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Thangaraj S, Liu H, Guo Y, Ding C, Kim IN, Sun J. Transitional traits determine the acclimation characteristics of the coccolithophore Chrysotila dentata to ocean warming and acidification. Environ Microbiol 2023. [PMID: 36721374 DOI: 10.1111/1462-2920.16343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/23/2023] [Indexed: 02/02/2023]
Abstract
Ocean warming and acidification interactively affect the coccolithophore physiology and drives major biogeochemical changes. While numerous studies investigated coccolithophore under short-term conditions, knowledge on how different transitional periods over long-exposure could influence the element, macromolecular and metabolic changes for its acclimation are largely unknown. We cultured the coccolithophore Chrysotila dentata, (culture generations of 1st, 10th, and 20th) under present (low-temperature low-carbon-dioxide [LTLC]) and projected (high-temperature high-carbon-dioxide [HTHC]) ocean conditions. We examined elemental and macromolecular component changes and sequenced a transcriptome. We found that with long-exposure, most physiological responses in HTHC cells decreased when compared with those in LTLC, however, HTHC cell physiology showed constant elevation between each generation. Specifically, compared to 1st generation, the 20th generation HTHC cells showed increases in quota carbon (Qc:29%), nitrogen (QN :101%), and subsequent changes in C:N-ratio (68%). We observed higher lipid accumulation than carbohydrates within HTHC cells under long-exposure, suggesting that lipids were used as an alternative energy source for cellular acclimation. Protein biosynthesis pathways increased their efficiency during long-term HTHC condition, indicating that cells produced more proteins than required to initiate acclimation. Our findings suggest that the coccolithophore resilience increased between the 1st-10th generation to initiate the acclimation process under ocean warming and acidifying conditions.
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Affiliation(s)
- Satheeswaran Thangaraj
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,Department of Marine Science, Incheon National University, Incheon, South Korea.,Department of Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai, India
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Yiyan Guo
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Changling Ding
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jun Sun
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
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2
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The genetic drivers for the successful invasive potential of a generalist bird, the House crow. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02684-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
In digital evolution, populations of computational organisms evolve via the same principles that govern natural selection in nature. These platforms have been used to great effect as a controlled system in which to conduct evolutionary experiments and develop novel evolutionary theory. In addition to their complex evolutionary dynamics, many digital evolution systems also produce rich ecological communities. As a result, digital evolution is also a powerful tool for research on eco-evolutionary dynamics. Here, we review the research to date in which digital evolution platforms have been used to address eco-evolutionary (and in some cases purely ecological) questions. This work has spanned a wide range of topics, including competition, facilitation, parasitism, predation, and macroecological scaling laws. We argue for the value of further ecological research in digital evolution systems and present some particularly promising directions for further research.
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Hu M, Chen S. Non-Target Site Mechanisms of Fungicide Resistance in Crop Pathogens: A Review. Microorganisms 2021; 9:microorganisms9030502. [PMID: 33673517 PMCID: PMC7997439 DOI: 10.3390/microorganisms9030502] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 01/15/2023] Open
Abstract
The rapid emergence of resistance in plant pathogens to the limited number of chemical classes of fungicides challenges sustainability and profitability of crop production worldwide. Understanding mechanisms underlying fungicide resistance facilitates monitoring of resistant populations at large-scale, and can guide and accelerate the development of novel fungicides. A majority of modern fungicides act to disrupt a biochemical function via binding a specific target protein in the pathway. While target-site based mechanisms such as alternation and overexpression of target genes have been commonly found to confer resistance across many fungal species, it is not uncommon to encounter resistant phenotypes without altered or overexpressed target sites. However, such non-target site mechanisms are relatively understudied, due in part to the complexity of the fungal genome network. This type of resistance can oftentimes be transient and noninheritable, further hindering research efforts. In this review, we focused on crop pathogens and summarized reported mechanisms of resistance that are otherwise related to target-sites, including increased activity of efflux pumps, metabolic circumvention, detoxification, standing genetic variations, regulation of stress response pathways, and single nucleotide polymorphisms (SNPs) or mutations. In addition, novel mechanisms of drug resistance recently characterized in human pathogens are reviewed in the context of nontarget-directed resistance.
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Affiliation(s)
- Mengjun Hu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
- Correspondence: (M.H.); (S.C.)
| | - Shuning Chen
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (M.H.); (S.C.)
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Mahtani-Williams S, Fulton W, Desvars-Larrive A, Lado S, Elbers JP, Halpern B, Herczeg D, Babocsay G, Lauš B, Nagy ZT, Jablonski D, Kukushkin O, Orozco-terWengel P, Vörös J, Burger PA. Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia. Genes (Basel) 2020; 11:genes11101218. [PMID: 33080926 PMCID: PMC7603136 DOI: 10.3390/genes11101218] [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: 08/31/2020] [Revised: 10/02/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022] Open
Abstract
Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius.
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Affiliation(s)
- Sarita Mahtani-Williams
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
- Fundación Charles Darwin, Avenida Charles Darwin s/n, Casilla 200144, Puerto Ayora EC-200350, Ecuador
| | - William Fulton
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
| | - Amelie Desvars-Larrive
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Institute of Food Safety, Food Technology and Veterinary Public Health, Vetmeduni Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
- Complexity Science Hub Vienna, Josefstädter Straße 39, A-1080 Vienna, Austria
| | - Sara Lado
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
| | - Jean Pierre Elbers
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
| | - Bálint Halpern
- MME Birdlife Hungary, Költő utca 21., H-1121 Budapest, Hungary; (B.H.); (G.B.)
| | - Dávid Herczeg
- Lendület Evolutionary Ecology Research Group, Centre for Agricultural Research, Plant Protection Institute, Herman Ottó út 15., H-1022 Budapest, Hungary;
| | - Gergely Babocsay
- MME Birdlife Hungary, Költő utca 21., H-1121 Budapest, Hungary; (B.H.); (G.B.)
- Mátra Museum of the Hungarian Natural History Museum, Kossuth Lajos utca 40., H-3200 Gyöngyös, Hungary
| | - Boris Lauš
- Association HYLA, Lipocac I., No. 7, C-10000 Zagreb, Croatia;
| | - Zoltán Tamás Nagy
- Independent Researcher, Hielscherstraße 25, D-13158 Berlin, Germany;
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, Mlynská Dolina, S-84215 Bratislava, Slovakia;
| | - Oleg Kukushkin
- Department of Biodiversity Studies and Ecological Monitoring, T. I. Vyazemsky Karadag Scientific Station–Nature Reserve–Branch of Institute of Biology of the Southern Seas of the Russian Academy of Sciences, Nauki Street 24, R-298188 Theodosia, Crimea;
- Department of Herpetology, Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, R-199034 Saint Petersburg, Russia
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
| | - Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, Baross u. 13., H-1088 Budapest, Hungary
- Molecular Taxonomy Laboratory, Hungarian Natural History Museum, Ludovika tér 2-6., H-1083 Budapest, Hungary
- Correspondence: (J.V.); (P.A.B.)
| | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Correspondence: (J.V.); (P.A.B.)
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Mathiasen P, Venegas-González A, Fresia P, Premoli AC. A relic of the past: current genetic patterns of the palaeoendemic tree Nothofagus macrocarpa were shaped by climatic oscillations in central Chile. ANNALS OF BOTANY 2020; 126:891-904. [PMID: 32578853 PMCID: PMC7539361 DOI: 10.1093/aob/mcaa111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS The Mediterranean-type forest of central Chile is considered a 'biodiversity hotspot' and a relic of a wider ancient distribution produced by past climatic oscillations. Nothofagus macrocarpa, commonly known as 'roble de Santiago', is a threatened palaeoendemic of this forest, poorly represented in the protected area system. This tree has been repeatedly misidentified as the sister species N. obliqua, which has affected its recognition and protection. Only a few populations of N. macrocarpa remain within a matrix of intensive land use that has been affected by recent forest fires. We tested the hypothesis that current populations of N. macrocarpa are a relic state of a previously widespread range, with the aim of contributing to its identification, its biogeographical history and the design of conservation measures using genetic information. METHODS We analysed remnant N. macrocarpa forests using nuclear (nDNA) and chloroplast DNA (cpDNA) sequences, conducted phylogenetic and phylogeographical analyses to reconstruct its biogeographical history, and assessed microsatellites [simple sequence repeats (SSRs)] to determine contemporary patters of diversity within and among all remnant populations. We also examined the degree of past, current and potential future isolation of N. macrocarpa populations using ecological niche models (ENMs). KEY RESULTS The species N. macrocarpa was confirmed by nDNA sequences, as previously suggested by chromosomal analysis. Small isolated populations of N. macrocarpa exhibited moderate to high genetic diversity according to SSRs. cpDNA analysis revealed a marked past latitudinal geographical structure, whereas analysis of SSRs did not find such current structure. ENM analyses revealed local expansion-contraction of the N. macrocarpa range during warmer periods, particularly in the northern and central ranges where basal-most cpDNA haplotypes were detected, and recent expansion to the south of the distribution. CONCLUSIONS Genetic patterns confirm that N. macrocarpa is a distinct species and suggest a marked latitudinal relic structure in at least two evolutionarily significant units, despite contemporary among-population gene flow. This information must be considered when choosing individuals (seeds and/or propagules) for restoration purposes, to avoid the admixture of divergent genetic stocks.
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Affiliation(s)
- Paula Mathiasen
- Laboratorio Ecotono, Universidad Nacional del Comahue, INIBIOMA-CONICET, Bariloche, Argentina
| | - Alejandro Venegas-González
- Hémera Centro de Observación de la Tierra, Escuela de Ingeniería Forestal, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Pablo Fresia
- Unidad de Biotecnología, INIA Las Brujas, Canelones, Uruguay
- Unidad de Bioinformática, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Andrea C Premoli
- Laboratorio Ecotono, Universidad Nacional del Comahue, INIBIOMA-CONICET, Bariloche, Argentina
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Milano N, Carvalho JT, Nolfi S. Moderate Environmental Variation Across Generations Promotes the Evolution of Robust Solutions. ARTIFICIAL LIFE 2019; 24:277-295. [PMID: 30681913 DOI: 10.1162/artl_a_00274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Previous evolutionary studies demonstrated how robust solutions can be obtained by evaluating agents multiple times in variable environmental conditions. Here we demonstrate how agents evolved in environments that vary across generations outperform agents evolved in environments that remain fixed. Moreover, we demonstrate that best performance is obtained when the environment varies at a moderate rate across generations, that is, when the environment does not vary every generation but every N generations. The advantage of exposing evolving agents to environments that vary across generations at a moderate rate is due, at least in part, to the fact that this condition maximizes the retention of changes that alter the behavior of the agents, which in turn facilitates the discovery of better solutions. Finally, we demonstrate that moderate environmental variations are advantageous also from an evolutionary computation perspective, that is, from the perspective of maximizing the performance that can be achieved within a limited computational budget.
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Affiliation(s)
- Nicola Milano
- Institute of Cognitive Sciences and Technologies, National Research Council.
| | - Jônata Tyska Carvalho
- Institute of Cognitive Sciences and Technologies, National Research Council.
- Federal University of Rio Grande, Center for Computational Sciences
| | - Stefano Nolfi
- Institute of Cognitive Sciences and Technologies, National Research Council
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8
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da Silva RF, Cardozo DM, Rodrigues GOL, Souza-Araújo CND, Migita NA, Andrade LALDA, Derchain S, Yunes JA, Guimarães F. CAISMOV24, a new human low-grade serous ovarian carcinoma cell line. BMC Cancer 2017; 17:756. [PMID: 29132324 PMCID: PMC5683553 DOI: 10.1186/s12885-017-3716-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 10/30/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The spontaneous immortalization of primary malignant cells is frequently assigned to their genetic instability during in vitro culturing. In this study, the new epithelial ovarian cancer cell line CAISMOV24 was described and compared with its original low-grade serous ovarian carcinoma. METHODS The in vitro culture was established with cells isolated from ascites of a 60-year-old female patient with recurrent ovarian cancer. The CAISMOV24 line was assessed for cell growth, production of soluble biomarkers, expression of surface molecules and screened for typical mutations found in serous ovarian carcinoma. Additionally, comparative genomic hybridization was employed to compare genomic alterations between the CAISMOV24 cell line and its primary malignant cells. RESULTS CAISMOV24 has been in continuous culture for more than 30 months and more than 100 in vitro passages. The cell surface molecules EpCAM, PVR and CD73 are overexpressed on CAISMOV24 cells compared to the primary malignant cells. CAISMOV24 continues to produce CA125 and HE4 in vitro. Although the cell line had developed alongside the accumulation of genomic alterations (28 CNV in primary cells and 37 CNV in CAISMOV24), most of them were related to CNVs already present in primary malignant cells. CAISMOV24 cell line harbored KRAS mutation with wild type TP53, therefore it is characterized as low-grade serous carcinoma. CONCLUSION Our results corroborate with the idea that genomic alterations, depicted by CNVs, can be used for subtyping epithelial ovarian carcinomas. Additionally, CAISMOV24 cell line was characterized as a low-grade serous ovarian carcinoma, which still resembles its primary malignant cells.
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Affiliation(s)
| | | | - Gisele Olinto Libanio Rodrigues
- Instituto de Biologia, University of Campinas, Campinas, SP Brazil
- Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas, SP Brazil
| | | | - Natacha Azussa Migita
- Instituto de Biologia, University of Campinas, Campinas, SP Brazil
- Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas, SP Brazil
| | | | - Sophie Derchain
- Faculdade de Ciências Médicas, University of Campinas, Campinas, SP Brazil
- Women’s Hospital “Professor Doutor José Aristodemo Pinotti” – CAISM, University of Campinas, Rua Alexander Fleming 101, Campinas, SP 13083-881 Brazil
| | - José Andrés Yunes
- Faculdade de Ciências Médicas, University of Campinas, Campinas, SP Brazil
- Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas, SP Brazil
| | - Fernando Guimarães
- Faculdade de Ciências Médicas, University of Campinas, Campinas, SP Brazil
- Women’s Hospital “Professor Doutor José Aristodemo Pinotti” – CAISM, University of Campinas, Rua Alexander Fleming 101, Campinas, SP 13083-881 Brazil
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Krams I, Eichler Inwood S, Trakimas G, Krams R, Burghardt GM, Butler DM, Luoto S, Krama T. Short-term exposure to predation affects body elemental composition, climbing speed and survival ability in Drosophila melanogaster. PeerJ 2016; 4:e2314. [PMID: 27602281 PMCID: PMC4991848 DOI: 10.7717/peerj.2314] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022] Open
Abstract
Factors such as temperature, habitat, larval density, food availability and food quality substantially affect organismal development. In addition, risk of predation has a complex impact on the behavioural and morphological life history responses of prey. Responses to predation risk seem to be mediated by physiological stress, which is an adaptation for maintaining homeostasis and improving survivorship during life-threatening situations. We tested whether predator exposure during the larval phase of development has any influence on body elemental composition, energy reserves, body size, climbing speed and survival ability of adult Drosophila melanogaster. Fruit fly larvae were exposed to predation by jumping spiders (Phidippus apacheanus), and the percentage of carbon (C) and nitrogen (N) content, extracted lipids, escape response and survival were measured from predator-exposed and control adult flies. The results revealed predation as an important determinant of adult phenotype formation and survival ability. D. melanogaster reared together with spiders had a higher concentration of body N (but equal body C), a lower body mass and lipid reserves, a higher climbing speed and improved adult survival ability. The results suggest that the potential of predators to affect the development and the adult phenotype of D. melanogaster is high enough to use predators as a more natural stimulus in laboratory experiments when testing, for example, fruit fly memory and learning ability, or when comparing natural populations living under different predation pressures.
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Affiliation(s)
- Indrikis Krams
- Department of Psychology, University of Tennessee, Knoxville, United States; Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia; Department of Risk Assessment and Epidemiology, Institute of Food Safety, Animal Health and Environment BIOR, Riga, Latvia
| | - Sarah Eichler Inwood
- Bredesen Center, Energy Science and Engineering, University of Tennessee , Knoxville , United States
| | - Giedrius Trakimas
- Centre for Ecology and Environmental Research, Vilnius University, Vilnius, Lithuania; Department of Biotechnology, Daugavpils University, Daugavpils, Latvia
| | - Ronalds Krams
- Department of Biotechnology, Daugavpils University , Daugavpils , Latvia
| | - Gordon M Burghardt
- Departments of Psychology and Ecology & Evolutionary Biology, University of Tennessee , Knoxville , TN , United States
| | - David M Butler
- Department of Plant Sciences, University of Tennessee , Knoxville , United States
| | - Severi Luoto
- School of Psychology, University of Auckland, Auckland, New Zealand; English, Drama and Writing Studies, University of Auckland, Auckland, New Zealand
| | - Tatjana Krama
- Department of Plant Protection, Estonian University of Life Science , Tartu , Estonia
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10
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Gupta A, LaBar T, Miyagi M, Adami C. Evolution of Genome Size in Asexual Digital Organisms. Sci Rep 2016; 6:25786. [PMID: 27181837 PMCID: PMC4867773 DOI: 10.1038/srep25786] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in some amoebas. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as mutation rate and population size. While comparative genomics has uncovered how some of these evolutionary factors influence genome size, we still do not understand what drives genome size evolution. Specifically, it is not clear how the primordial mutational processes of base substitutions, insertions, and deletions influence genome size evolution in asexual organisms. Here, we use digital evolution to investigate genome size evolution by tracking genome edits and their fitness effects in real time. In agreement with empirical data, we find that mutation rate is inversely correlated with genome size in asexual populations. We show that at low point mutation rate, insertions are significantly more beneficial than deletions, driving genome expansion and the acquisition of phenotypic complexity. Conversely, the high mutational load experienced at high mutation rates inhibits genome growth, forcing the genomes to compress their genetic information. Our analyses suggest that the inverse relationship between mutation rate and genome size is a result of the tradeoff between evolving phenotypic innovation and limiting the mutational load.
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Affiliation(s)
- Aditi Gupta
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Thomas LaBar
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Miyagi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Christoph Adami
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824, USA.,Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
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Weigel EG, Testa ND, Peer A, Garnett SC. Context matters: sexual signaling loss in digital organisms. Ecol Evol 2015; 5:3725-36. [PMID: 26380700 PMCID: PMC4567875 DOI: 10.1002/ece3.1631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/07/2015] [Accepted: 07/13/2015] [Indexed: 11/11/2022] Open
Abstract
Sexual signals are important in attracting and choosing mates; however, these signals and their associated preferences are often costly and frequently lost. Despite the prevalence of signaling system loss in many taxa, the factors leading to signal loss remain poorly understood. Here, we test the hypothesis that complexity in signal loss scenarios is due to the context-dependent nature of the many factors affecting signal loss itself. Using the Avida digital life platform, we evolved 50 replicates of ∼250 lineages, each with a unique combination of parameters, including whether signaling is obligate or facultative; genetic linkage between signaling and receiving genes; population size; and strength of preference for signals. Each of these factors ostensibly plays a crucial role in signal loss, but was found to do so only under specific conditions. Under obligate signaling, genetic linkage, but not population size, influenced signal loss; under facultative signaling, genetic linkage does not have significant influence. Somewhat surprisingly, only a total loss of preference in the obligate signaling populations led to total signal loss, indicating that even a modest amount of preference is enough to maintain signaling systems. Strength of preference proved to be the strongest single force preventing signal loss, as it consistently overcame the potential effects of drift within our study. Our findings suggest that signaling loss is often dependent on not just preference for signals, population size, and genetic linkage, but also whether signals are required to initiate mating. These data provide an understanding of the factors (and their interactions) that may facilitate the maintenance of sexual signals.
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Affiliation(s)
- Emily G Weigel
- Department of Integrative Biology, Michigan State University 288 Farm Lane Road RM 203, East Lansing, Michigan, 48824 ; BEACON Center for the Study of Evolution in Action, Michigan State University East Lansing, Michigan, 48824
| | - Nicholas D Testa
- Department of Integrative Biology, Michigan State University 288 Farm Lane Road RM 203, East Lansing, Michigan, 48824 ; BEACON Center for the Study of Evolution in Action, Michigan State University East Lansing, Michigan, 48824
| | - Alex Peer
- Department of Computer Sciences, University of Wisconsin-Madison Madison, Wisconsin, 53706
| | - Sara C Garnett
- Department of Integrative Biology, Michigan State University 288 Farm Lane Road RM 203, East Lansing, Michigan, 48824 ; BEACON Center for the Study of Evolution in Action, Michigan State University East Lansing, Michigan, 48824
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12
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Heredity and self-organization: partners in the generation and evolution of phenotypes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015. [PMID: 25708463 DOI: 10.1016/bs.ircmb.2014.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In this review we examine the role of self-organization in the context of the evolution of morphogenesis. We provide examples to show that self-organized behavior is ubiquitous, and suggest it is a mechanism that can permit high levels of biodiversity without the invention of ever-increasing numbers of genes. We also examine the implications of self-organization for understanding the "internal descriptions" of organisms and the concept of a genotype-phenotype map.
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Lehmann KDS, Goldman BW, Dworkin I, Bryson DM, Wagner AP. From cues to signals: evolution of interspecific communication via aposematism and mimicry in a predator-prey system. PLoS One 2014; 9:e91783. [PMID: 24614755 PMCID: PMC3948874 DOI: 10.1371/journal.pone.0091783] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/14/2014] [Indexed: 11/19/2022] Open
Abstract
Current theory suggests that many signaling systems evolved from preexisting cues. In aposematic systems, prey warning signals benefit both predator and prey. When the signal is highly beneficial, a third species often evolves to mimic the toxic species, exploiting the signaling system for its own protection. We investigated the evolutionary dynamics of predator cue utilization and prey signaling in a digital predator-prey system in which prey could evolve to alter their appearance to mimic poison-free or poisonous prey. In predators, we observed rapid evolution of cue recognition (i.e. active behavioral responses) when presented with sufficiently poisonous prey. In addition, active signaling (i.e. mimicry) evolved in prey under all conditions that led to cue utilization. Thus we show that despite imperfect and dishonest signaling, given a high cost of consuming poisonous prey, complex systems of interspecific communication can evolve via predator cue recognition and prey signal manipulation. This provides evidence supporting hypotheses that cues may serve as stepping-stones in the evolution of more advanced communication and signaling systems that incorporate information about the environment.
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Affiliation(s)
- Kenna D. S. Lehmann
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - Brian W. Goldman
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - Ian Dworkin
- Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - David M. Bryson
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - Aaron P. Wagner
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
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