Maillard F, Elie N, Villain-Naud N, Lepoittevin M, Martinez AS, Lelong C. Male triploid oysters of Crassostrea gigas exhibit defects in mitosis and meiosis during early spermatogenesis. FEBS Open Bio 2021; 12:1438-1452. [PMID: 34935310 PMCID: PMC9340784 DOI: 10.1002/2211-5463.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 11/07/2022] Open
Abstract
The Pacific oyster, Crassostrea gigas is a successive irregular hermaphrodite mollusc which has an annual breeding cycle. Oysters are naturally diploid organisms, but triploid oysters have been developed for use in shellfish aquaculture, with the aim of obtaining sterile animals with commercial value. However, studies have shown that some triploid oysters are partially able to undergo gametogenesis, with numerous proliferating cells closed to diploids (3n alpha) or a partial one with an accumulation of locked germ cells (3n beta). The aim of our study therefore was to understand the regulation of spermatogenesis in both groups of triploid oysters (alpha and beta) from the beginning of spermatogenesis, during mitosis and meiosis events. Our results demonstrate that the reduced spermatogenesis in triploids results from a deregulation of the development of the germinal lineage and the establishment of the gonadal tract led by a lower number of tubules. Morphological cellular investigation also revealed an abnormal condensation of germ cell nuclei and the presence of clear patches in the nucleoplasm of triploid cells, which were more pronounced in beta oysters. Furthermore, studies of molecular and cellular regulation showed a downregulation of mitotic spindle checkpoint in beta oysters, resulting in disturbance of chromosomal segregation, notably on Spindle Assembly Checkpoint involved in the binding of microtubules to chromosomes. Taken together, our results suggest that the lower reproductive ability of triploid oysters may be due to cellular and molecular events such as impairment of spermatogenesis and disruptions of mitosis and meiosis, occurring early and at various stages of the gametogenetic cycle.
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Affiliation(s)
- Floriane Maillard
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Nicolas Elie
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Microscopie Appliquée à la Biologie, SF4206 Interaction Cellule-Organisme-Environnement (ICORE), Université de Caen Normandie, Esplanade de la paix, 14032, Caen CEDEX, France
| | - Nadège Villain-Naud
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Mélanie Lepoittevin
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Anne-Sophie Martinez
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France
| | - Christophe Lelong
- Unité de Formation et de Recherches (UFR) des sciences, Université de Caen Normandie, 14032, Caen CEDEX, France.,Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE2030, Museum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231, Paris CEDEX, France.,Oestrogènes et Reproduction (OeReCa), EA2608, Université de Caen Normandie, Esplanade de la paix, 14032, Caen CEDEX, France
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7
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Adiguzel Y. Information-theoretic approach in allometric scaling relations of DNA and proteins. Chem Biol Drug Des 2021; 99:331-343. [PMID: 34855304 DOI: 10.1111/cbdd.13988] [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: 05/18/2021] [Revised: 10/06/2021] [Accepted: 11/14/2021] [Indexed: 11/28/2022]
Abstract
Allometric scaling relations can be observed in between molecular parameters. Hence, we looked for presence of such relation among sizes (i.e., lengths) of proteins and genes. Protein lengths exist in the literature as the number of amino acids. They can also be derived from the mRNA lengths. Here, we looked for allometric scaling relation by using such data and simultaneously, the data was compared with the sizes of genes and proteins that were obtained from our modified information-theoretic approach. Results implied presence of scaling relation in the calculated results. This was expected due to the implemented modification in the information-theoretic calculation. Relation in the literature-based data was lacking high goodness of fit value. It could be due to physical factors and selective pressures, which ended up in deviations of the literature-sourced values from those in the model. Genome size is correlated with cell size. Intracellular volume, which is related to the DNA size, would require certain number of proteins, the sizes of which can therefore be correlated with the protein sizes. Cell sizes, genome sizes, and average protein and gene sizes, along with the number of proteins, namely the expression levels of the genes, are the physical factors, and the molecular factors influence those physical factors. The selective pressures on those can act through the connection between those physical factors and limit the dynamic ranges. Biological measures could be prone to such forces and are likely to deviate from expected models, regardless of the validity of assumptions, unless those are also implemented in the models. Yet, present discrepancies could be pointing at the need for model improvement, data imperfection, invalid assumptions, etc. Still, current work highlights possible use of information-theoretic approach in allometric scaling relations' studies.
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Affiliation(s)
- Yekbun Adiguzel
- Department of Medical Biology, School of Medicine, Atilim University, Ankara, Turkey
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8
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Hultgren KM, Chak STC, Bjelajac J, Macdonald KS. Correlated evolution of larval development, egg size and genome size across two genera of snapping shrimp. J Evol Biol 2021; 34:1827-1839. [PMID: 34626036 DOI: 10.1111/jeb.13945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 01/21/2023]
Abstract
Across plants and animals, genome size is often correlated with life-history traits: large genomes are correlated with larger seeds, slower development, larger body size and slower cell division. Among decapod crustaceans, caridean shrimps are among the most variable both in terms of genome size variation and life-history characteristics such as larval development mode and egg size, but the extent to which these traits are associated in a phylogenetic context is largely unknown. In this study, we examine correlations among egg size, larval development and genome size in two different genera of snapping shrimp, Alpheus and Synalpheus, using phylogenetically informed analyses. In both Alpheus and Synalpheus, egg size is strongly linked to larval development mode: species with abbreviated development had significantly larger eggs than species with extended larval development. We produced the first comprehensive dataset of genome size in Alpheus (n = 37 species) and demonstrated that genome size was strongly and positively correlated with egg size in both Alpheus and Synalpheus. Correlated trait evolution analyses showed that in Alpheus, changes in genome size were clearly dependent on egg size. In Synalpheus, evolutionary path analyses suggest that changes in development mode (from extended to abbreviated) drove increases in egg volume; larger eggs, in turn, resulted in larger genomes. These data suggest that variation in reproductive traits may underpin the high degree of variation in genome size seen in a wide variety of caridean shrimp groups more generally.
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Affiliation(s)
| | - Solomon T C Chak
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA.,Biological Sciences Department, SUNY College at Old Westbury, Old Westbury, New York, USA
| | - Jeremy Bjelajac
- Department of Biology, Seattle University, Seattle, Washington, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
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9
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Paule J, von Döhren J, Sagorny C, Nilsson MA. Genome Size Dynamics in Marine Ribbon Worms (Nemertea, Spiralia). Genes (Basel) 2021; 12:1347. [PMID: 34573329 PMCID: PMC8468679 DOI: 10.3390/genes12091347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/28/2022] Open
Abstract
Nemertea is a phylum consisting of 1300 mostly marine species. Nemertea is distinguished by an eversible muscular proboscis, and most of the species are venomous. Genomic resources for this phylum are scarce despite their value in understanding biodiversity. Here, we present genome size estimates of Nemertea based on flow cytometry and their relationship to different morphological and developmental traits. Ancestral genome size estimations were done across the nemertean phylogeny. The results increase the available genome size estimates for Nemertea three-fold. Our analyses show that Nemertea has a narrow genome size range (0.43-3.89 pg) compared to other phyla in Lophotrochozoa. A relationship between genome size and evolutionary rate, developmental modes, and habitat was found. Trait analyses show that the highest evolutionary rate of genome size is found in upper intertidal, viviparous species with direct development. Despite previous findings, body size in nemerteans was not correlated with genome size. A relatively small genome (1.18 pg) is assumed for the most recent common ancestor of all extant nemerteans. The results provide an important basis for future studies in nemertean genomics, which will be instrumental to understanding the evolution of this enigmatic and often neglected phylum.
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Affiliation(s)
- Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany;
| | - Jörn von Döhren
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, D-53121 Bonn, Germany; (J.v.D.); (C.S.)
| | - Christina Sagorny
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, D-53121 Bonn, Germany; (J.v.D.); (C.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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10
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Malerba ME, Marshall DJ. Larger cells have relatively smaller nuclei across the Tree of Life. Evol Lett 2021; 5:306-314. [PMID: 34367657 PMCID: PMC8327945 DOI: 10.1002/evl3.243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/13/2021] [Accepted: 06/07/2021] [Indexed: 01/13/2023] Open
Abstract
Larger cells have larger nuclei, but the precise relationship between cell size and nucleus size remains unclear, and the evolutionary forces that shape this relationship are debated. We compiled data for almost 900 species - from yeast to mammals - at three scales of biological organisation: among-species, within-species, and among-lineages of a species that was artificially selected for cell size. At all scales, we showed that the ratio of nucleus size to cell size (the 'N: C' ratio) decreased systematically in larger cells. Size evolution appears more constrained in nuclei than cells: cell size spans across six orders of magnitude, whereas nucleus size varies by only three. The next important challenge is to determine the drivers of this apparently ubiquitous relationship in N:C ratios across such a diverse array of organisms.
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Affiliation(s)
- Martino E. Malerba
- Centre of Geometric Biology, School of Biological SciencesMonash UniversityMelbourneAustralia
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityVictoriaAustralia
| | - Dustin J. Marshall
- Centre of Geometric Biology, School of Biological SciencesMonash UniversityMelbourneAustralia
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11
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Wang X, Morton JA, Pellicer J, Leitch IJ, Leitch AR. Genome downsizing after polyploidy: mechanisms, rates and selection pressures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1003-1015. [PMID: 34077584 DOI: 10.1111/tpj.15363] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 05/20/2023]
Abstract
An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO2 uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.
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Affiliation(s)
- Xiaotong Wang
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Joseph A Morton
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia sn, Barcelona, 08038, Spain
| | | | - Andrew R Leitch
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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12
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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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13
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Wang Q, Ren X, Liu P, Li J, Lv J, Wang J, Zhang H, Wei W, Zhou Y, He Y, Li J. Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication. Mol Ecol Resour 2021; 22:334-344. [PMID: 34240531 DOI: 10.1111/1755-0998.13463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022]
Abstract
A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1.47 Gb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.
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Affiliation(s)
- Qiong Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xianyun Ren
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jitao Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jianjian Lv
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiajia Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Haien Zhang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Wei Wei
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yuxin Zhou
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yuying He
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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14
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Jernfors T, Danforth J, Kesäniemi J, Lavrinienko A, Tukalenko E, Fajkus J, Dvořáčková M, Mappes T, Watts PC. Expansion of rDNA and pericentromere satellite repeats in the genomes of bank voles Myodes glareolus exposed to environmental radionuclides. Ecol Evol 2021; 11:8754-8767. [PMID: 34257925 PMCID: PMC8258220 DOI: 10.1002/ece3.7684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
Altered copy number of certain highly repetitive regions of the genome, such as satellite DNA within heterochromatin and ribosomal RNA loci (rDNA), is hypothesized to help safeguard the genome against damage derived from external stressors. We quantified copy number of the 18S rDNA and a pericentromeric satellite DNA (Msat-160) in bank voles (Myodes glareolus) inhabiting the Chernobyl Exclusion Zone (CEZ), an area that is contaminated by radionuclides and where organisms are exposed to elevated levels of ionizing radiation. We found a significant increase in 18S rDNA and Msat-160 content in the genomes of bank voles from contaminated locations within the CEZ compared with animals from uncontaminated locations. Moreover, 18S rDNA and Msat-160 copy number were positively correlated in the genomes of bank voles from uncontaminated, but not in the genomes of animals inhabiting contaminated, areas. These results show the capacity for local-scale geographic variation in genome architecture and are consistent with the genomic safeguard hypothesis. Disruption of cellular processes related to genomic stability appears to be a hallmark effect in bank voles inhabiting areas contaminated by radionuclides.
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Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - John Danforth
- Department of Biochemistry & Molecular BiologyRobson DNA Science CentreArnie Charbonneau Cancer InstituteCumming School of MedicineUniversity of CalgaryCalgaryCanada
| | - Jenni Kesäniemi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anton Lavrinienko
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Eugene Tukalenko
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- National Research Center for Radiation Medicine of the National Academy of Medical ScienceKyivUkraine
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and ProteomicsCentral European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
- Laboratory of Functional Genomics and ProteomicsNCBRFaculty of ScienceMasaryk UniversityBrnoCzech Republic
- Department of Cell Biology and RadiobiologyInstitute of Biophysics of the Czech Academy of SciencesBrnoCzech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and ProteomicsCentral European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Tapio Mappes
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Phillip C. Watts
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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15
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Jurado-Escobar R, Doña I, Perkins JR, Laguna JJ, Muñoz-Cano R, García-Sánchez A, Ayuso P, Torres MJ, Mayorga C, Cornejo-García JA. Polymorphisms in eicosanoid-related biosynthesis enzymes associated with acute urticaria/angioedema induced by nonsteroidal anti-inflammatory drug hypersensitivity. Br J Dermatol 2021; 185:815-824. [PMID: 33955560 DOI: 10.1111/bjd.20440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND Nonsteroidal anti-inflammatory drugs (NSAIDs) are the main triggers of drug hypersensitivity, with NSAID-induced acute urticaria/angioedema (NIUA) the most frequent phenotype. NSAID hypersensitivity is caused by cyclooxygenase 1 inhibition, which leads to an imbalance in prostaglandin (PG) and cysteinyl leukotriene (CysLT) synthesis. As only susceptible individuals develop NSAID hypersensitivity, genetic factors are believed to be involved; however, no study has assessed the overall genetic variability of key enzymes in PG and CysLT synthesis in NSAID hypersensitivity. OBJECTIVES To evaluate simultaneously variants in the main genes involved in PG and CysLT biosynthesis in NIUA. METHODS Two independent cohorts of patients were recruited in Spain, alongside NSAID-tolerant controls. The discovery cohort included only patients with NIUA; the replication cohort included patients with NSAID-exacerbated respiratory disease (NERD). A set of tagging single-nucleotide polymorphisms (tagSNPs) in PTGS1, PTGS2, ALOX5 and LTC4S was genotyped using mass spectrometry coupled with endpoint polymerase chain reaction. RESULTS The study included 1272 individuals. Thirty-five tagSNPs were successfully genotyped in the discovery cohort, with three being significantly associated after Bonferroni correction (rs10306194 and rs1330344 in PTGS1; rs28395868 in ALOX5). These polymorphisms were genotyped in the replication cohort: rs10306194 and rs28395868 remained associated with NIUA, and rs28395868 was marginally associated with NERD. Odds ratios (ORs) in the combined analysis (discovery and replication NIUA populations) were 1·7 for rs10306194 [95% confidence interval (CI) 1·34-2·14; Pcorrected = 2·83 × 10-4 ) and 2·19 for rs28395868 (95% CI 1·43-3·36; Pcorrected = 0·002). CONCLUSIONS Variants of PTGS1 and ALOX5 may play a role in NIUA and NERD, supporting the proposed mechanisms of NSAID-hypersensitivity and shedding light on their genetic basis.
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Affiliation(s)
- R Jurado-Escobar
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Departments of, Department of, Medicine, University of Malaga, Malaga, Spain
| | - I Doña
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario de Málaga, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain
| | - J R Perkins
- Department of, Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain.,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.,The Biomedical Research Institute of Malaga (IBIMA), Malaga, Spain
| | - J J Laguna
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Unidad de Alergia, Hospital Central de la Cruz Roja, Madrid, Spain
| | - R Muñoz-Cano
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Allergy Section, Pneumology Department, Hospital Clinic, Universitat de Barcelona, ARADyAL, Barcelona, Spain
| | - A García-Sánchez
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Biochemistry, Pharmacogenetics Unit, University Hospital of Salamanca, Salamanca, Spain
| | - P Ayuso
- ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Department of Pharmacology, University of Extremadura, Caceres, Spain
| | - M J Torres
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Departments of, Department of, Medicine, University of Malaga, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario de Málaga, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Malaga, Spain
| | - C Mayorga
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,Allergy Unit, Hospital Regional Universitario de Málaga, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain.,Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Malaga, Spain
| | - J A Cornejo-García
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, ARADyAL, Malaga, Spain.,ARADyAL Network, Instituto de Salud Carlos III, Madrid, Spain
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16
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Rees TAV, Raven JA. The maximum growth rate hypothesis is correct for eukaryotic photosynthetic organisms, but not cyanobacteria. THE NEW PHYTOLOGIST 2021; 230:601-611. [PMID: 33449358 PMCID: PMC8048539 DOI: 10.1111/nph.17190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/23/2020] [Indexed: 05/12/2023]
Abstract
The (maximum) growth rate (µmax ) hypothesis predicts that cellular and tissue phosphorus (P) concentrations should increase with increasing growth rate, and RNA should also increase as most of the P is required to make ribosomes. Using published data, we show that though there is a strong positive relationship between the µmax of all photosynthetic organisms and their P content (% dry weight), leading to a relatively constant P productivity, the relationship with RNA content is more complex. In eukaryotes there is a strong positive relationship between µmax and RNA content expressed as % dry weight, and RNA constitutes a relatively constant 25% of total P. In prokaryotes the rRNA operon copy number is the important determinant of the amount of RNA present in the cell. The amount of phospholipid expressed as % dry weight increases with increasing µmax in microalgae. The relative proportions of each of the five major P-containing constituents is remarkably constant, except that the proportion of RNA is greater and phospholipids smaller in prokaryotic than eukaryotic photosynthetic organisms. The effect of temperature differences between studies was minor. The evidence for and against P-containing constituents other than RNA being involved with ribosome synthesis and functioning is discussed.
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Affiliation(s)
- T. A. V. Rees
- Leigh Marine LaboratoryInstitute of Marine ScienceUniversity of AucklandAuckland1142New Zealand
| | - John A. Raven
- Division of Plant ScienceUniversity of Dundee at the James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- Climate Change ClusterFaculty of ScienceUniversity of TechnologySydney, UltimoNSW2007Australia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWA6009Australia
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17
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Verberk WC, Atkinson D, Hoefnagel KN, Hirst AG, Horne CR, Siepel H. Shrinking body sizes in response to warming: explanations for the temperature-size rule with special emphasis on the role of oxygen. Biol Rev Camb Philos Soc 2021; 96:247-268. [PMID: 32959989 PMCID: PMC7821163 DOI: 10.1111/brv.12653] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 01/04/2023]
Abstract
Body size is central to ecology at levels ranging from organismal fecundity to the functioning of communities and ecosystems. Understanding temperature-induced variations in body size is therefore of fundamental and applied interest, yet thermal responses of body size remain poorly understood. Temperature-size (T-S) responses tend to be negative (e.g. smaller body size at maturity when reared under warmer conditions), which has been termed the temperature-size rule (TSR). Explanations emphasize either physiological mechanisms (e.g. limitation of oxygen or other resources and temperature-dependent resource allocation) or the adaptive value of either a large body size (e.g. to increase fecundity) or a short development time (e.g. in response to increased mortality in warm conditions). Oxygen limitation could act as a proximate factor, but we suggest it more likely constitutes a selective pressure to reduce body size in the warm: risks of oxygen limitation will be reduced as a consequence of evolution eliminating genotypes more prone to oxygen limitation. Thus, T-S responses can be explained by the 'Ghost of Oxygen-limitation Past', whereby the resulting (evolved) T-S responses safeguard sufficient oxygen provisioning under warmer conditions, reflecting the balance between oxygen supply and demands experienced by ancestors. T-S responses vary considerably across species, but some of this variation is predictable. Body-size reductions with warming are stronger in aquatic taxa than in terrestrial taxa. We discuss whether larger aquatic taxa may especially face greater risks of oxygen limitation as they grow, which may be manifested at the cellular level, the level of the gills and the whole-organism level. In contrast to aquatic species, terrestrial ectotherms may be less prone to oxygen limitation and prioritize early maturity over large size, likely because overwintering is more challenging, with concomitant stronger end-of season time constraints. Mechanisms related to time constraints and oxygen limitation are not mutually exclusive explanations for the TSR. Rather, these and other mechanisms may operate in tandem. But their relative importance may vary depending on the ecology and physiology of the species in question, explaining not only the general tendency of negative T-S responses but also variation in T-S responses among animals differing in mode of respiration (e.g. water breathers versus air breathers), genome size, voltinism and thermally associated behaviour (e.g. heliotherms).
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Affiliation(s)
- Wilco C.E.P. Verberk
- Department of Animal Ecology and Physiology, Institute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - David Atkinson
- Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolL69 7ZBU.K.
| | - K. Natan Hoefnagel
- Department of Animal Ecology and Physiology, Institute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
- Faculty of Science and Engineering, Ocean Ecosystems — Energy and Sustainability Research Institute GroningenUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Andrew G. Hirst
- School of Environmental SciencesUniversity of LiverpoolLiverpoolL69 3GPU.K.
- Centre for Ocean Life, DTU AquaTechnical University of DenmarkLyngbyDenmark
| | - Curtis R. Horne
- School of Environmental SciencesUniversity of LiverpoolLiverpoolL69 3GPU.K.
| | - Henk Siepel
- Department of Animal Ecology and Physiology, Institute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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18
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Kozłowski J, Konarzewski M, Czarnoleski M. Coevolution of body size and metabolic rate in vertebrates: a life-history perspective. Biol Rev Camb Philos Soc 2020; 95:1393-1417. [PMID: 32524739 PMCID: PMC7540708 DOI: 10.1111/brv.12615] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022]
Abstract
Despite many decades of research, the allometric scaling of metabolic rates (MRs) remains poorly understood. Here, we argue that scaling exponents of these allometries do not themselves mirror one universal law of nature but instead statistically approximate the non-linearity of the relationship between MR and body mass. This 'statistical' view must be replaced with the life-history perspective that 'allows' organisms to evolve myriad different life strategies with distinct physiological features. We posit that the hypoallometric allometry of MRs (mass scaling with an exponent smaller than 1) is an indirect outcome of the selective pressure of ecological mortality on allocation 'decisions' that divide resources among growth, reproduction, and the basic metabolic costs of repair and maintenance reflected in the standard or basal metabolic rate (SMR or BMR), which are customarily subjected to allometric analyses. Those 'decisions' form a wealth of life-history variation that can be defined based on the axis dictated by ecological mortality and the axis governed by the efficiency of energy use. We link this variation as well as hypoallometric scaling to the mechanistic determinants of MR, such as metabolically inert component proportions, internal organ relative size and activity, cell size and cell membrane composition, and muscle contributions to dramatic metabolic shifts between the resting and active states. The multitude of mechanisms determining MR leads us to conclude that the quest for a single-cause explanation of the mass scaling of MRs is futile. We argue that an explanation based on the theory of life-history evolution is the best way forward.
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Affiliation(s)
- Jan Kozłowski
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa7, 30‐387KrakówPoland
| | - Marek Konarzewski
- Institute of BiologyUniversity of BiałystokCiołkowskiego 1J, 15‐245, BiałystokPoland
| | - Marcin Czarnoleski
- Institute of Environmental SciencesJagiellonian UniversityGronostajowa7, 30‐387KrakówPoland
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19
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Moura MN, Cardoso DC, Lima Baldez BC, Cristiano MP. Intraspecific variation in the karyotype length and genome size of fungus-farming ants (genus Mycetophylax), with remarks on procedures for the estimation of genome size in the Formicidae by flow cytometry. PLoS One 2020; 15:e0237157. [PMID: 32760102 PMCID: PMC7410318 DOI: 10.1371/journal.pone.0237157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 11/19/2022] Open
Abstract
Ants (Formicidae) present considerable diversity in chromosome numbers, which vary from n = 1 to n = 60, although this variation is not proportional to that in genome size, for which estimates range from 0.18 pg to 0.77 pg. Intraspecific variation in the chromosome number and karyotype structure has been reported among species, although the variation among populations of the same species has received much less attention, and there are few data on genome size. Here, we studied the karyotype length and genome size of different populations of the fungus-farming ants Mycetophylax conformis (Mayr, 1884) and Mycetophylax morschi (Emery, 1888). We also provide remarks on procedure for the estimation of ant genome size by Flow Cytometry (FCM) analysis. Chromosome number and morphology did not vary among the populations of M. conformis or the cytotypes of M. morschi, but karyotype length and genome size were significantly distinct among the populations of these ants. Our results on the variation in karyotype length and genome size among M. morschi and M. conformis populations reveal considerable diversity that would be largely overlooked by more traditional descriptions of karyotypes, which were also supported by the estimates of genome size obtained using flow cytometry. Changes in the amount of DNA reflect variation in the fine structure of the chromosomes, which may represent the first steps of karyotype evolution and may occur previously to any changes in the chromosome number.
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Affiliation(s)
- Mariana Neves Moura
- Programa de Pós-graduação em Ecologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Danon Clemes Cardoso
- Departamento de Biodiversidade, Evolução e Meio Ambiente/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Brenda Carla Lima Baldez
- Programa de Pós-graduação em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
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20
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Hjelmen CE, Holmes VR, Burrus CG, Piron E, Mynes M, Garrett MA, Blackmon H, Johnston JS. Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA. Evolution 2020; 74:1423-1436. [PMID: 32438451 DOI: 10.1111/evo.14022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/05/2020] [Accepted: 05/17/2020] [Indexed: 12/11/2022]
Abstract
Many cells in the thorax of Drosophila were found to stall during replication, a phenomenon known as underreplication. Unlike underreplication in nuclei of salivary and follicle cells, this stall occurs with less than one complete round of replication. This stall point allows precise estimations of early-replicating euchromatin and late-replicating heterochromatin regions, providing a powerful tool to investigate the dynamics of structural change across the genome. We measure underreplication in 132 species across the Drosophila genus and leverage these data to propose a model for estimating the rate at which additional DNA is accumulated as heterochromatin and euchromatin and also predict the minimum genome size for Drosophila. According to comparative phylogenetic approaches, the rates of change of heterochromatin differ strikingly between Drosophila subgenera. Although these subgenera differ in karyotype, there were no differences by chromosome number, suggesting other structural changes may influence accumulation of heterochromatin. Measurements were taken for both sexes, allowing the visualization of genome size and heterochromatin changes for the hypothetical path of XY sex chromosome differentiation. Additionally, the model presented here estimates a minimum genome size in Sophophora remarkably close to the smallest insect genome measured to date, in a species over 200 million years diverged from Drosophila.
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Affiliation(s)
- Carl E Hjelmen
- Department of Biology, Texas A&M University, College Station, Texas.,Department of Entomology, Texas A&M University, College Station, Texas
| | | | - Crystal G Burrus
- Department of Biology, Texas A&M University, College Station, Texas
| | - Elizabeth Piron
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Melissa Mynes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Margaret A Garrett
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas
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21
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Davesne D, Schmitt AD, Fernandez V, Benson RBJ, Sanchez S. Three-dimensional characterization of osteocyte volumes at multiple scales, and its relationship with bone biology and genome evolution in ray-finned fishes. J Evol Biol 2020; 33:808-830. [PMID: 32144878 DOI: 10.1111/jeb.13612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022]
Abstract
Osteocytes, cells embedded within the bone mineral matrix, inform on key aspects of vertebrate biology. In particular, a relationship between volumes of the osteocytes and bone growth and/or genome size has been proposed for several tetrapod lineages. However, the variation in osteocyte volume across different scales is poorly characterized and mostly relies on incomplete, two-dimensional information. In this study, we characterize the variation of osteocyte volumes in ray-finned fishes (Actinopterygii), a clade including more than half of modern vertebrate species in which osteocyte biology is poorly known. We use X-ray synchrotron micro-computed tomography (SRµCT) to achieve a three-dimensional visualization of osteocyte lacunae and direct measurement of their size (volumes). Our specimen sample is designed to characterize variation in osteocyte lacuna morphology at three scales: within a bone, among the bones of one individual and among species. At the intra-bone scale, we find that osteocyte lacunae vary noticeably in size between zones of organized and woven bone (being up to six times larger in woven bone), and across cyclical bone deposition. This is probably explained by differences in bone deposition rate, with larger osteocyte lacunae contained in bone that deposits faster. Osteocyte lacuna volumes vary 3.5-fold among the bones of an individual, and this cannot readily be explained by variation in bone growth rate or other currently observable factors. Finally, we find that genome size provides the best explanation of variation in osteocyte lacuna volume among species: actinopterygian taxa with larger genomes (polyploid taxa in particular) have larger osteocyte lacunae (with a ninefold variation in median osteocyte volume being measured). Our findings corroborate previous two-dimensional studies in tetrapods that also observed similar patterns of intra-individual variation and found a correlation with genome size. This opens new perspectives for further studies on bone evolution, physiology and palaeogenomics in actinopterygians, and vertebrates as a whole.
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Affiliation(s)
- Donald Davesne
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Armin D Schmitt
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Vincent Fernandez
- European Synchrotron Radiation Facility, Grenoble, France.,Imaging and Analysis Centre, Natural History Museum, London, UK
| | | | - Sophie Sanchez
- European Synchrotron Radiation Facility, Grenoble, France.,Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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22
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Gibeaux R, Miller K, Acker R, Kwon T, Heald R. Xenopus Hybrids Provide Insight Into Cell and Organism Size Control. Front Physiol 2018; 9:1758. [PMID: 30564147 PMCID: PMC6288844 DOI: 10.3389/fphys.2018.01758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/20/2018] [Indexed: 01/08/2023] Open
Abstract
Determining how size is controlled is a fundamental question in biology that is poorly understood at the organismal, cellular, and subcellular levels. The Xenopus species, X. laevis and X. tropicalis differ in size at all three of these levels. Despite these differences, fertilization of X. laevis eggs with X. tropicalis sperm gives rise to viable hybrid animals that are intermediate in size. We observed that although hybrid and X. laevis embryogenesis initiates from the same sized zygote and proceeds synchronously through development, hybrid animals were smaller by the tailbud stage, and a change in the ratio of nuclear size to cell size was observed shortly after zygotic genome activation (ZGA), suggesting that differential gene expression contributes to size differences. Transcriptome analysis at the onset of ZGA identified twelve transcription factors paternally expressed in hybrids. A screen of these X. tropicalis factors by expression in X. laevis embryos revealed that Hes7 and Ventx2 significantly reduced X. laevis body length size by the tailbud stage, although nuclear to cell size scaling relationships were not affected as in the hybrid. Together, these results suggest that transcriptional regulation contributes to biological size control in Xenopus.
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Affiliation(s)
- Romain Gibeaux
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Kelly Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Rachael Acker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
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Arkorful M, Gazo K, Zweig A, Ott L, Mendelson T, deCarvalho T. Larger sperm size may contribute to reproductive isolation between Etheostoma species. JOURNAL OF YOUNG INVESTIGATORS 2018; 35:92-96. [PMID: 31097926 PMCID: PMC6516065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Etheostoma is a genus of North American darter fish whose species have similar habitats and breeding seasons, yet hybridization is rare. Behavioral barriers have been demonstrated to play a key role in maintaining species boundaries. Further, conspecific (same species) sperm precedence has also been observed when the gametes of two different species come into contact. In this study, we investigated if physical characteristics of sperm could be a mechanism for the lower fertilization success of heterospecific (different species) males when eggs are simultaneously exposed to conspecific and heterospecific sperm. We chose to examine the sperm of two closely related species, E. zonale and E. barrenense. Using toluidine blue and immunofluorescent labeling methods, we compared head diameter and tail length of sperm cells between the two species. We found that head diameter was significantly larger for E. barrenense sperm compared to E. zonale. This difference in cell morphology may point to a physical mechanism underlying conspecific sperm precedence in Etheostoma. Our results are the first to describe a morphological difference in sperm between species in this genus and provide initial evidence for the role of sperm morphology in prezygotic reproductive isolation.
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Affiliation(s)
- Mercy Arkorful
- Howard Community College, 10901 Little Patuxent Pkwy, Columbia, MD 21044
| | - Katrina Gazo
- Howard Community College, 10901 Little Patuxent Pkwy, Columbia, MD 21044
| | - Aaron Zweig
- Montgomery College, Mannakee St., Rockville, MD 20850
| | - Laura Ott
- College of Natural and Mathematical Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Tamra Mendelson
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Tagide deCarvalho
- College of Natural and Mathematical Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
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Guislain A, Beisner BE, Köhler J. Variation in species light acquisition traits under fluctuating light regimes: implications for non‐equilibrium coexistence. OIKOS 2018. [DOI: 10.1111/oik.05297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Alexis Guislain
- Dept of Ecosystem Research, Leibniz‐Inst. of Freshwater Ecology and Inland Fisheries Berlin Germany
- Dept of Ecology and Ecosystem Modeling, Univ. of Potsdam Potsdam Germany
| | - Beatrix E. Beisner
- Dept of Ecosystem Research, Leibniz‐Inst. of Freshwater Ecology and Inland Fisheries Berlin Germany
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), and Dept of Biological Sciences, Univ. of Québec at Montréal, Montréal Québec Canada
| | - Jan Köhler
- Dept of Ecosystem Research, Leibniz‐Inst. of Freshwater Ecology and Inland Fisheries Berlin Germany
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Bilinski P, Albert PS, Berg JJ, Birchler JA, Grote MN, Lorant A, Quezada J, Swarts K, Yang J, Ross-Ibarra J. Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. PLoS Genet 2018; 14:e1007162. [PMID: 29746459 DOI: 10.1371/journal.pgen.1007162.g001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/20/2017] [Indexed: 05/23/2023] Open
Abstract
While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.
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Affiliation(s)
- Paul Bilinski
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jeremy J Berg
- Center for Population Biology, University of California, Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Mark N Grote
- Department of Anthropology, University of California, Davis, Davis, California, United States of America
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Juvenal Quezada
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Kelly Swarts
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Jinliang Yang
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Center for Population Biology, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California, Davis, Davis, California, United States of America
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Brittingham HA, Koski MH, Ashman TL. Higher ploidy is associated with reduced range breadth in the Potentilleae tribe. AMERICAN JOURNAL OF BOTANY 2018; 105:700-710. [PMID: 29608209 DOI: 10.1002/ajb2.1046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Polyploids are predicted to have greater niche breadth and larger ranges than diploids because of higher ecological tolerances, self-compatibility, and increased genetic variation. However, empirical support for this prediction is mixed, and most studies compare diploids and polyploids, rather than accounting for quantitative variation in ploidy. We test the prediction that species of higher ploidy have greater range breadth and abiotic breadth than those of lower ploidy. METHODS We estimate range breadth (latitudinal range, altitudinal range, and range size) and abiotic breadth (range in temperature, precipitation, and ultraviolet-B irradiance) for 109 species in the Potentilleae tribe of Rosaceae. We assess the contribution of ploidy to variation in range breadth, while accounting for shared evolutionary history and time of species divergence using phylogenetic comparative methods. KEY RESULTS Ploidy varied widely among species from 2× to 12×. Phylogenetic relatedness explained little of the variation in ploidy, range breadth, and abiotic breadth. Transitions to higher ploidy were associated with reduced latitudinal and altitudinal ranges, smaller overall range size, and reduced abiotic breadth for temperature and UV-B. CONCLUSIONS In contrast to predictions, this study shows that transitions to higher ploidy are associated with reduced range size and abiotic breadth. It also highlights the importance of considering continuous variation in ploidy when evaluating ecological correlates with ploidy. We discuss how genome duplication may contribute to the observed negative relationship between ploidy and range breadth.
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Affiliation(s)
- Hayley A Brittingham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260
| | - Matthew H Koski
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260
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Musci RV, Hamilton KL, Miller BF. Targeting mitochondrial function and proteostasis to mitigate dynapenia. Eur J Appl Physiol 2018; 118:1-9. [PMID: 28986697 PMCID: PMC5756099 DOI: 10.1007/s00421-017-3730-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/30/2017] [Indexed: 12/25/2022]
Abstract
Traditionally, interventions to treat skeletal muscle aging have largely targeted sarcopenia-the age-related loss of skeletal muscle mass. Dynapenia refers to the age-related loss in skeletal muscle function due to factors outside of muscle mass, which helps to inform treatment strategies for aging skeletal muscle. There is evidence that mechanisms to maintain protein homeostasis and proteostasis, deteriorate with age. One key mechanism to maintain proteostasis is protein turnover, which is an energetically costly process. When there is a mismatch between cellular energy demands and energy provision, inelastic processes related to metabolism are maintained, but there is competition for the remaining energy between the elastic processes of somatic maintenance and growth. With aging, mitochondrial dysfunction reduces ATP generation capacity, constraining the instantaneous supply of energy, thus compromising growth and somatic maintenance processes. Further, with age the need for somatic maintenance increases because of the accumulation of protein damage. In this review, we highlight the significant role mitochondria have in maintaining skeletal muscle proteostasis through increased energy provision, protein turnover, and substrate flux. In addition, we provide evidence that improving mitochondrial function could promote a cellular environment that is conducive to somatic maintenance, and consequently for mitigating dynapenia. Finally, we highlight interventions, such as aerobic exercise, that could be used to improve mitochondrial function and improve outcomes related to dynapenia.
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Affiliation(s)
- Robert V Musci
- Translational Research on Aging and Chronic Disease Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, 80523-1582, USA
| | - Karyn L Hamilton
- Translational Research on Aging and Chronic Disease Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, 80523-1582, USA
| | - Benjamin F Miller
- Translational Research on Aging and Chronic Disease Laboratory, Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, 80523-1582, USA.
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Štubňová E, Hodálová I, Kučera J, Mártonfiová L, Svitok M, Slovák M. Karyological patterns in the European endemic genus Soldanella L.: Absolute genome size variation uncorrelated with cytotype chromosome numbers. AMERICAN JOURNAL OF BOTANY 2017; 104:1241-1253. [PMID: 28790087 DOI: 10.3732/ajb.1700153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Detailed knowledge about the karyological diversity of organisms undoubtedly represents one of the crucial steps toward a better understanding of their evolutionary trends and history. We investigated the cytotype and absolute genome size (AGS) patterns in the European mountain-dwelling genus Soldanella (Primulaceae) in light of its geographic distribution and ecological diversification. METHODS Our chromosome number survey was based on 34 newly determined and 125 previously published chromosome counts. AGS was estimated on the basis of propidium iodide (PI) flow cytometry (299 individuals, 110 populations). KEY RESULTS We confirmed the existence of two cytotypes with the same ploidy level, i.e., euploid 2n = 40 and dysploid 2n = 38. The overall infrageneric AGS variation ranged between 2.97 and 3.99 pg (25.6% variation). The 2n = 40 cytotype harbors a modest amount of continuous AGS variation. With regard to its distribution area and ecology, the cytotype is ubiquitous. By contrast, the 2n = 38 cytotype was detected only in six forest-dwelling taxa with AGS variation segregated into three discrete, geographically separated groups. The AGS variation of the 2n = 38 cytotype was strongly correlated with elevation and longitude. CONCLUSIONS Despite the apparent morphological and ecological variation, members of the genus Soldanella have not undergone any pronounced cytotype and AGS diversification during their evolutionary history. The lack of correlation between chromosome numbers and AGS indicates that the evolutionary mechanism behind the origin of the dysploid cytotype 2n = 38 was a chromosomal fusion.
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Affiliation(s)
- Eliška Štubňová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
| | - Iva Hodálová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
| | - Jaromír Kučera
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
| | - Lenka Mártonfiová
- Pavol Jozef Šafárik University, Botanical Garden, Mánesova 23, SK-04352 Košice, Slovak Republic
| | - Marek Svitok
- Technical University, Faculty of Ecology, T. G. Masaryka 2117/24, SK-96053 Zvolen, Slovak Republic
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84523 Bratislava, Slovak Republic
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van der Woude E, Smid HM. Effects of Isometric Brain-Body Size Scaling on the Complexity of Monoaminergic Neurons in a Minute Parasitic Wasp. BRAIN, BEHAVIOR AND EVOLUTION 2017; 89:185-194. [PMID: 28478445 DOI: 10.1159/000468974] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/07/2017] [Indexed: 01/24/2023]
Abstract
Trichogramma evanescens parasitic wasps show large phenotypic plasticity in brain and body size, resulting in a 5-fold difference in brain volume among genetically identical sister wasps. Brain volume scales linearly with body volume in these wasps. This isometric brain scaling forms an exception to Haller's rule, which states that small animals have relatively larger brains than large animals. The large plasticity in brain size may be facilitated by plasticity in neuron size, in the number of neurons, or both. Here, we investigated whether brain isometry requires plasticity in the number and size of monoaminergic neurons that express serotonin (5HT), octopamine (OA), and dopamine (DA). Genetically identical small and large T. evanescens appear to have the same number of 5HT-, OA-, and DA-like immunoreactive cell bodies in their brains, but these cell bodies differ in diameter. This indicates that brain isometry can be facilitated by plasticity in the size of monoaminergic neurons, rather than plasticity in numbers of monoaminergic neurons. Selection pressures on body miniaturization may have resulted in the evolution of miniaturized neural pathways that allow even the smallest wasps to find suitable hosts. Plasticity in the size of neural components may be among the mechanisms that underlie isometric brain scaling while maintaining cognitive abilities in the smallest individuals.
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Affiliation(s)
- Emma van der Woude
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
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30
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Chansler MT, Ferguson CJ, Fehlberg SD, Prather LA. The role of polyploidy in shaping morphological diversity in natural populations of Phlox amabilis. AMERICAN JOURNAL OF BOTANY 2016; 103:1546-1558. [PMID: 27589933 DOI: 10.3732/ajb.1600183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Studies of natural populations of polyploids increasingly highlight complex patterns of variation in ploidy and geographic distribution of cytotypes. As our understanding of the complexity of polyploidy grows, our understanding of the morphological correlates of polyploidy should expand as well. Here we examine in what ways, and to what degree, polyploidy affects the overall phenotype of a species across its distribution when there are three ploidies and geographic complexity in cytotype distribution. METHODS We measured 31 morphological traits from stems, leaves, and flowers from up to 25 individuals from 11 sites across the distribution of Phlox amabilis. Chromosome counts and flow cytometry confirmed and expanded upon earlier research documenting diploid, tetraploid, and hexaploid populations, and also identified a site with two ploidies. Univariate and multivariate statistics were used to characterize the morphological effects of polyploidy. KEY RESULTS We detected significant associations between morphology and ploidy in 11 traits spread across vegetative and reproductive structures. Generally, diploid individuals differed from polyploid individuals to a greater extent, and in different ways, than tetraploid and hexaploid plants differed from each other. Multivariate morphometrics demonstrated that the two primary axes of overall variation are driven by morphological traits associated with polyploidy, and individuals of different ploidies can be discriminated with 95% success. CONCLUSIONS Polyploidy plays a major role in shaping overall morphological diversity in natural populations of P. amabilis.
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Affiliation(s)
- Matthew T Chansler
- Herbarium and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
| | - Carolyn J Ferguson
- Herbarium and Division of Biology, Kansas State University, Manhattan, Kansas 66506 USA
| | - Shannon D Fehlberg
- Research, Conservation, and Collections, Desert Botanical Garden, 1201 North Galvin Parkway, Phoenix, Arizona 85008 USA
| | - L Alan Prather
- Herbarium and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Jensen L, Grant JR, Laughinghouse HD, Katz LA. Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa. Evolution 2016; 70:1322-33. [DOI: 10.1111/evo.12935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/04/2016] [Accepted: 04/19/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Lindy Jensen
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Current Address: Department of Molecular and Integrative Physiology; University of Michigan; Ann Arbor Michigan 48109
| | - Jessica R. Grant
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
| | | | - Laura A. Katz
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Program in Organismic and Evolutionary Biology; University of Massachusetts; Amherst Massachusetts 01003
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Carta A, Peruzzi L. Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality in Liliaceae. THE NEW PHYTOLOGIST 2016; 210:709-16. [PMID: 26595257 DOI: 10.1111/nph.13769] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/20/2015] [Indexed: 05/08/2023]
Abstract
The factors driving genome size evolution in Liliaceae were examined. In particular, we investigated whether species with larger genomes are confined to less stressful environments with a longer vegetative season. We tested our hypotheses by correlating the genome size with other plant traits and environmental variables. To determine the adaptive nature of the genome size, we also compared the performances of Brownian motion (BM) processes with those inferred by Ornstein-Uhlenbeck (OU) models of trait evolution. A positive correlation of genome size with plant size, mean temperature and habitat moisture and a negative correlation with altitude and precipitation seasonality were found. Models of trait evolution revealed a deviation from a drift process or BM. Instead, changes in genome size were significantly associated with precipitation regimes according to an OU process. Specifically, the evolutionary optima towards which the genome size evolves were higher for humid climates and lower for drier ones. Taken together, our results indicate that the genome size increase in Liliaceae is constrained by climate seasonality.
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Affiliation(s)
- Angelino Carta
- Unit of Botany, Department of Biology, Università of Pisa, via Derna 1, Pisa, 56126, Italy
| | - Lorenzo Peruzzi
- Unit of Botany, Department of Biology, Università of Pisa, via Derna 1, Pisa, 56126, Italy
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Henry TA, Bainard JD, Newmaster SG. Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing. Genome 2015; 57:555-66. [PMID: 25727714 DOI: 10.1139/gen-2014-0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.
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Affiliation(s)
- Thomas A Henry
- Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Suda J, Meyerson LA, Leitch IJ, Pyšek P. The hidden side of plant invasions: the role of genome size. THE NEW PHYTOLOGIST 2015; 205:994-1007. [PMID: 25323486 DOI: 10.1111/nph.13107] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/11/2014] [Indexed: 05/11/2023]
Abstract
The ecological role of genome size in plant biology, biogeography, and morphology has garnered increasing attention as the methods and technology associated with measuring cytological characteristics have become more reliable and accessible. However, how plant genome size influences plant invasions and at what stage in the invasion this influence occurs have been little explored. Several large-scale analyses of published data have yielded valuable interspecific comparisons, but experimental studies that manipulate environmental factors are needed, particularly below the species level, to fully understand the role that genome size plays in plant invasion. In this review, we summarize the available knowledge, discuss the integration of genome size data into invasion research, and suggest how it can be applied to detect and manage invasive species. We also explore how global climate change could exert selective pressures on plant populations with varying genome sizes, thereby increasing the distribution range and invasiveness of some populations while decreasing others. Finally, we outline avenues for future research, including considerations of large-scale studies of intraspecific variation in genome size of invasive populations, testing the interaction of genome size with other factors in macroecological analyses of invasions, as well as the role this trait may play in plant-enemy interactions.
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Affiliation(s)
- Jan Suda
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, CZ-128 01, Czech Republic
| | - Laura A Meyerson
- University of Rhode Island, 1 Greenhouse Road, Kingston, RI, 02881, USA
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Petr Pyšek
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, CZ-252 43, Czech Republic
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, Prague, CZ-128 44, Czech Republic
- Centre for Invasion Biology, Stellenbosch University, Matieland, 7602, South Africa
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Maciak S, Michalak P. Cell size and cancer: a new solution to Peto's paradox? Evol Appl 2015; 8:2-8. [PMID: 25667599 PMCID: PMC4310577 DOI: 10.1111/eva.12228] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/01/2014] [Indexed: 01/06/2023] Open
Abstract
Cancer, one of the leading health concerns for humans, is by no means a human-unique malady. Accumulating evidence shows that cancer kills domestic and wild animals at a similar rate to humans and can even pose a conservation threat to certain species. Assuming that each physiologically active and proliferating cell is at risk of malignant transformation, any evolutionary increase in the number of cells (and thus body mass) will lead to a higher cancer frequency, all else being equal. However, available data fail to support the prediction that bigger animals are affected by cancer more than smaller ones. The unexpected lack of correlation between body size (and life span) and cancer risk across taxa was dubbed Peto's paradox. In this perspective, several plausible explanations of Peto's paradox are presented, with the emphasis on a largely underappreciated relation of cell size to both metabolism and cell division rates across species, which we believe are key factors underlying the paradox. We conclude that larger organisms have bigger and slowly dividing cells with lower energy turnover, all significantly reducing the risk of cancer initiation. Solving Peto's paradox will enhance our understanding the evolution of cancer and may provide new implications for cancer prevention and treatment.
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Affiliation(s)
- Sebastian Maciak
- Virginia Bioinformatics Institute, Virginia TechBlacksburg, VA, USA
- Institute of Biology, University of BialystokBialystok, Poland
| | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia TechBlacksburg, VA, USA
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Pandit MK, White SM, Pocock MJO. The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis. THE NEW PHYTOLOGIST 2014; 203:697-703. [PMID: 24697788 DOI: 10.1111/nph.12799] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/05/2014] [Indexed: 05/28/2023]
Abstract
Understanding how species' traits relate to their status (e.g. invasiveness or rarity) is important because it can help to efficiently focus conservation and management effort and infer mechanisms affecting plant status. This is particularly important for invasiveness, in which proactive action is needed to restrict the establishment of potentially invasive plants. We tested the ability of genome size (DNA 1C-values) to explain invasiveness and compared it with cytogenetic traits (chromosome number and ploidy level). We considered 890 species from 62 genera, from across the angiosperm phylogeny and distributed from tropical to boreal latitudes. We show that invasiveness was negatively related to genome size and positively related to chromosome number (and ploidy level), yet there was a positive relationship between genome size and chromosome number; that is, our result was not caused by collinearity between the traits. Including both traits in explanatory models greatly increased the explanatory power of each. This demonstrates the potential unifying role that genome size, chromosome number and ploidy have as species' traits, despite the diverse impacts they have on plant physiology. It provides support for the continued cataloguing of cytogenetic traits and genome size of the world's flora.
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Affiliation(s)
- Maharaj K Pandit
- Department of Environmental Studies, Centre for Inter-disciplinary Studies of Mountain & Hill Environment, University of Delhi, Delhi, 110007, India
| | - Steven M White
- Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, Oxfordshire, OX1 3LB, UK
| | - Michael J O Pocock
- Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
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Coward J, Harding A. Size Does Matter: Why Polyploid Tumor Cells are Critical Drug Targets in the War on Cancer. Front Oncol 2014; 4:123. [PMID: 24904834 PMCID: PMC4033620 DOI: 10.3389/fonc.2014.00123] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/11/2014] [Indexed: 12/14/2022] Open
Abstract
Tumor evolution presents a formidable obstacle that currently prevents the development of truly curative treatments for cancer. In this perspective, we advocate for the hypothesis that tumor cells with significantly elevated genomic content (polyploid tumor cells) facilitate rapid tumor evolution and the acquisition of therapy resistance in multiple incurable cancers. We appeal to studies conducted in yeast, cancer models, and cancer patients, which all converge on the hypothesis that polyploidy enables large phenotypic leaps, providing access to many different therapy-resistant phenotypes. We develop a flow-cytometry based method for quantifying the prevalence of polyploid tumor cells, and show the frequency of these cells in patient tumors may be higher than is generally appreciated. We then present recent studies identifying promising new therapeutic strategies that could be used to specifically target polyploid tumor cells in cancer patients. We argue that these therapeutic approaches should be incorporated into new treatment strategies aimed at blocking tumor evolution by killing the highly evolvable, therapy-resistant polyploid cell subpopulations, thus helping to maintain patient tumors in a drug sensitive state.
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Affiliation(s)
- Jermaine Coward
- Mater Medical Research Institute, Princess Alexandra Hospital , Woolloongabba, QLD , Australia
| | - Angus Harding
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute , Brisbane, QLD , Australia
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38
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Adams GR, Bamman MM. Characterization and regulation of mechanical loading-induced compensatory muscle hypertrophy. Compr Physiol 2013; 2:2829-70. [PMID: 23720267 DOI: 10.1002/cphy.c110066] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In mammalian systems, skeletal muscle exists in a dynamic state that monitors and regulates the physiological investment in muscle size to meet the current level of functional demand. This review attempts to consolidate current knowledge concerning development of the compensatory hypertrophy that occurs in response to a sustained increase in the mechanical loading of skeletal muscle. Topics covered include: defining and measuring compensatory hypertrophy, experimental models, loading stimulus parameters, acute responses to increased loading, hyperplasia, myofiber-type adaptations, the involvement of satellite cells, mRNA translational control, mechanotransduction, and endocrinology. The authors conclude with their impressions of current knowledge gaps in the field that are ripe for future study.
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Affiliation(s)
- Gregory R Adams
- Department of Physiology and Biophysics, University of California Irvine, Irvine, California, USA.
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Ujvari B, Pearse AM, Swift K, Hodson P, Hua B, Pyecroft S, Taylor R, Hamede R, Jones M, Belov K, Madsen T. Anthropogenic selection enhances cancer evolution in Tasmanian devil tumours. Evol Appl 2013; 7:260-5. [PMID: 24567746 PMCID: PMC3927887 DOI: 10.1111/eva.12117] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/30/2013] [Indexed: 01/06/2023] Open
Abstract
The Tasmanian Devil Facial Tumour Disease (DFTD) provides a unique opportunity to elucidate the long-term effects of natural and anthropogenic selection on cancer evolution. Since first observed in 1996, this transmissible cancer has caused local population declines by >90%. So far, four chromosomal DFTD variants (strains) have been described and karyotypic analyses of 253 tumours showed higher levels of tetraploidy in the oldest strain. We propose that increased ploidy in the oldest strain may have evolved in response to effects of genomic decay observed in asexually reproducing organisms. In this study, we focus on the evolutionary response of DFTD to a disease suppression trial. Tumours collected from devils subjected to the removal programme showed accelerated temporal evolution of tetraploidy compared with tumours from other populations where no increase in tetraploid tumours were observed. As ploidy significantly reduces tumour growth rate, we suggest that the disease suppression trial resulted in selection favouring slower growing tumours mediated by an increased level of tetraploidy. Our study reveals that DFTD has the capacity to rapidly respond to novel selective regimes and that disease eradication may result in novel tumour adaptations, which may further imperil the long-term survival of the world's largest carnivorous marsupial.
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Affiliation(s)
- Beata Ujvari
- Faculty of Veterinary Science, University of Sydney Sydney, NSW, Australia
| | - Anne-Maree Pearse
- Animal Health Laboratory Department of Primary Industries, Parks and Water and Environment Launceston Tas., Australia
| | - Kate Swift
- Animal Health Laboratory Department of Primary Industries, Parks and Water and Environment Launceston Tas., Australia
| | - Pamela Hodson
- Animal Health Laboratory Department of Primary Industries, Parks and Water and Environment Launceston Tas., Australia
| | - Bobby Hua
- Animal Health Laboratory Department of Primary Industries, Parks and Water and Environment Launceston Tas., Australia
| | - Stephen Pyecroft
- Animal Health Laboratory Department of Primary Industries, Parks and Water and Environment Launceston Tas., Australia ; School of Animal & Veterinary Science, Faculty of Science, University of Adelaide Adelaide, SA, Australia
| | - Robyn Taylor
- Animal Health Laboratory Department of Primary Industries, Parks and Water and Environment Launceston Tas., Australia
| | - Rodrigo Hamede
- School of Zoology, University of Tasmania Hobart, Tas., Australia
| | - Menna Jones
- School of Zoology, University of Tasmania Hobart, Tas., Australia
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney Sydney, NSW, Australia
| | - Thomas Madsen
- School of Biological Sciences, University of Wollongong Wollongong, NSW, Australia
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Smith JDL, Bickham JW, Gregory TR. Patterns of genome size diversity in bats (order Chiroptera). Genome 2013; 56:457-72. [PMID: 24168629 DOI: 10.1139/gen-2013-0046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite being a group of particular interest in considering relationships between genome size and metabolic parameters, bats have not been well studied from this perspective. This study presents new estimates for 121 "microbat" species from 12 families and complements a previous study on members of the family Pteropodidae ("megabats"). The results confirm that diversity in genome size in bats is very limited even compared with other mammals, varying approximately 2-fold from 1.63 pg in Lophostoma carrikeri to 3.17 pg in Rhinopoma hardwickii and averaging only 2.35 pg ± 0.02 SE (versus 3.5 pg overall for mammals). However, contrary to some other vertebrate groups, and perhaps owing to the narrow range observed, genome size correlations were not apparent with any chromosomal, physiological, flight-related, developmental, or ecological characteristics within the order Chiroptera. Genome size is positively correlated with measures of body size in bats, though the strength of the relationships differs between pteropodids ("megabats") and nonpteropodids ("microbats").
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Affiliation(s)
- Jillian D L Smith
- a Department of Integrative Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
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41
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Jalal M, Wojewodzic MW, Laane CMM, Hessen DO. Larger Daphnia at lower temperature: a role for cell size and genome configuration? Genome 2013; 56:511-9. [DOI: 10.1139/gen-2013-0004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Experiments with Daphnia magna and Daphnia pulex raised at 10 and 20 °C yielded larger adult size at the lower temperature. This must reflect increased cell size, increased cell numbers, or a combination of both. As it is difficult to achieve good estimates on cell size in crustaceans, we, therefore, measured nucleus and genome size using flow cytometry at 10 and 20 °C. DNA was stained with propidium iodide, ethidium bromide, and DAPI. Both nucleus and genome size estimates were elevated at 10 °C compared with 20 °C, suggesting that larger body size at low temperature could partly be accredited to an enlarged nucleus and thus cell size. Confocal microscopy observations confirmed the staining properties of fluorochromes. As differences in nucleotide numbers in response of growth temperature within a life span is unlikely, these results seem accredited to changed DNA–fluorochrome binding properties, presumably reflecting increased DNA condensation at low temperature. This implies that genome size comparisons may be impacted by ambient temperature in ectotherms. It also suggests that temperature-induced structural changes in the genome could affect cell size and for some species even body size.
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Affiliation(s)
- Marwa Jalal
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Marcin W. Wojewodzic
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Carl Morten M. Laane
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Dag O. Hessen
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
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42
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Dobeš C, Lückl A, Hülber K, Paule J. Prospects and limits of the flow cytometric seed screen--insights from Potentilla sensu lato (Potentilleae, Rosaceae). THE NEW PHYTOLOGIST 2013; 198:605-616. [PMID: 23425259 PMCID: PMC3618378 DOI: 10.1111/nph.12149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/14/2012] [Indexed: 05/03/2023]
Abstract
The flow cytometric seed screen allows for identification of reproductive modes of seed formation and inference of the ploidy of contributing gametes. However, the lack of a mathematical formalization to infer male/female genomic contributions, and the prerequisite of a binucleate female contribution to the endosperm limits its applicability. We evaluated this assumption combining a DNA-based progeny survey with a comparison of the cytology of reproductive pathways co-occurring within single individuals representing 14 Potentilleae species from six phylogenetic lineages. A numerical framework valid for sexual and pseudogamous taxa was developed, enabling quantification of female and male genomes contributing to embryo and endosperm independent of gametophyte origins, numbers of sperm involved and ploidy of parents. The inference strongly depended on accurate peak index estimation. The endosperm of Potentilleae species received a binucleate female contribution in five evolutionary lineages whereas endosperm formation remained uncertain in the Tormentillae. A modified flow cytometric seed screen protocol was developed to cope with low endosperm contents. Evolutionary conservation of a binucleate female contribution to the endosperm suggested wide applicability of flow cytometric seed screen - at least in the Potentilleae. However, alternative progeny surveys and precise embryo/endosperm ploidy estimates are required for a comprehensive understanding of the cytology of seed formation.
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Affiliation(s)
- Christoph Dobeš
- Department of Pharmacognosy, Pharmacobotany, University of ViennaAlthanstrasse 14, A–1090, Vienna, Austria
| | - Andrea Lückl
- Department of Pharmacognosy, Pharmacobotany, University of ViennaAlthanstrasse 14, A–1090, Vienna, Austria
| | - Karl Hülber
- Department of Conservation Biology, Vegetation and Landscape Ecology, University of ViennaRennweg 14, A–1030, Vienna, Austria
- Vienna Institute for Nature Conservation & AnalysesGiessergasse 6/7, A-1090, Vienna, Austria
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute & Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 25, D–60325, Frankfurt am Main, Germany
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43
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Choleva L, Janko K. Rise and Persistence of Animal Polyploidy: Evolutionary Constraints and Potential. Cytogenet Genome Res 2013; 140:151-70. [DOI: 10.1159/000353464] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Bainard JD, Bainard LD, Henry TA, Fazekas AJ, Newmaster SG. A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits. THE NEW PHYTOLOGIST 2012; 196:1240-1250. [PMID: 23078229 DOI: 10.1111/j.1469-8137.2012.04370.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 08/30/2012] [Indexed: 05/03/2023]
Abstract
Genome size (C-value) and endopolyploidy (endoreduplication index, EI) are known to correlate with various morphological and ecological traits, in addition to phylogenetic placement. A phylogenetically controlled multivariate analysis was used to explore the relationships between DNA content and phenotype in angiosperms. Seeds from 41 angiosperm species (17 families) were grown in a common glasshouse experiment. Genome size (2C-value and 1Cx-value) and EI (in four tissues: leaf, stem, root, petal) were determined using flow cytometry. The phylogenetic signal was calculated for each measure of DNA content, and phylogenetic canonical correlation analysis (PCCA) explored how the variation in genome size and EI was correlated with 18 morphological and ecological traits. Phylogenetic signal (λ) was strongest for EI in all tissues, and λ was stronger for the 2C-value than the 1Cx-value. PCCA revealed that EI was correlated with pollen length, stem height, seed mass, dispersal mechanism, arbuscular mycorrhizal association, life history and flowering time, and EI and genome size were both correlated with stem height and life history. PCCA provided an effective way to explore multiple factors of DNA content variation and phenotypic traits in a phylogenetic context. Traits that were correlated significantly with DNA content were linked to plant competitive ability.
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Affiliation(s)
- Jillian D Bainard
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Luke D Bainard
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Thomas A Henry
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Aron J Fazekas
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Steven G Newmaster
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
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45
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Ardila‐Garcia AM, Gregory TR. An exploration of genome size diversity in dragonflies and damselflies (Insecta: Odonata). J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00557.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - T. R. Gregory
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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46
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Beaulieu JM, Leitch IJ, Patel S, Pendharkar A, Knight CA. Genome size is a strong predictor of cell size and stomatal density in angiosperms. THE NEW PHYTOLOGIST 2008; 179:975-986. [PMID: 18564303 DOI: 10.1111/j.1469-8137.2008.02528.x] [Citation(s) in RCA: 251] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Across eukaryotes phenotypic correlations with genome size are thought to scale from genome size effects on cell size. However, for plants the genome/cell size link has only been thoroughly documented within ploidy series and small subsets of herbaceous species. Here, the first large-scale comparative analysis is made of the relationship between genome size and cell size across 101 species of angiosperms of varying growth forms. Guard cell length and epidermal cell area were used as two metrics of cell size and, in addition, stomatal density was measured. There was a significant positive relationship between genome size and both guard cell length and epidermal cell area and a negative relationship with stomatal density. Independent contrast analyses revealed that these traits are undergoing correlated evolution with genome size. However, the relationship was growth form dependent (nonsignificant results within trees/shrubs), although trees had the smallest genome/cell sizes and the highest stomatal density. These results confirm the generality of the genome size/cell size relationship. The results also suggest that changes in genome size, with concomitant influences on stomatal size and density, may influence physiology, and perhaps play an important genetic role in determining the ecological and life-history strategy of a species.
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Affiliation(s)
- Jeremy M Beaulieu
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AD, UK
| | - Sunil Patel
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Arjun Pendharkar
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Charles A Knight
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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47
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Leitch IJ, Beaulieu JM, Cheung K, Hanson L, Lysak MA, Fay MF. Punctuated genome size evolution in Liliaceae. J Evol Biol 2007; 20:2296-308. [PMID: 17956392 DOI: 10.1111/j.1420-9101.2007.01416.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most angiosperms possess small genomes (mode 1C = 0.6 pg, median 1C = 2.9 pg). Those with truly enormous genomes (i.e. > or = 35 pg) are phylogenetically restricted to a few families and include Liliaceae - with species possessing some of the largest genomes so far reported for any plant as well as including species with much smaller genomes. To gain insights into when and where genome size expansion took place during the evolution of Liliaceae and the mode and tempo of this change, data for 78 species were superimposed onto a phylogenetic tree and analysed. Results suggest that genome size in Liliaceae followed a punctuated rather than gradual mode of evolution and that most of the diversification evolved recently rather than early in the evolution of the family. We consider that the large genome sizes of Liliaceae may have emerged passively rather than being driven primarily by selection.
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Affiliation(s)
- I J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
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48
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Meagher TR, Vassiliadis C. Phenotypic impacts of repetitive DNA in flowering plants. THE NEW PHYTOLOGIST 2005; 168:71-80. [PMID: 16159322 DOI: 10.1111/j.1469-8137.2005.01527.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The discovery that nuclear DNA content varies widely among species, and even within species, was unexpected because it was thought that the number of genes required for an organism should be common across taxa. We now know that the bulk of nuclear DNA content variation is caused by repetitive DNA sequences characterized according to the nature of repeat (tandem vs dispersed) or chromosomal location/mechanism of replication (pericentromeric, telomeric or subtelomeric, microsatellites, minisatellites, satellites, transposable elements, retroelements). Variation in repetitive DNA, manifested as variation in nuclear DNA content, has been shown to have broad ecological and life-history consequences. For example, large genome size appears to limit fitness in extreme environmental conditions. Within species, variation in DNA content has been coupled to growth and development, such as maturation time in crop species. In Silene latifolia, DNA content is negatively correlated with flower size, a character that, in turn, has well documented ecological significance. These intraspecific studies suggest a connection between repetitive DNA and quantitative genetic determination of continuous characters. Novel insights into mechanisms by which repetitive DNA influences phenotype will lead to models of evolutionary change that extend well beyond the conventional view of evolution by allelic substitution.
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Affiliation(s)
- Thomas R Meagher
- Centre for Evolution, Genes & Genomics, School of Biology, Sir Harold Mitchell Building, University of St Andrews, St Andrews, Fife KY16 9TH, UK.
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49
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Baack EJ, Whitney KD, Rieseberg LH. Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species. THE NEW PHYTOLOGIST 2005; 167:623-30. [PMID: 15998412 PMCID: PMC2442926 DOI: 10.1111/j.1469-8137.2005.01433.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Hybridization and polyploidy can induce rapid genomic changes, including the gain or loss of DNA, but the magnitude and timing of such changes are not well understood. The homoploid hybrid system in Helianthus (three hybrid-derived species and their two parents) provides an opportunity to examine the link between hybridization and genome size changes in a replicated fashion. Flow cytometry was used to estimate the nuclear DNA content in multiple populations of three homoploid hybrid Helianthus species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus), the parental species (Helianthus annuus and Helianthus petiolaris), synthetic hybrids, and natural hybrid-zone populations. Results confirm that hybrid-derived species have 50% more nuclear DNA than the parental species. Despite multiple origins, hybrid species were largely consistent in their DNA content across populations, although H. deserticola showed significant interpopulation differences. First- and sixth-generation synthetic hybrids and hybrid-zone plants did not show an increase from parental DNA content. First-generation hybrids differed in DNA content according to the maternal parent. In summary, hybridization by itself does not lead to increased nuclear DNA content in Helianthus, and the evolutionary forces responsible for the repeated increases in DNA content seen in the hybrid-derived species remain mysterious.
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Affiliation(s)
- Eric J Baack
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.
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50
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Bruusgaard JC, Liestøl K, Ekmark M, Kollstad K, Gundersen K. Number and spatial distribution of nuclei in the muscle fibres of normal mice studied in vivo. J Physiol 2003; 551:467-78. [PMID: 12813146 PMCID: PMC2343230 DOI: 10.1113/jphysiol.2003.045328] [Citation(s) in RCA: 173] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We present here a new technique with which to visualize nuclei in living muscle fibres in the intact animal, involving injection of labelled DNA into single cells. This approach allowed us to determine the position of all of nuclei within a sarcolemma without labelling satellite cells. In contrast to what has been reported in tissue culture, we found that the nuclei were immobile, even when observed over several days. Nucleic density was uniform along the fibre except for the endplate and some myotendinous junctions, where the density was higher. The perijunctional region had the same number of nuclei as the rest of the fibre. In the extensor digitorum longus (EDL) muscle, the extrajunctional nuclei were elongated and precisely aligned to the long axis of the fibre. In the soleus, the nuclei were rounder and not well aligned. When comparing small and large fibres in the soleus, the number of nuclei varied approximately in proportion to cytoplasmic volume, while in the EDL the number was proportional to surface area. Statistical analysis revealed that the nuclei were not randomly distributed in either the EDL or the soleus. For each fibre, actual distributions were compared with computer simulations in which nuclei were assumed to repel each other, which optimizes the distribution of nuclei with respect to minimizing transport distances. The simulated patterns were regular, with clear row-like structures when the density of nuclei was low. The non-random and often row-like distribution of nuclei observed in muscle fibres may thus reflect regulatory mechanisms whereby nuclei repel each other in order to minimize transport distances.
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Affiliation(s)
- J C Bruusgaard
- Department of Biology, University of Oslo, Blindern, Norway
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