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Caporale LH. Evolutionary feedback from the environment shapes mechanisms that generate genome variation. J Physiol 2024; 602:2601-2614. [PMID: 38194279 DOI: 10.1113/jp284411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
Darwin recognized that 'a grand and almost untrodden field of inquiry will be opened, on the causes and laws of variation.' However, because the Modern Synthesis assumes that the intrinsic probability of any individual mutation is unrelated to that mutation's potential adaptive value, attention has been focused on selection rather than on the intrinsic generation of variation. Yet many examples illustrate that the term 'random' mutation, as widely understood, is inaccurate. The probabilities of distinct classes of variation are neither evenly distributed across a genome nor invariant over time, nor unrelated to their potential adaptive value. Because selection acts upon variation, multiple biochemical mechanisms can and have evolved that increase the relative probability of adaptive mutations. In effect, the generation of heritable variation is in a feedback loop with selection, such that those mechanisms that tend to generate variants that survive recurring challenges in the environment would be captured by this survival and thus inherited and accumulated within lineages of genomes. Moreover, because genome variation is affected by a wide range of biochemical processes, genome variation can be regulated. Biochemical mechanisms that sense stress, from lack of nutrients to DNA damage, can increase the probability of specific classes of variation. A deeper understanding of evolution involves attention to the evolution of, and environmental influences upon, the intrinsic variation generated in gametes, in other words upon the biochemical mechanisms that generate variation across generations. These concepts have profound implications for the types of questions that can and should be asked, as omics databases become more comprehensive, detection methods more sensitive, and computation and experimental analyses even more high throughput and thus capable of revealing the intrinsic generation of variation in individual gametes. These concepts also have profound implications for evolutionary theory, which, upon reflection it will be argued, predicts that selection would increase the probability of generating adaptive mutations, in other words, predicts that the ability to evolve itself evolves.
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Yudin NS, Larkin DM. Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds. Vavilovskii Zhurnal Genet Selektsii 2023; 27:463-470. [PMID: 37867610 PMCID: PMC10587008 DOI: 10.18699/vjgb-23-56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 10/24/2023] Open
Abstract
It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adaptation. Local cattle and sheep breeds have been formed over thousands of years under the influence of domestication, as well as selection aimed at adaptation to the local environment and meeting human needs. Previously, we identified a number of candidate genes in genome regions potentially selected during domestication and adaptation to the climatic conditions of Russia, in local breeds of cattle and sheep using whole genome genotyping data. However, these data are of low resolution and do not reveal most nucleotide substitutions. The aim of the work was to create, using the whole genome sequencing data, a list of genes associated with domestication, selection and adaptation in Russian cattle and sheep breeds, as well as to identify candidate genes and metabolic pathways for selection for cold adaptation. We used our original data on the search for signatures of selection in the genomes of Russian cattle (Yakut, Kholmogory, Buryat, Wagyu) and sheep (Baikal, Tuva) breeds. We used the HapFLK, DCMS, FST and PBS methods to identify DNA regions with signatures of selection. The number of candidate genes in potentially selective regions was 946 in cattle and 151 in sheep. We showed that the studied Russian cattle and sheep breeds have at least 10 genes in common, apparently involved in the processes of adaptation/selection, including adaptation to a cold climate, including the ASTN2, PM20D1, TMEM176A, and GLIS1 genes. Based on the intersection with the list of selected genes in at least two Arctic/Antarctic mammal species, 20 and 8 genes, have been identified in cattle and sheep, respectively, that are potentially involved in cold adaptation. Among them, the most promising for further research are the ASPH, NCKAP5L, SERPINF1, and SND1 genes. Gene ontology analysis indicated the existence of possible common biochemical pathways for adaptation to cold in domestic and wild mammals associated with cytoskeleton disassembly and apoptosis.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
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3
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Rybnikov SR, Frenkel Z, Hübner S, Weissman DB, Korol AB. Modeling the evolution of recombination plasticity: A prospective review. Bioessays 2023; 45:e2200237. [PMID: 37246937 DOI: 10.1002/bies.202200237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 05/30/2023]
Abstract
Meiotic recombination is one of the main sources of genetic variation, a fundamental factor in the evolutionary adaptation of sexual eukaryotes. Yet, the role of variation in recombination rate and other recombination features remains underexplored. In this review, we focus on the sensitivity of recombination rates to different extrinsic and intrinsic factors. We briefly present the empirical evidence for recombination plasticity in response to environmental perturbations and/or poor genetic background and discuss theoretical models developed to explain how such plasticity could have evolved and how it can affect important population characteristics. We highlight a gap between the evidence, which comes mostly from experiments with diploids, and theory, which typically assumes haploid selection. Finally, we formulate open questions whose solving would help to outline conditions favoring recombination plasticity. This will contribute to answering the long-standing question of why sexual recombination exists despite its costs, since plastic recombination may be evolutionary advantageous even in selection regimes rejecting any non-zero constant recombination.
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Affiliation(s)
- Sviatoslav R Rybnikov
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Sariel Hübner
- Galilee Research Institute (MIGAL), Tel-Hai College, Kiryat Shmona, Israel
| | | | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
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Murashov AK, Pak ES, Mar J, O’Brien K, Fisher-Wellman K, Bhat KM. Paternal Western diet causes transgenerational increase in food consumption in Drosophila with parallel alterations in the offspring brain proteome and microRNAs. FASEB J 2023; 37:e22966. [PMID: 37227156 PMCID: PMC10234493 DOI: 10.1096/fj.202300239rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
Abstract
Several lines of evidence indicate that ancestral diet might play an important role in determining offspring's metabolic traits. However, it is not yet clear whether ancestral diet can affect offspring's food choices and feeding behavior. In the current study, taking advantage of Drosophila model system, we demonstrate that paternal Western diet (WD) increases offspring food consumption up to the fourth generation. Paternal WD also induced alterations in F1 offspring brain proteome. Using enrichment analyses of pathways for upregulated and downregulated proteins, we found that upregulated proteins had significant enrichments in terms related to translation and translation factors, whereas downregulated proteins displayed enrichments in small molecule metabolic processes, TCA cycles, and electron transport chain (ETC). Using MIENTURNET miRNA prediction tool, dme-miR-10-3p was identified as the top conserved miRNA predicted to target proteins regulated by ancestral diet. RNAi-based knockdown of miR-10 in the brain significantly increased food consumption, implicating miR-10 as a potential factor in programming feeding behavior. Together, these findings suggest that ancestral nutrition may influence offspring feeding behavior through alterations in miRNAs.
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Affiliation(s)
- Alexander K. Murashov
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Elena S. Pak
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Jordan Mar
- Department of Molecular Medicine, University of South Florida, Tampa, FL
| | - Kevin O’Brien
- Department of Biostatistics, College of Allied Health Sciences, East Carolina University, Greenville, NC
| | - Kelsey Fisher-Wellman
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL
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5
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Moniruzzaman M, Datta U, Saha NC, Bhowmick AR, Mukherjee J. Abiotic factors and heavy metals defining eco-physiological niche in fish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162328. [PMID: 36863592 DOI: 10.1016/j.scitotenv.2023.162328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Ecosystem dynamics undergoing alterations in structure and function highlights the need to look into the relations between ecological parameters and organismal fitness and tolerance. Ecophysiological studies are used to understand how organisms adapt to and cope up with environmental stress. Current study uses a process-based approach to model physiochemical parameters regarding seven different fish species. Species respond to climatic variations via acclimation or adaptation through physiological plasticity. Four sites are differentiated into two types based on the water quality parameters and metal contamination. Seven fish species are clustered into two groups, each group depicting separate pattern of response in similar habitat. In this manner, biomarkers from three different physiological axes- stress, reproduction, and neurology were taken to determine the organism's ecological niche. Cortisol, Testosterone, Estradiol, and AChE are the signature molecules estimated for the said physiological axes. The ordination technique, nonmetric multidimensional scaling, has been utilized to visualize the differentiated physiological response to changing environmental conditions. Then, Bayesian Model Averaging (BMA) was used to identify the factors that play a key role in refining the stress physiology and determining the niche. Current study confirms different species belonging to similar habitats respond to various environmental and physiological factors in a different manner as various biomarkers respond in a species-specific pattern that induces the choice of habitat preference controlling its ecophysiological niche. In the present study, it is quite apparent that adaptive mechanism of fish to environmental stress is achieved through modification of physiological mechanisms through a panel of biochemical markers. These markers organize a cascade of physiological event at various levels including reproduction.
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Affiliation(s)
- Mahammed Moniruzzaman
- Department of Zoology, University of Calcutta, Kolkata 700019, India; Estuarine and Coastal Studies Foundation, Howrah, West Bengal, India
| | - Urbi Datta
- Department of Mathematics, Institute of Chemical Technology, Mumbai, India
| | - Nimai Chandra Saha
- Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India
| | | | - Joyita Mukherjee
- Department of Zoology, Krishna Chandra College, Hetampur, Birbhum, West Bengal, India.
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Fu Y, Liu X, Xia Y, Guo X, Guo J, Zhang J, Zhao W, Wu Y, Wang J, Zhong F. Whole-cell-catalyzed hydrogenation/deuteration of aryl halides with a genetically repurposed photodehalogenase. Chem 2023. [DOI: 10.1016/j.chempr.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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7
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von Mücke-Heim IA, Urbina-Treviño L, Bordes J, Ries C, Schmidt MV, Deussing JM. Introducing a depression-like syndrome for translational neuropsychiatry: a plea for taxonomical validity and improved comparability between humans and mice. Mol Psychiatry 2023; 28:329-340. [PMID: 36104436 PMCID: PMC9812782 DOI: 10.1038/s41380-022-01762-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/09/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
Depressive disorders are the most burdensome psychiatric disorders worldwide. Although huge efforts have been made to advance treatment, outcomes remain unsatisfactory. Many factors contribute to this gridlock including suboptimal animal models. Especially limited study comparability and replicability due to imprecise terminology concerning depressive-like states are major problems. To overcome these issues, new approaches are needed. Here, we introduce a taxonomical concept for modelling depression in laboratory mice, which we call depression-like syndrome (DLS). It hinges on growing evidence suggesting that mice possess advanced socioemotional abilities and can display non-random symptom patterns indicative of an evolutionary conserved disorder-like phenotype. The DLS approach uses a combined heuristic method based on clinical depression criteria and the Research Domain Criteria to provide a biobehavioural reference syndrome for preclinical rodent models of depression. The DLS criteria are based on available, species-specific evidence and are as follows: (I) minimum duration of phenotype, (II) significant sociofunctional impairment, (III) core biological features, (IV) necessary depressive-like symptoms. To assess DLS presence and severity, we have designed an algorithm to ensure statistical and biological relevance of findings. The algorithm uses a minimum combined threshold for statistical significance and effect size (p value ≤ 0.05 plus moderate effect size) for each DLS criterion. Taken together, the DLS is a novel, biologically founded, and species-specific minimum threshold approach. Its long-term objective is to gradually develop into an inter-model validation standard and microframework to improve phenotyping methodology in translational research.
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Affiliation(s)
- Iven-Alex von Mücke-Heim
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Molecular Neurogenetics, Munich, Germany ,grid.419548.50000 0000 9497 5095Department of Translational Research, Max Planck Institute of Psychiatry, Munich, Germany ,grid.4372.20000 0001 2105 1091International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Lidia Urbina-Treviño
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Molecular Neurogenetics, Munich, Germany
| | - Joeri Bordes
- grid.4372.20000 0001 2105 1091International Max Planck Research School for Translational Psychiatry, Munich, Germany ,grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Neurobiology of Stress Resilience, Munich, Germany
| | - Clemens Ries
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Molecular Neurogenetics, Munich, Germany ,grid.4372.20000 0001 2105 1091International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Mathias V. Schmidt
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Neurobiology of Stress Resilience, Munich, Germany
| | - Jan M. Deussing
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Molecular Neurogenetics, Munich, Germany
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Mukherjee S, Kuang Z, Ghosh S, Detroja R, Carmi G, Tripathy S, Barash D, Frenkel-Morgenstern M, Nevo E, Li K. Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis. BIOLOGY 2022; 11:biology11081110. [PMID: 35892966 PMCID: PMC9331176 DOI: 10.3390/biology11081110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary The microevolutionary dynamics of soil bacteria under microclimatic differences are largely unexplored in contrast to our improving knowledge of their vast diversity. In this study, we performed a comparative metagenomic analysis of two sharply divergent rocks and soil types at the Evolution Plateau (EP) in eastern Upper Galilee, Israel. We have identified the significant differences in bacterial taxonomic diversity, functions, and patterns of RNA-based gene regulation between the bacteria from two different soil types. Furthermore, we have identified several species with a significant genetic divergence of the same species between the two soil types, highlighting the soil bacteria’s incipient sympatric speciation. Abstract Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.
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Affiliation(s)
- Sumit Mukherjee
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
- Correspondence: (S.M.); (K.L.)
| | - Zhuoran Kuang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
| | - Samrat Ghosh
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Gon Carmi
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata 700054, India; (S.G.); (S.T.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201009, India
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel;
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (R.D.); (G.C.); (M.F.-M.)
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel;
| | - Kexin Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730050, China;
- Correspondence: (S.M.); (K.L.)
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Brown JI, Harrigan RJ, Lavretsky P. Evolutionary and Ecological Drivers of Local Adaptation and Speciation in a North American Avian Species Complex. Mol Ecol 2022; 31:2578-2593. [PMID: 35263000 DOI: 10.1111/mec.16423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for non-model organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in a climate refugia arising during a glacial period in in a southwestern North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that likely reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.
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Affiliation(s)
- Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
| | - Ryan J Harrigan
- Center for Tropical Research, University of California, Los Angeles, La Kretz Hall, Suite 300, Los Angeles, CA, 90095, U.S.A
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, 79668, USA
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10
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de Sousa AA, Todorov OS, Proulx MJ. A natural history of vertebrate vision loss: Insight from mammalian vision for human visual function. Neurosci Biobehav Rev 2022; 134:104550. [PMID: 35074313 DOI: 10.1016/j.neubiorev.2022.104550] [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: 03/27/2020] [Revised: 10/08/2021] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
Research on the origin of vision and vision loss in naturally "blind" animal species can reveal the tasks that vision fulfills and the brain's role in visual experience. Models that incorporate evolutionary history, natural variation in visual ability, and experimental manipulations can help disentangle visual ability at a superficial level from behaviors linked to vision but not solely reliant upon it, and could assist the translation of ophthalmological research in animal models to human treatments. To unravel the similarities between blind individuals and blind species, we review concepts of 'blindness' and its behavioral correlates across a range of species. We explore the ancestral emergence of vision in vertebrates, and the loss of vision in blind species with reference to an evolution-based classification scheme. We applied phylogenetic comparative methods to a mammalian tree to explore the evolution of visual acuity using ancestral state estimations. Future research into the natural history of vision loss could help elucidate the function of vision and inspire innovations in how to address vision loss in humans.
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Affiliation(s)
- Alexandra A de Sousa
- Centre for Health and Cognition, Bath Spa University, Bath, United Kingdom; UKRI Centre for Accessible, Responsible & Transparent Artificial Intelligence (ART:AI), University of Bath, United Kingdom.
| | - Orlin S Todorov
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Michael J Proulx
- UKRI Centre for Accessible, Responsible & Transparent Artificial Intelligence (ART:AI), University of Bath, United Kingdom; Department of Psychology, REVEAL Research Centre, University of Bath, Bath, United Kingdom
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11
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Abu Bakar N, Lau Yii Chung B, Smykla J, Karsani SA, Alias SA. Protein homeostasis, regulation of energy production and activation of DNA damage-repair pathways are involved in the heat stress response of Pseudogymnoascus spp. Environ Microbiol 2021; 24:1849-1864. [PMID: 34528369 DOI: 10.1111/1462-2920.15776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 11/30/2022]
Abstract
Proteome changes can be used as an instrument to measure the effects of climate change, predict the possible future state of an ecosystem and the direction in which is headed. In this study, proteomic and GO functional enrichment analysis of six Pseudogymnoascus spp. isolated from various global biogeographical regions were carried out to determine their response to heat stress. In total, 2,122 proteins were identified with high confidence. Comparative quantitative analysis showed that changes in proteome profiles varied greatly between isolates from different biogeographical regions. Although the identities of the proteins that changed varied between the different regions, the functions they governed were similar. Gene Ontology analysis showed enrichment of proteins involved in multiple protective mechanisms, including the modulation of protein homeostasis, regulation of energy production, and activation of DNA damage and repair pathways. Our proteomic analysis did not show any clear relationship between protein changes and the strains' biogeographical origins. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nurlizah Abu Bakar
- Institute of Ocean and Earth Sciences, C308, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,National Antarctic Research Centre, B303, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Benjamin Lau Yii Chung
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Jerzy Smykla
- Department of Biodiversity, Institute of Nature Conservation Polish Academy of Sciences, Mickiewicza 33, 31-120 Krakow, Poland
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, C308, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,National Antarctic Research Centre, B303, Institute of Advanced Studies Building, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
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12
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Yap KN, Yamada K, Zikeli S, Kiaris H, Hood WR. Evaluating endoplasmic reticulum stress and unfolded protein response through the lens of ecology and evolution. Biol Rev Camb Philos Soc 2020; 96:541-556. [PMID: 33164297 DOI: 10.1111/brv.12667] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/13/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
Considerable progress has been made in understanding the physiological basis for variation in the life-history patterns of animals, particularly with regard to the roles of oxidative stress and hormonal regulation. However, an underappreciated and understudied area that could play a role in mediating inter- and intraspecific variation of life history is endoplasmic reticulum (ER) stress, and the resulting unfolded protein response (UPRER ). ER stress response and the UPRER maintain proteostasis in cells by reducing the intracellular load of secretory proteins and enhancing protein folding capacity or initiating apoptosis in cells that cannot recover. Proper modulation of the ER stress response and execution of the UPRER allow animals to respond to intracellular and extracellular stressors and adapt to constantly changing environments. ER stress responses are heritable and there is considerable individual variation in UPRER phenotype in animals, suggesting that ER stress and UPRER phenotype can be subjected to natural selection. The variation in UPRER phenotype presumably reflects the way animals respond to ER stress and environmental challenges. Most of what we know about ER stress and the UPRER in animals has either come from biomedical studies using cell culture or from experiments involving conventional laboratory or agriculturally important models that exhibit limited genetic diversity. Furthermore, these studies involve the assessment of experimentally induced qualitative changes in gene expression as opposed to the quantitative variations that occur in naturally existing populations. Almost all of these studies were conducted in controlled settings that are often quite different from the conditions animals experience in nature. Herein, we review studies that investigated ER stress and the UPRER in relation to key life-history traits including growth and development, reproduction, bioenergetics and physical performance, and ageing and senescence. We then ask if these studies can inform us about the role of ER stress and the UPRER in mediating the aforementioned life-history traits in free-living animals. We propose that there is a need to conduct experiments pertaining to ER stress and the UPRER in ecologically relevant settings, to characterize variation in ER stress and the UPRER in free-living animals, and to relate the observed variation to key life-history traits. We urge others to integrate multiple physiological systems and investigate how interactions between ER stress and oxidative stress shape life-history trade-offs in free-living animals.
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Affiliation(s)
- Kang Nian Yap
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, U.S.A
| | - KayLene Yamada
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, U.S.A
| | - Shelby Zikeli
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, U.S.A
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, and Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, 29208, U.S.A
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, U.S.A
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Gardon T, Morvan L, Huvet A, Quillien V, Soyez C, Le Moullac G, Le Luyer J. Microplastics induce dose-specific transcriptomic disruptions in energy metabolism and immunity of the pearl oyster Pinctada margaritifera. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115180. [PMID: 32673975 DOI: 10.1016/j.envpol.2020.115180] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/19/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
A combined approach integrating bioenergetics and major biological activities is essential to properly understand the impact of microplastics (MP) on marine organisms. Following experimental exposure of polystyrene microbeads (micro-PS of 6 and 10 μm) at 0.25, 2.5, and 25 μg L-1, which demonstrated a dose-dependent decrease of energy balance in the pearl oyster Pinctada margaritifera, a transcriptomic study was conducted on mantle tissue. Transcriptomic data helped us to decipher the molecular mechanisms involved in P. margaritifera responses to micro-PS and search more broadly for effects on energetically expensive maintenance functions. Genes related to the detoxification process were impacted by long-term micro-PS exposure through a decrease in antioxidant response functioning, most likely leading to oxidative stress and damage, especially at higher micro-PS doses. The immune response was also found to be dose-specific, with a stress-related activity stimulated by the lowest dose present after a 2-month exposure period. This stress response was not observed following exposure to higher doses, reflecting an energy-limited capacity of pearl oysters to cope with prolonged stress and a dramatic shift to adjust to pessimum conditions, mostly limited and hampered by a lowered energetic budget. This preliminary experiment lays the foundation for exploring pathways and gene expression in P. margaritifera, and marine mollusks in general, under MP exposure. We also propose a conceptual framework to properly assess realistic MP effects on organisms and population resilience in future investigations.
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Affiliation(s)
- Tony Gardon
- Ifremer, Institut Louis-Malardé, IRD, Univ Polynésie Française, EIO, F-98719, Taravao, Tahiti, Polynésie française, France
| | - Lucie Morvan
- Ifremer, Institut Louis-Malardé, IRD, Univ Polynésie Française, EIO, F-98719, Taravao, Tahiti, Polynésie française, France
| | - Arnaud Huvet
- Univ Brest, Ifremer, CNRS, IRD, LEMAR, F-29280, Plouzané, France
| | - Virgile Quillien
- Ifremer, Institut Louis-Malardé, IRD, Univ Polynésie Française, EIO, F-98719, Taravao, Tahiti, Polynésie française, France; Univ Brest, Ifremer, CNRS, IRD, LEMAR, F-29280, Plouzané, France
| | - Claude Soyez
- Ifremer, Institut Louis-Malardé, IRD, Univ Polynésie Française, EIO, F-98719, Taravao, Tahiti, Polynésie française, France
| | - Gilles Le Moullac
- Ifremer, Institut Louis-Malardé, IRD, Univ Polynésie Française, EIO, F-98719, Taravao, Tahiti, Polynésie française, France
| | - Jérémy Le Luyer
- Ifremer, Institut Louis-Malardé, IRD, Univ Polynésie Française, EIO, F-98719, Taravao, Tahiti, Polynésie française, France.
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14
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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15
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Polonca S. Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates. MICROBIAL ECOLOGY 2020; 79:853-864. [PMID: 31707464 DOI: 10.1007/s00248-019-01455-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.
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Affiliation(s)
- Stefanic Polonca
- Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia.
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16
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Maina JN, Igbokwe CO. Comparative morphometric analysis of lungs of the semifossorial giant pouched rat (Cricetomys gambianus) and the subterranean Nigerian mole rat (Cryptomys foxi). Sci Rep 2020; 10:5244. [PMID: 32251351 PMCID: PMC7090082 DOI: 10.1038/s41598-020-61873-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022] Open
Abstract
Lungs of the rodent species, the African giant pouched rat (Cricetomys gambianus) and the Nigerian mole rat (Cryptomys foxi) were investigated. Significant morphometric differences exist between the two species. The volume of the lung per unit body mass was 2.7 times larger; the respiratory surface area 3.4 times greater; the volume of the pulmonary capillary blood 2 times more; the harmonic mean thickness of the blood-gas (tissue) barrier (τht) ~29% thinner and; the total pulmonary morphometric diffusing capacity (DLo2) for O2 2.3 times more in C. foxi. C. gambianus occupies open burrows that are ventilated with air while C. foxi lives in closed burrows. The less morphometrically specialized lungs of C. gambianus may be attributed to its much larger body mass (~6 times more) and possibly lower metabolic rate and its semifossorial life whereas the 'superior' lungs of C. foxi may largely be ascribed to the subterranean hypoxic and hypercapnic environment it occupies. Compared to other rodents species that have been investigated hitherto, the τht was mostly smaller in the lungs of the subterranean species and C. foxi has the highest mass-specific DLo2. The fossorial- and the subterranean rodents have acquired various pulmonary structural specializations that relate to habitats occupied.
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Affiliation(s)
- John N Maina
- Department of Zoology, University of Johannesburg, Auckland Park Campus, Kingsway, Johannesburg, 2006, South Africa.
| | - Casmir O Igbokwe
- Department of Zoology, University of Johannesburg, Auckland Park Campus, Kingsway, Johannesburg, 2006, South Africa
- Visiting Postdoctoral Fellow, Department of Veterinary Anatomy, Faculty of Veterinary Medicine, University of Nigeria, Nsukka, Nigeria
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17
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Díaz-Hung ML, Martínez G, Hetz C. Emerging roles of the unfolded protein response (UPR) in the nervous system: A link with adaptive behavior to environmental stress? INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 350:29-61. [PMID: 32138903 DOI: 10.1016/bs.ircmb.2020.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Stressors elicit a neuroendocrine response leading to increased levels of glucocorticoids, allowing the organism to adapt to environmental changes and maintain homeostasis. Glucocorticoids have a broad effect in the body, modifying the activity of the immune system, metabolism, and behavior through the activation of receptors in the limbic system. Chronic exposition to stressors operates as a risk factor for psychiatric diseases such as depression and posttraumatic stress disorder. Among the cellular alterations observed as a consequence of environmental stress, alterations to organelle function at the level of mitochondria and endoplasmic reticulum (ER) are emerging as possible factors contributing to neuronal dysfunction. ER proteostasis alterations elicit the unfolded protein response (UPR), a conserved signaling network that re-establish protein homeostasis. In addition, in the context of brain function, the UPR has been associated to neurodevelopment, synaptic plasticity and neuronal connectivity. Recent studies suggest a role of the UPR in the adaptive behavior to stress, suggesting a mechanistic link between environmental and cellular stress. Here, we revise recent evidence supporting an evolutionary connection between the neuroendocrine system and the UPR to modulate behavioral adaptive responses.
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Affiliation(s)
- Mei-Li Díaz-Hung
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile; Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Gabriela Martínez
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile; Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile; Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile; Center for Geroscience, Brain Health and Metabolism, Santiago, Chile; Buck Institute for Research on Aging, Novato, CA, United States.
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18
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Song D, Chen X, Xu M, Hai R, Zhou A, Tian R, Van Nostrand JD, Kempher ML, Guo J, Sun G, Zhou J. Adaptive Evolution of Sphingobium hydrophobicum C1 T in Electronic Waste Contaminated River Sediment. Front Microbiol 2019; 10:2263. [PMID: 31632374 PMCID: PMC6783567 DOI: 10.3389/fmicb.2019.02263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
Abstract
Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1T, characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1T can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1T and other Sphingobium strains, numerous C1T-unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1T. Moreover, presence of type IV secretion systems may allow strain C1T to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies.
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Affiliation(s)
- Da Song
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xingjuan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rong Hai
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, CA, United States
| | - Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Renmao Tian
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Megan L Kempher
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jun Guo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Guoping Sun
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
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19
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Lövy M, Šumbera R, Heth G, Nevo E. Presumed ecological speciation in blind mole rats: does soil type influence mate preferences? ETHOL ECOL EVOL 2019. [DOI: 10.1080/03949370.2019.1646809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Matěj Lövy
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Radim Šumbera
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Giora Heth
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
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20
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Charles ED, Muhamadali H, Goodacre R, Pittman JK. Biochemical signatures of acclimation by Chlamydomonas reinhardtii to different ionic stresses. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Touska F, Turnquist B, Vlachova V, Reeh PW, Leffler A, Zimmermann K. Heat-resistant action potentials require TTX-resistant sodium channels Na V1.8 and Na V1.9. J Gen Physiol 2018; 150:1125-1144. [PMID: 29970412 PMCID: PMC6080895 DOI: 10.1085/jgp.201711786] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 12/31/2017] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
Nociceptors prevent damage by being able to detect and transmit noxious stimuli, such as hot temperatures. Touska et al. show that the TTX-resistant NaV channels, NaV1.8 and NaV1.9, are required for heat-resistant nociceptors to encode noxious heat and that the current through NaV1.9 increases at higher temperatures. Damage-sensing nociceptors in the skin provide an indispensable protective function thanks to their specialized ability to detect and transmit hot temperatures that would block or inflict irreversible damage in other mammalian neurons. Here we show that the exceptional capacity of skin C-fiber nociceptors to encode noxiously hot temperatures depends on two tetrodotoxin (TTX)-resistant sodium channel α-subunits: NaV1.8 and NaV1.9. We demonstrate that NaV1.9, which is commonly considered an amplifier of subthreshold depolarizations at 20°C, undergoes a large gain of function when temperatures rise to the pain threshold. We also show that this gain of function renders NaV1.9 capable of generating action potentials with a clear inflection point and positive overshoot. In the skin, heat-resistant nociceptors appear as two distinct types with unique and possibly specialized features: one is blocked by TTX and relies on NaV1.9, and the second type is insensitive to TTX and composed of both NaV1.8 and NaV1.9. Independent of rapidly gated TTX-sensitive NaV channels that form the action potential at pain threshold, NaV1.8 is required in all heat-resistant nociceptors to encode temperatures higher than ∼46°C, whereas NaV1.9 is crucial for shaping the action potential upstroke and keeping the NaV1.8 voltage threshold within reach.
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Affiliation(s)
- Filip Touska
- Klinik für Anästhesiologie am Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.,Department of Cellular Neurophysiology, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Brian Turnquist
- Department of Mathematics and Computer Science, Bethel University, St. Paul, MN
| | - Viktorie Vlachova
- Department of Cellular Neurophysiology, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Peter W Reeh
- Department of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Leffler
- Klinik für Anästhesiologie und Intensivmedizin, Medizinische Hochschule Hannover, Hannover, Germany
| | - Katharina Zimmermann
- Klinik für Anästhesiologie am Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
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22
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Cardonatto MC, Melchor RN. Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers. PeerJ 2018; 6:e4787. [PMID: 29844958 PMCID: PMC5969051 DOI: 10.7717/peerj.4787] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/27/2018] [Indexed: 11/27/2022] Open
Abstract
Large cylindrical sediment-filled structures interpreted as mammal burrows occur within the loess-paleosol sequence of the late Miocene Cerro Azul Formation of central Argentina. A total of 115 burrow fills from three localities were measured. They are typically shallowly dipping, subcylindrical, unbranched structures with rounded ends and lacking enlargements. The horizontal diameter of the burrows range between 0.15 and 1.50 m, with most of the burrows in the interval of 0.39 to 0.98 m. Geometric morphometric analysis of transverse cross-sections support their distinct subcircular and elliptical (horizontally flattened) shapes. Burrow fills are typically laminated in the lower part and massive in the upper part. The laminated intervals reflect pulses of flowing water entering the abandoned burrow during moderate rains, whereas massive intervals reflect mass flow input of dense sediment-water mixtures during heavy rains that produced sheet floods. Approximately 1% of the burrows contained fragmentary, disarticulated and weathered mammal bones that were introduced in the open burrow by currents along with other sedimentary particles. Analysis of the tetrapod burrow fossil record suggests that Miocene burrows, including those studied herein, reflect a remarkable increase in the average size of the fossorial fauna. We conclude that large late Miocene mammals dug burrows essentially as a shelter against environmental extremes and to escape predation. The simple architecture of the burrows suggests that the producers essentially foraged aboveground. Several mammal groups acquired fossorial habits in response to cold and seasonally dry climatic conditions that prevailed during the late Miocene in southern South America. The considerable range of horizontal diameters of the studied burrows can be attributed to a variety of producers, including dasypodids, the notoungulate Paedotherium minor, Glyptodontidae and Proscelidodon sp.
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Affiliation(s)
- María Cristina Cardonatto
- Departamento de Geología, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Santa Rosa, La Pampa, Argentina
| | - Ricardo Néstor Melchor
- Instituto de Ciencias de la Tierra y Ambientales de La Pampa, Universidad Nacional de La Pampa and Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Rosa, La Pampa, Argentina
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23
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Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High- Altitude Stresses in Tibet. Sci Rep 2018; 8:4671. [PMID: 29549310 PMCID: PMC5856782 DOI: 10.1038/s41598-018-22483-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/30/2018] [Indexed: 11/20/2022] Open
Abstract
Animals living at high altitudes have evolved distinct phenotypic and genotypic adaptations against stressful environments. We studied the adaptive patterns of altitudinal stresses on transcriptome turnover in subterranean plateau zokors (Myospalax baileyi) in the high-altitude Qinghai-Tibetan Plateau. Transcriptomes of zokors from three populations with distinct altitudes and ecologies (Low: 2846 m, Middle: 3282 m, High: 3,714 m) were sequenced and compared. Phylogenetic and principal component analyses classified them into three divergent altitudinal population clusters. Genetic polymorphisms showed that the population at H, approaching the uppermost species boundary, harbors the highest genetic polymorphism. Moreover, 1056 highly up-regulated UniGenes were identified from M to H. Gene ontologies reveal genes like EPAS1 and COX1 were overexpressed under hypoxia conditions. EPAS1, EGLN1, and COX1 were convergent in high-altitude adaptation against stresses in other species. The fixation indices (FST and GST)-based outlier analysis identified 191 and 211 genes, highly differentiated among L, M, and H. We observed adaptive transcriptome changes in Myospalax baileyi, across a few hundred meters, near the uppermost species boundary, regardless of their relatively stable underground burrows’ microclimate. The highly variant genes identified in Myospalax were involved in hypoxia tolerance, hypercapnia tolerance, ATP-pathway energetics, and temperature changes.
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24
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Wieczynski DJ, Turner PE, Vasseur DA. Temporally Autocorrelated Environmental Fluctuations Inhibit the Evolution of Stress Tolerance. Am Nat 2018; 191:E195-E207. [PMID: 29750560 DOI: 10.1086/697200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
As global environmental conditions continue to change at an unprecedented rate, many species will experience increases in natural and anthropogenic stress. Generally speaking, selection is expected to favor adaptations that reduce the negative impact of environmental stress (i.e., stress tolerance). However, natural environmental variables typically fluctuate, exhibiting various degrees of temporal autocorrelation, known as environmental colors, which may complicate evolutionary responses to stress. Here we combine experiments and theory to show that temporal environmental autocorrelation can determine long-term evolutionary responses to stress without affecting the total amount of stress experienced over time. Experimental evolution of RNA virus lineages in differing environmental autocorrelation treatments agreed closely with predictions from our theoretical models that stress tolerance is favored in less autocorrelated (whiter) environments but disfavored in more autocorrelated (redder) environments. This is explained by an interaction between environmental autocorrelation and a phenotypic trade-off between stress tolerance and reproductive ability. The degree to which environmental autocorrelation influences evolutionary trajectories depends on the shape of this trade-off as well as the relative level of tolerance exhibited by novel mutants. These results suggest that long-term evolutionary dynamics depend not only on the overall strength of selection but also on the way that selection is distributed over time.
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25
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Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
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26
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An ZF, Zhao K, Wei LN, Wang ZJ, Li SH, Wei L, Wei DB. p53 gene cloning and response to hypoxia in the plateau zokor, Myospalax baileyi. ANIM BIOL 2018. [DOI: 10.1163/15707563-18000004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The plateau zokor (Myospalax baileyi) is a specialized subterranean rodent that lives on the Qinghai-Tibet Plateau. The species has evolved a series of strategies to adapt to its hypoxic environment and hypercapnia. p53 is a tumour suppressor gene that plays a crucial role in the cellular response to hypoxia by inducing cell cycle arrest, cell apoptosis, DNA damage repair and angiogenesis. To investigate the sequence characteristics of p53 and the response to hypoxia in plateau zokor, we cloned the p53 coding DNA sequence, analysed it, and measured the expression level of p53 at different altitudes in plateau zokor and rats. Our results show that the coding DNA sequence is 1179 bp, consisting of 392 amino acid residues. Compared to human p53, the subterranean rodents have two mutation sites in common with the human hotspots in the DNA-binding domain. Compared to subterranean rodents, plateau zokor have a mutation at residue 309. In addition, subterranean rodents have two convergent sites at residues 78 and 84. The expression levels of p53 in plateau zokor tissues increase significantly from 2260 m to 3300 m, but there was no significant difference in rats at those altitudes. Our results suggest that subterranean rodents have two mutation sites in common with the human hotspots in the DNA-binding domain, the mutation of Gly309Asp is a unique mutation site of plateau zokor p53, and there are two convergent sites enhancing subterranean rodent adaptation to hypoxic conditions. In addition, p53 is sensitive to the oxygen concentration in plateau zokor, and hypoxia upregulates the levels of p53. Generally, plateau zokor use this strategy to adapt to a hypoxic environment.
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Affiliation(s)
- Zhi-fang An
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
- 2Research Center for High Altitude Medicine, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
| | - Kang Zhao
- 3College of Medical, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
| | - Lin-na Wei
- 4College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
| | - Zhi-jie Wang
- 4College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
| | - Su-hua Li
- 2Research Center for High Altitude Medicine, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
| | - Lian Wei
- 4College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
| | - Deng-bang Wei
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
- 4College of Eco-Environmental Engineering, Qinghai University, 251 Ningda Road, Xining, Qinghai 810016, China
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Raghuram GV, Gupta D, Subramaniam S, Gaikwad A, Khare NK, Nobre M, Nair NK, Mittra I. Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries. BMC Mol Biol 2017; 18:21. [PMID: 28793862 PMCID: PMC5550992 DOI: 10.1186/s12867-017-0098-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022] Open
Abstract
Background We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA. Results To test this hypothesis, we generated small DNA fragments by sonicating high molecular weight DNA (HMW DNA) to mimic circulating cfDNA. Sonication of HMW DNA isolated from cancerous and non-cancerous human cells, bacteria and plant generated fragments 300–3000 bp in size which are similar to that reported for circulating cfDNA. We show here that while HMW DNAs were incapable of entering into cells, sonicated DNA (sDNA) from different sources could do so indiscriminately without heed to species or kingdom boundaries. Thus, sDNA from human cells and those from bacteria and plant could enter into nuclei of mouse cells and sDNA from human, bacterial and plant sources could spontaneously enter into bacteria. The intracellular sDNA associated themselves with host cell chromosomes and integrated into their genomes. Furthermore, sDNA, but not HMW DNA, from all four sources could phosphorylate H2AX and activate the pro-inflammatory transcription factor NFκB in mouse cells, indicating that sDNAs had acquired biological activities. Conclusions Our results show that small fragments of DNA from different sources can indiscriminately enter into other cells across species and kingdom boundaries to integrate into their genomes and activate biological processes. This raises the possibility that fragmented DNA that are generated following organismal cell-death may have evolutionary implications by acting as mobile genetic elements that are involved in horizontal gene transfer. Electronic supplementary material The online version of this article (doi:10.1186/s12867-017-0098-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gorantla Venkata Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Deepika Gupta
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Siddharth Subramaniam
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Ashwini Gaikwad
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen Kumar Khare
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Malcolm Nobre
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen Kumar Nair
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India.
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Angeletti D, Cimmaruta R, Sebbio C, Bellisario B, Carere C, Nascetti G. Environmental heterogeneity promotes microgeographic genetic divergence in the Mediterranean killifish Aphanius fasciatus(Cyprinodontidae). ETHOL ECOL EVOL 2017. [DOI: 10.1080/03949370.2016.1188159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Dario Angeletti
- Department of Ecological and Biological Sciences, Ichthyogenic Experimental Marine Center (CISMAR), Tuscia University, Borgo Le Saline, 01016 Tarquinia (Viterbo), Italy
| | - Roberta Cimmaruta
- Department of Ecological and Biological Sciences, Ichthyogenic Experimental Marine Center (CISMAR), Tuscia University, Borgo Le Saline, 01016 Tarquinia (Viterbo), Italy
| | - Claudia Sebbio
- Department of Ecological and Biological Sciences, Ichthyogenic Experimental Marine Center (CISMAR), Tuscia University, Borgo Le Saline, 01016 Tarquinia (Viterbo), Italy
- Department of Monitoring of Environmental Quality, Italian National Institute for Environmental Protection and Research (ISPRA), Via di Castel Romano 100, 00128 Rome, Italy
| | - Bruno Bellisario
- Department of Ecological and Biological Sciences, Ichthyogenic Experimental Marine Center (CISMAR), Tuscia University, Borgo Le Saline, 01016 Tarquinia (Viterbo), Italy
| | - Claudio Carere
- Department of Ecological and Biological Sciences, Ichthyogenic Experimental Marine Center (CISMAR), Tuscia University, Borgo Le Saline, 01016 Tarquinia (Viterbo), Italy
- Laboratory of Experimental and Comparative Ethology, University of Paris 13, Sorbonne Paris Cité, Paris, France
| | - Giuseppe Nascetti
- Department of Ecological and Biological Sciences, Ichthyogenic Experimental Marine Center (CISMAR), Tuscia University, Borgo Le Saline, 01016 Tarquinia (Viterbo), Italy
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Maor-Landaw K, Waldman Ben-Asher H, Karako-Lampert S, Salmon-Divon M, Prada F, Caroselli E, Goffredo S, Falini G, Dubinsky Z, Levy O. Mediterranean versus Red sea corals facing climate change, a transcriptome analysis. Sci Rep 2017; 7:42405. [PMID: 28181588 PMCID: PMC5299404 DOI: 10.1038/srep42405] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/09/2017] [Indexed: 01/08/2023] Open
Abstract
The anthropogenic increase in atmospheric CO2 that drives global warming and ocean acidification raises serious concerns regarding the future of corals, the main carbonate biomineralizers. Here we used transcriptome analysis to study the effect of long-term gradual temperature increase (annual rate), combined with lowered pH values, on a sub-tropical Red Sea coral, Stylophora pistillata, and on a temperate Mediterranean symbiotic coral Balanophyllia europaea. The gene expression profiles revealed a strong effect of both temperature increase and pH decrease implying for synergism response. The temperate coral, exposed to a twice as high range of seasonal temperature fluctuations than the Red Sea species, faced stress more effectively. The compensatory strategy for coping apparently involves deviating cellular resources into a massive up-regulation of genes in general, and specifically of genes involved in the generation of metabolic energy. Our results imply that sub-lethal, prolonged exposure to stress can stimulate evolutionary increase in stress resilience.
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Affiliation(s)
- Keren Maor-Landaw
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Sarit Karako-Lampert
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | | | - Fiorella Prada
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, Section of Biology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Erik Caroselli
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, Section of Biology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Stefano Goffredo
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, Section of Biology, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Giuseppe Falini
- Dipartimento di Chimica 'G. Ciamician', Alma Mater Studiorum Università di Bologna, Bologna, Italy
| | - Zvy Dubinsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
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Perl T, Kis-Papo T, Nevo E. Fungal biodiversity in the hypersaline Dead Sea: extinction and evolution. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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Marcy AE, Hadly EA, Sherratt E, Garland K, Weisbecker V. Getting a head in hard soils: Convergent skull evolution and divergent allometric patterns explain shape variation in a highly diverse genus of pocket gophers (Thomomys). BMC Evol Biol 2016; 16:207. [PMID: 27724858 PMCID: PMC5057207 DOI: 10.1186/s12862-016-0782-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/30/2016] [Indexed: 01/11/2023] Open
Abstract
Background High morphological diversity can occur in closely related animals when selection favors morphologies that are subject to intrinsic biological constraints. A good example is subterranean rodents of the genus Thomomys, one of the most taxonomically and morphologically diverse mammalian genera. Highly procumbent, tooth-digging rodent skull shapes are often geometric consequences of increased body size. Indeed, larger-bodied Thomomys species tend to inhabit harder soils. We used geometric morphometric analyses to investigate the interplay between soil hardness (the main extrinsic selection pressure on fossorial mammals) and allometry (i.e. shape change due to size change; generally considered the main intrinsic factor) on crania and humeri in this fast-evolving mammalian clade. Results Larger Thomomys species/subspecies tend to have more procumbent cranial shapes with some exceptions, including a small-bodied species inhabiting hard soils. Counter to earlier suggestions, cranial shape within Thomomys does not follow a genus-wide allometric pattern as even regional subpopulations differ in allometric slopes. In contrast, humeral shape varies less with body size and with soil hardness. Soft-soil taxa have larger humeral muscle attachment sites but retain an orthodont (non-procumbent) cranial morphology. In intermediate soils, two pairs of sister taxa diverge through differential modifications on either the humerus or the cranium. In the hardest soils, both humeral and cranial morphology are derived through large muscle attachment sites and a high degree of procumbency. Conclusions Our results show that conflict between morphological function and intrinsic allometric patterning can quickly and differentially alter the rodent skeleton, especially the skull. In addition, we found a new case of convergent evolution of incisor procumbency among large-, medium-, and small-sized species inhabiting hard soils. This occurs through different combinations of allometric and non-allometric changes, contributing to shape diversity within the genus. The strong influence of allometry on cranial shape appears to confirm suggestions that developmental change underlies mammalian cranial shape divergences, but this requires confirmation from ontogenetic studies. Our findings illustrate how a variety of intrinsic processes, resulting in species-level convergence, could sustain a genus-level range across a variety of extrinsic environments. This might represent a mechanism for observations of genus-level niche conservation despite species extinctions in mammals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0782-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ariel E Marcy
- School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. .,Department of Biology, Stanford University, Stanford, 94305-5020, CA, USA.
| | - Elizabeth A Hadly
- Department of Biology, Stanford University, Stanford, 94305-5020, CA, USA
| | - Emma Sherratt
- Department of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Kathleen Garland
- School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Vera Weisbecker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
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Li J, Xu H, Song Y, Tang L, Gong Y, Yu R, Shen L, Wu X, Liu Y, Zeng W. Geography Plays a More Important Role than Soil Composition on Structuring Genetic Variation of Pseudometallophyte Commelina communis. FRONTIERS IN PLANT SCIENCE 2016; 7:1085. [PMID: 27499758 PMCID: PMC4956667 DOI: 10.3389/fpls.2016.01085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/11/2016] [Indexed: 05/14/2023]
Abstract
Pseudometallophytes are excellent models to study microevolution and local adaptation to soil pollution, as they can grow both on metalliferous and contrasting non-metalliferous soils. Although, there has been accumulating evidence for the effects of edaphic conditions and geographical isolation on the genetic structure of pesudometallophytes, it is still a difficult problem in evolutionary biology to assess their relative importance. In this study, we investigated the spatial patterns of genetic variability, population differentiation and genetic groups in pseudometallophyte Commelina communis with 12 microsatellite loci. Eight metallicolous and six non-metallicolous populations of C. communis were sampled from cupriferous sites and surrounding non-contaminated areas in China. Neither significant reduction in genetic diversity nor apparent founder and bottleneck effects were observed in metallicolous populations of C. communis. Based on Bayesian and Neighbor-Joining clustering analyses and a principal coordinates analysis, all sampled populations were found to be mainly separated into three genetic groups, corresponding well to their geographical locations rather than edaphic origins. Moreover, a significant and strong correlation between population genetic divergence and geographical distance were detected by Mantel test (r = 0.33; P < 0.05) and multiple matrix regression with randomization (MMRR; βD = 0.57, P < 0.01). However, the effect of copper concentration on genetic patterns of C. communis was not significant (MMRR; βE = -0.17, P = 0.12). Our study clearly demonstrated that the extreme edaphic conditions in metalliferous areas had limited effects on the genetic variability in C. communis. Geographic distance played a more important role in affecting the genetic structure of C. communis than soil composition did. In C. communis, the geographically disjunctive populations on metalliferous soils had multiple origins and evolved independently from nearby non-metallicolous populations.
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Affiliation(s)
- Jiaokun Li
- School of Metallurgy and Environment, Central South University, ChangshaChina
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Hui Xu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Yunpeng Song
- College of Life Sciences, Central China Normal University, WuhanChina
| | - Lulu Tang
- School of Life Sciences, Central South University, ChangshaChina
| | - Yanbing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, WuhanChina
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
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Kelley JL, Arias-Rodriguez L, Patacsil Martin D, Yee MC, Bustamante CD, Tobler M. Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments. Mol Biol Evol 2016; 33:1419-34. [PMID: 26861137 PMCID: PMC4868117 DOI: 10.1093/molbev/msw020] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments.
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Affiliation(s)
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | | | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA
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Buse J, Fassbender S, Entling MH, Pavlicek T. Microclimatic Divergence in a Mediterranean Canyon Affects Richness, Composition, and Body Size in Saproxylic Beetle Assemblages. PLoS One 2015; 10:e0129323. [PMID: 26047491 PMCID: PMC4457890 DOI: 10.1371/journal.pone.0129323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/07/2015] [Indexed: 11/18/2022] Open
Abstract
Large valleys with opposing slopes may act as a model system with which the effects of strong climatic gradients on biodiversity can be evaluated. The advantage of such comparisons is that the impact of a change of climate can be studied on the same species pool without the need to consider regional differences. The aim of this study was to compare the assemblage of saproxylic beetles on such opposing slopes at Lower Nahal Oren, Mt. Carmel, Israel (also known as "Evolution Canyon") with a 200-800% higher solar radiation on the south-facing (SFS) compared to the north-facing slope (NFS). We tested specific hypotheses of species richness patterns, assemblage structure, and body size resulting from interslope differences in microclimate. Fifteen flight-interception traps per slope were distributed over three elevation levels ranging from 50 to 100 m a.s.l. Richness of saproxylic beetles was on average 34% higher on the SFS compared with the NFS, with no detected influence of elevation levels. Both assemblage structure and average body size were determined by slope aspect, with more small-bodied beetles found on the SFS. Both the increase in species richness and the higher prevalence of small species on the SFS reflect ecological rules present on larger spatial grain (species-energy hypothesis and community body size shift hypothesis), and both can be explained by the metabolic theory of ecology. This is encouraging for the complementary use of micro- and macroclimatic gradients to study impacts of climate warming on biodiversity.
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Affiliation(s)
- Jörn Buse
- University Koblenz-Landau, Institute for Environmental Sciences, Ecosystem Analysis, Fortstrasse 7, Landau, Germany
| | - Samuel Fassbender
- University Koblenz-Landau, Institute for Environmental Sciences, Ecosystem Analysis, Fortstrasse 7, Landau, Germany
| | - Martin H. Entling
- University Koblenz-Landau, Institute for Environmental Sciences, Ecosystem Analysis, Fortstrasse 7, Landau, Germany
| | - Tomas Pavlicek
- University of Haifa, Institute of Evolution, Mt. Carmel, Haifa, Israel
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p53 gene discriminates two ecologically divergent sister species of pine voles. Heredity (Edinb) 2015; 115:444-51. [PMID: 25990877 DOI: 10.1038/hdy.2015.44] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/10/2015] [Accepted: 03/24/2015] [Indexed: 12/11/2022] Open
Abstract
Genes with relevant roles in the differentiation of closely-related species are likely to have diverged simultaneously with the species and more accurately reproduce the species tree. The Lusitanian (Microtus lusitanicus) and Mediterranean (M. duodecimcostatus) pine voles are two recently separated sister species with fossorial lifestyles whose different ecological, physiological and morphological phenotypes reflect the better adaptation of M. duodecimcostatus to the underground habitat. Here we asked whether the differentiation of M. lusitanicus and M. duodecimcostatus involved genetic variations within the tumour suppressor p53 gene, given its role in stress-associated responses. We performed a population-genetic analysis through sequencing of exons and introns of p53 in individuals from sympatric and allopatric populations of both the species in the Iberian Peninsula in which a unidirectional introgression of mitochondrial DNA was previously observed. We were able to discriminate the two species to a large extent. We show that M. duodecimcostatus is composed of one genetically unstructured group of populations sharing a P53 protein that carries a mutation in the DNA-binding region not observed in M. lusitanicus, raising the possibility that this mutation may have been central in the evolutionary history of M. duodecimcostatus. Our results provide suggestive evidence for the involvement of a master transcription factor in the separation of M. lusitanicus and M. duodecimcostatus during Microtus radiation in the Quaternary presumably via a differential adaptive role of the novel p53 in M. duodecimcostatus.
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Osundeko O, Dean AP, Davies H, Pittman JK. Acclimation of Microalgae to Wastewater Environments Involves Increased Oxidative Stress Tolerance Activity. ACTA ACUST UNITED AC 2014; 55:1848-57. [DOI: 10.1093/pcp/pcu113] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Prado FE, Fernández-Turiel JL, Tsarouchi M, Psaras GK, González JA. Variation of Seed Mineral Concentrations in Seven Quinoa Cultivars Grown in Two Agroecological Sites. Cereal Chem 2014. [DOI: 10.1094/cchem-08-13-0157-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fernando E. Prado
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Naturales e IML, Universidad Nacional de Tucumán. Miguel Lillo 205, CP 4000 San Miguel de Tucumán-Argentina
- Corresponding author. Phone: +54-381-4239456. Fax: +54-381-4330633
| | | | - Martha Tsarouchi
- Section of Plant Biology, Department of Biology, University of Patras, GR 26500, Patras, Greece
| | - George K. Psaras
- Section of Plant Biology, Department of Biology, University of Patras, GR 26500, Patras, Greece
| | - Juan A. González
- Laboratorio de Ecología, Fundación Miguel Lillo. Miguel Lillo 251, CP 4000 San Miguel de Tucumán, Argentina
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Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat Commun 2014; 5:3966. [DOI: 10.1038/ncomms4966] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 04/28/2014] [Indexed: 12/20/2022] Open
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Nevo E. Evolution in action: adaptation and incipient sympatric speciation with gene flow across life at “Evolution Canyon”, Israel. Isr J Ecol Evol 2014. [DOI: 10.1080/15659801.2014.986879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Various major evolutionary problems are still open, controversial or unsettled. These include even the basic evolutionary processes of adaptation and speciation. The “Evolution Canyon” model is a microscale natural laboratory that can highlight some of the basic problems requiring clarification (Nevo list of “Evolution Canyon” publications at http://evolution.haifa.ac.il). This is especially true if an interdisciplinary approach is practiced including ecological functional genomics, transcriptomics, proteomics, metabolomics and phenomics. Here I overview and reanalyze the incipient sympatric adaptive ecological speciation of five model organisms at “Evolution Canyon”, across life: the soil bacterium, Bacillus simplex; wild barley, the progenitor of cultivated barley, Hordeum spontaneum; the tiny beetle Oryzaephilus surinamensis; the cosmopolitan fruit-fly, Drosophila melanogaster, and the Africa-originated spiny mouse, Acomys cahirinus. All five models of organisms display evolution in action of microclimatic adaptation and incipient sympatric adaptive ecological speciation on the tropical and temperate abutting slopes, separated on average by only 250 meters. Some distant species converge in their micro-climatic adaptations to the hot and dry “African”, south-facing slope (SFS or AS) and to the cool and humid “European”, north-facing slope (NSF or ES). Natural selection overrules ongoing inter-slope gene-flow between the free interbreeding populations within and between slopes, and leads to adaptive incipient sympatric ecological speciation on the dramatically opposite abutting xeric savannoid and mesic forested slopes.
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Shen Y, Lansky E, Traber M, Nevo E. Increases in both acute and chronic temperature potentiate tocotrienol concentrations in wild barley at 'Evolution Canyon'. Chem Biodivers 2014; 10:1696-705. [PMID: 24078602 DOI: 10.1002/cbdv.201300133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Indexed: 12/16/2022]
Abstract
Biosynthesis of tocols (vitamin E isoforms) is linked to response to temperature in plants. 'Evolution Canyon', an ecogeographical microcosm extending over an average of 200 meters (range 100-400) wide area in the Carmel Mountains of northern Israel, has been suggested as a model for studying global warming. Both domestic (Hordeum vulgare) and wild (Hordeum spontaneum) barley compared with wheat, oat, corn, rice, and rye show high tocotrienol/tocopherol ratios. Therefore, we hypothesized that tocol distribution might change in response to global warming. α-, β-, γ-, and δ-tocopherol, and α-, β-, γ-, and δ-tocotrienol concentrations were measured in wild barley (H. spontaneum) seeds harvested from the xeric (African) and mesic (European) slopes of Evolution Canyon over a six-year period from 2005-2011. Additionally, we examined seeds from areas contiguous to and distant from the part of the Canyon severely burned during the Carmel Fire of December 2010. Increased α-tocotrienol (p<0.01) was correlated with 1) temperature increases, 2) to the hotter 'African' slope in contrast to the cooler 'European' slope, and 3) to propinquity to the fire. The study illustrates the role of α-tocotrienol in both chronic and acute temperature adaptation in wild barley and suggests future research into thermoregulatory mechanisms in plants.
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Affiliation(s)
- Yu Shen
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel, (phone: +972 4 8240448).
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Marco-Jiménez F, Naturil-Alfonso C, Jiménez-Trigos E, García-Diego F, Lavara R, Vicente JS. Foetal and postnatal exposure to high temperatures alter growth pattern but do not modify reproductive function in male rabbits. Int J Hyperthermia 2014; 30:86-95. [DOI: 10.3109/02656736.2013.878042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Ren J, Chen L, Sun D, You FM, Wang J, Peng Y, Nevo E, Beiles A, Sun D, Luo MC, Peng J. SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors. BMC Evol Biol 2013; 13:169. [PMID: 23937410 PMCID: PMC3751623 DOI: 10.1186/1471-2148-13-169] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 08/02/2013] [Indexed: 11/10/2022] Open
Abstract
Background Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers. Results In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a FST-outlier method. Significant correlations between loci and ecogeographical factors were observed. Conclusions Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors.
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Affiliation(s)
- Jing Ren
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
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Westberg E, Ohali S, Shevelevich A, Fine P, Barazani O. Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient. Ecol Evol 2013; 3:2471-84. [PMID: 24567822 PMCID: PMC3930051 DOI: 10.1002/ece3.646] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 02/01/2023] Open
Abstract
In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common-garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common-garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net-house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations. This article describes the use of several types of data to estimate the influence of the environment on intraspecific genetic variation in populations originating from a steep climatic gradient. In addition to molecular marker data, we made use of phenotypic evaluation from common garden experiments, and a broad GIS based environmental data with edaphic information gathered in the field. This study, among others, lead to the identification of an outlier locus with an association to trichome formation and herbivore defense, and its ecological adaptive value is discussed.
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Affiliation(s)
- Erik Westberg
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität MainzD-55099, Mainz, Germany
| | - Shachar Ohali
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
| | - Anatoly Shevelevich
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem76100, Rehovot, Israel
| | - Pinchas Fine
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization50250, Bet Dagan, Israel
| | - Oz Barazani
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization50250, Bet Dagan, Israel
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Nevo E. Stress, adaptation, and speciation in the evolution of the blind mole rat, Spalax, in Israel. Mol Phylogenet Evol 2012; 66:515-25. [PMID: 23032572 DOI: 10.1016/j.ympev.2012.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 09/06/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
Abstract
Environmental stress played a major role in the evolution of the blind mole rat superspecies Spalax ehrenbergi, affecting its adaptive evolution and ecological speciation underground. Spalax is safeguarded all of its life underground from aboveground climatic fluctuations and predators. However, it encounters multiple stresses in its underground burrows including darkness, energetics, hypoxia, hypercapnia, food scarcity, and pathogenicity. Consequently, it evolved adaptive genomic, proteomic, and phenomic complexes to cope with those stresses. Here I describe some of these adaptive complexes, and their theoretical and applied perspectives. Spalax mosaic molecular and organismal evolution involves reductions or regressions coupled with expansions or progressions caused by evolutionary tinkering and natural genetic engineering. Speciation of Spalax in Israel occurred in the Pleistocene, during the last 2.00-2.35 Mya, generating four species associated intimately with four climatic regimes with increasing aridity stress southwards and eastwards representing an ecological speciational adaptive trend: (Spalax golani, 2n=54→S. galili, 2n=52→S. carmeli, 2n=58→S. judaei, 2n=60). Darwinian ecological speciation occurred gradually with relatively little genetic change by Robertsonian chromosomal and genic mutations. Spalax genome sequencing has just been completed. It involves multiple adaptive complexes to life underground and is an evolutionary model to a few hundred underground mammals. It involves great promise in the future for medicine, space flight, and deep-sea diving.
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Affiliation(s)
- Eviatar Nevo
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 31905, Israel.
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Ma X, Sela H, Jiao G, Li C, Wang A, Pourkheirandish M, Weiner D, Sakuma S, Krugman T, Nevo E, Komatsuda T, Korol A, Chen G. Population-genetic analysis of HvABCG31 promoter sequence in wild barley (Hordeum vulgare ssp. spontaneum). BMC Evol Biol 2012; 12:188. [PMID: 23006777 PMCID: PMC3544613 DOI: 10.1186/1471-2148-12-188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 09/18/2012] [Indexed: 01/31/2023] Open
Abstract
Background The cuticle is an important adaptive structure whose origin played a crucial role in the transition of plants from aqueous to terrestrial conditions. HvABCG31/Eibi1 is an ABCG transporter gene, involved in cuticle formation that was recently identified in wild barley (Hordeum vulgare ssp. spontaneum). To study the genetic variation of HvABCG31 in different habitats, its 2 kb promoter region was sequenced from 112 wild barley accessions collected from five natural populations from southern and northern Israel. The sites included three mesic and two xeric habitats, and differed in annual rainfall, soil type, and soil water capacity. Results Phylogenetic analysis of the aligned HvABCG31 promoter sequences clustered the majority of accessions (69 out of 71) from the three northern mesic populations into one cluster, while all 21 accessions from the Dead Sea area, a xeric southern population, and two isolated accessions (one from a xeric population at Mitzpe Ramon and one from the xeric ‘African Slope’ of “Evolution Canyon”) formed the second cluster. The southern arid populations included six haplotypes, but they differed from the consensus sequence at a large number of positions, while the northern mesic populations included 15 haplotypes that were, on average, more similar to the consensus sequence. Most of the haplotypes (20 of 22) were unique to a population. Interestingly, higher genetic variation occurred within populations (54.2%) than among populations (45.8%). Analysis of the promoter region detected a large number of transcription factor binding sites: 121–128 and 121–134 sites in the two southern arid populations, and 123–128,125–128, and 123–125 sites in the three northern mesic populations. Three types of TFBSs were significantly enriched: those related to GA (gibberellin), Dof (DNA binding with one finger), and light. Conclusions Drought stress and adaptive natural selection may have been important determinants in the observed sequence variation of HvABCG31 promoter. Abiotic stresses may be involved in the HvABCG31 gene transcription regulations, generating more protective cuticles in plants under stresses.
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Affiliation(s)
- Xiaoying Ma
- Extreme Stress Resistance and Biotechnology Laboratory, Cold and Arid Regions Environmental and Engineering Institute, Chinese Academy of Sciences, Lanzhou 730000, China
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Coelho SM, Simon N, Ahmed S, Cock JM, Partensky F. Ecological and evolutionary genomics of marine photosynthetic organisms. Mol Ecol 2012; 22:867-907. [PMID: 22989289 DOI: 10.1111/mec.12000] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/10/2012] [Accepted: 07/15/2012] [Indexed: 01/05/2023]
Abstract
Environmental (ecological) genomics aims to understand the genetic basis of relationships between organisms and their abiotic and biotic environments. It is a rapidly progressing field of research largely due to recent advances in the speed and volume of genomic data being produced by next generation sequencing (NGS) technologies. Building on information generated by NGS-based approaches, functional genomic methodologies are being applied to identify and characterize genes and gene systems of both environmental and evolutionary relevance. Marine photosynthetic organisms (MPOs) were poorly represented amongst the early genomic models, but this situation is changing rapidly. Here we provide an overview of the recent advances in the application of ecological genomic approaches to both prokaryotic and eukaryotic MPOs. We describe how these approaches are being used to explore the biology and ecology of marine cyanobacteria and algae, particularly with regard to their functions in a broad range of marine ecosystems. Specifically, we review the ecological and evolutionary insights gained from whole genome and transcriptome sequencing projects applied to MPOs and illustrate how their genomes are yielding information on the specific features of these organisms.
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Affiliation(s)
- Susana M Coelho
- UPMC-Université Paris 06, Station Biologique de Roscoff, Roscoff, France.
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Tavita K, Mikkel K, Tark-Dame M, Jerabek H, Teras R, Sidorenko J, Tegova R, Tover A, Dame RT, Kivisaar M. Homologous recombination is facilitated in starving populations of Pseudomonas putida by phenol stress and affected by chromosomal location of the recombination target. Mutat Res 2012; 737:12-24. [PMID: 22917545 DOI: 10.1016/j.mrfmmm.2012.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 07/18/2012] [Accepted: 07/25/2012] [Indexed: 06/01/2023]
Abstract
Homologous recombination (HR) has a major impact in bacterial evolution. Most of the knowledge about the mechanisms and control of HR in bacteria has been obtained in fast growing bacteria. However, in their natural environment bacteria frequently meet adverse conditions which restrict the growth of cells. We have constructed a test system to investigate HR between a plasmid and a chromosome in carbon-starved populations of the soil bacterium Pseudomonas putida restoring the expression of phenol monooxygenase gene pheA. Our results show that prolonged starvation of P. putida in the presence of phenol stimulates HR. The emergence of recombinants on selective plates containing phenol as an only carbon source for the growth of recombinants is facilitated by reactive oxygen species and suppressed by DNA mismatch repair enzymes. Importantly, the chromosomal location of the HR target influences the frequency and dynamics of HR events. In silico analysis of binding sites of nucleoid-associated proteins (NAPs) revealed that chromosomal DNA regions which flank the test system in bacteria exhibiting a lower HR frequency are enriched in binding sites for a subset of NAPs compared to those which express a higher frequency of HR. We hypothesize that the binding of these proteins imposes differences in local structural organization of the genome that could affect the accessibility of the chromosomal DNA to HR processes and thereby the frequency of HR.
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Affiliation(s)
- Kairi Tavita
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Tartu, Estonia
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"Evolution Canyon," a potential microscale monitor of global warming across life. Proc Natl Acad Sci U S A 2012; 109:2960-5. [PMID: 22308456 DOI: 10.1073/pnas.1120633109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Climatic change and stress is a major driving force of evolution. The effects of climate change on living organisms have been shown primarily on regional and global scales. Here I propose the "Evolution Canyon" (EC) microscale model as a potential life monitor of global warming in Israel and the rest of the world. The EC model reveals evolution in action at a microscale involving biodiversity divergence, adaptation, and incipient sympatric speciation across life from viruses and bacteria through fungi, plants, and animals. The EC consists of two abutting slopes separated, on average, by 200 m. The tropical, xeric, savannoid, "African" south-facing slope (AS = SFS) abuts the forested "European" north-facing slope (ES = NFS). The AS receives 200-800% higher solar radiation than the ES. The ES represents the south European forested maquis. The AS and ES exhibit drought and shade stress, respectively. Major adaptations on the AS are because of solar radiation, heat, and drought, whereas those on the ES relate to light stress and photosynthesis. Preliminary evidence suggests the extinction of some European species on the ES and AS. In Drosophila, a 10-fold higher migration was recorded in 2003 from the AS to ES. I advance some predictions that could be followed in diverse species in EC. The EC microclimatic model is optimal to track global warming at a microscale across life from viruses and bacteria to mammals in Israel, and in additional ECs across the planet.
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