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De Blasio FV, Freiesleben De Blasio B. Rapid clade divergence and phyletic gradualism in an interacting particle model of sympatric speciation. Biosystems 2024; 239:105198. [PMID: 38575052 DOI: 10.1016/j.biosystems.2024.105198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
The coexistence of cladogenesis, i.e., the branching of lineages along an evolutionary tree as observed in the fossil record, and anagenesis, which is the progressive evolution within populations, lacks a clear explanation. In this study, we examine a simple model that simulates the evolutionary changes occurring within populations inhabiting the same environment in sympatry, and driven by ecological competition. Our model characterizes populations through a set of evolving morphological traits represented by mathematical points within a two-dimensional morphospace. Such points may reproduce or die due to overcrowding, implying competition in morphospace as suggested by the ecological phenomenon of character displacement. By focusing on the morphospace rather than physical space, the model effectively captures the simultaneous evolution of coexisting populations. Central to the model is the delicate balance between the range of competition and the range of reproduction within the morphospace. Interesting patterns emerge when the ratio between the competition to reproducetion ranges, referred to as CR ratio, changes from values slightly smaller to significantly larger than unity. When competition acts over short distances relative to the reproduction range (low CR), the phylogenetic tree takes on a nearly uniform appearance, gradually transforming into a more bush-like structure for slightly higher CR values. With further increases in CR, evolutionary lineages become more discernible, and the morphogenetic pattern shifts from a bush-like shape to a more tree-like arrangement and few branches for very large CRs. At specific time sections, the synthetic phylogenetic tree appears as an assembly of clusters of individuals within the morphospace. These clusters, interpretable as simulated models of species, exhibit distinct separation within the morphospace and are subject to dynamic inter-cluster repulsion. Notably, clusters tend to be resistant to change. They maintain relatively constant abundances while gradually shifting their positions within the morphospace-a phase that aligns with the concept of phyletic gradualism. However, this predictable pattern is occasionally upset by the abrupt divisions into multiple groups, interpreted as cladogenesis events. The intricacies of the splitting process are explored, revealing that in scenarios with large CR values, the splitting can emerge much more rapidly than phyletic changes. This accelerated process of splitting is initiated by one or few individuals at the fringes of a cluster, where competition is minimal. The newly generated cluster then undergoes deformation, swiftly followed by divergence and splitting (seen as branching in the synthetic phylogenetic tree), as if an inherent "repulsion" triggered the division between species. The simple rules implied in the interacting-particle model may provide insight into the coexistence of gradualism and cladogenesis along lineages, illustrating the capacity for rapid shifts during cladogenesis and the more gradual process of anagenesis.
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Affiliation(s)
- Fabio Vittorio De Blasio
- Università degli Studi di Milano-Bicocca, Department of Earth and Environmental Sciences, Milano, 20126, Italy.
| | - Birgitte Freiesleben De Blasio
- Department of Methods Development and Analytics, Norwegian Institute of Public Health, P.O.Box 222, 0213, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1122 Blindern, 0318, Oslo, Norway.
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2
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He H, Yang H, Foo R, Chan W, Zhu F, Liu Y, Zhou X, Ma L, Wang LF, Zhai W. Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto). J Genet Genomics 2023; 50:554-562. [PMID: 37182682 DOI: 10.1016/j.jgg.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the micro-evolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.
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Affiliation(s)
- Haopeng He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hechuan Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Wharton Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Yunsong Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore.
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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Brandon AA, Almeida D, Powder KE. Neural crest cells as a source of microevolutionary variation. Semin Cell Dev Biol 2023; 145:42-51. [PMID: 35718684 PMCID: PMC10482117 DOI: 10.1016/j.semcdb.2022.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 05/03/2022] [Accepted: 06/03/2022] [Indexed: 11/28/2022]
Abstract
Vertebrates have some of the most complex and diverse features in animals, from varied craniofacial morphologies to colorful pigmentation patterns and elaborate social behaviors. All of these traits have their developmental origins in a multipotent embryonic lineage of neural crest cells. This "fourth germ layer" is a vertebrate innovation and the source of a wide range of adult cell types. While others have discussed the role of neural crest cells in human disease and animal domestication, less is known about their role in contributing to adaptive changes in wild populations. Here, we review how variation in the development of neural crest cells and their derivatives generates considerable phenotypic diversity in nature. We focus on the broad span of traits under natural and sexual selection whose variation may originate in the neural crest, with emphasis on behavioral factors such as intraspecies communication that are often overlooked. In all, we encourage the integration of evolutionary ecology with developmental biology and molecular genetics to gain a more complete understanding of the role of this single cell type in trait covariation, evolutionary trajectories, and vertebrate diversity.
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Affiliation(s)
- A Allyson Brandon
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Daniela Almeida
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Kara E Powder
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
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Zhu M, Yang Y, Yang H, Zhao Z, Zhang H, Blair HT, Zheng W, Wang M, Fang C, Yu Q, Zhou H, Qi H. Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits. BMC Genomics 2023; 24:392. [PMID: 37434152 DOI: 10.1186/s12864-023-09479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. RESULTS We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. CONCLUSIONS Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.
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Affiliation(s)
- Mengting Zhu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China.
| | - Hongmei Zhang
- First Affiliated Hospital, School of Medical College, Shihezi University, Shihezi, Xinjiang, China
| | - Hugh T Blair
- Institute Veterinary, Animal & Biomedical Sciences, Massey University, Auckland, Palmerston North, New Zealand
| | - Wei Zheng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Mingyuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chenhui Fang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Huaqian Zhou
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hangdong Qi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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Oliveira-Christe R, de Carvalho GC, Wilke ABB, Marrelli MT. Assessment of wing geometric morphometrics of urban Culex quinquefasciatus (Diptera: Culicidae) populations. Acta Trop 2023:106971. [PMID: 37331646 DOI: 10.1016/j.actatropica.2023.106971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Culex quinquefasciatus is a cosmopolitan species distributed throughout tropical and subtropical areas of the world. The species is of great epidemiological importance as it is responsible for vectoring the causative agent of lymphatic filariasis and several arboviruses, including West Nile virus. Wing geometric morphometrics has been widely used to assess phenotypic variations in mosquito species. Here, we hypothesize that Cx. quinquefasciatus populations in urban parks in the city of São Paulo, Brazil, have been subjected to anthropogenic selective pressures that are responsible for driving their ecology and behavior. Mosquitoes were collected by CDC traps in five municipal parks in the city of São Paulo. Eighteen anatomical landmark coordinates on each female right wing were digitized. Canonical variate analysis, wireframe graphs, cross-validated reclassification tests and the neighbor-joining method were used to assess phenotypical dissimilarity in wing shape between populations. Centroid size was calculated to assess differences in wing size between populations, which can result from different environmental conditions during immature mosquito development. Moderately heterogeneous wing shape and wing size patterns were found in the populations analyzed, indicating that selective pressures in the urban environment are affecting the wing patterns of Cx. quinquefasciatus populations in the city of São Paulo, Brazil.
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Affiliation(s)
- Rafael Oliveira-Christe
- Institute of Tropical Medicine, University of São Paulo, Av. Dr. Eneas Carvalho de Aguiar 470, São Paulo, SP, Brazil; (R.O.C.).
| | - Gabriela Cristina de Carvalho
- Department of Epidemiology, School of Public Health, University of São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP, Brazil.
| | - André Barretto Bruno Wilke
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
| | - Mauro Toledo Marrelli
- Institute of Tropical Medicine, University of São Paulo, Av. Dr. Eneas Carvalho de Aguiar 470, São Paulo, SP, Brazil; (R.O.C.).
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Yamaoka Y, Saruuljavkhlan B, Alfaray RI, Linz B. Pathogenomics of Helicobacter pylori. Curr Top Microbiol Immunol 2023; 444:117-155. [PMID: 38231217 DOI: 10.1007/978-3-031-47331-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The human stomach bacterium Helicobacter pylori, the causative agent of gastritis, ulcers and adenocarcinoma, possesses very high genetic diversity. H. pylori has been associated with anatomically modern humans since their origins over 100,000 years ago and has co-evolved with its human host ever since. Predominantly intrafamilial and local transmission, along with genetic isolation, genetic drift, and selection have facilitated the development of distinct bacterial populations that are characteristic for large geographical areas. H. pylori utilizes a large arsenal of virulence and colonization factors to mediate the interaction with its host. Those include various adhesins, the vacuolating cytotoxin VacA, urease, serine protease HtrA, the cytotoxin-associated genes pathogenicity island (cagPAI)-encoded type-IV secretion system and its effector protein CagA, all of which contribute to disease development. While many pathogenicity-related factors are present in all strains, some belong to the auxiliary genome and are associated with specific phylogeographic populations. H. pylori is naturally competent for DNA uptake and recombination, and its genome evolution is driven by extraordinarily high recombination and mutation rates that are by far exceeding those in other bacteria. Comparative genome analyses revealed that adaptation of H. pylori to individual hosts is associated with strong selection for particular protein variants that facilitate immune evasion, especially in surface-exposed and in secreted virulence factors. Recent studies identified single-nucleotide polymorphisms (SNPs) in H. pylori that are associated with the development of severe gastric disease, including gastric cancer. Here, we review the current knowledge about the pathogenomics of H. pylori.
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Affiliation(s)
- Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, 60286, East Java, Indonesia
| | - Bodo Linz
- Division of Microbiology, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
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Fu S, Wang Q, Wang R, Zhang Y, Lan R, He F, Yang Q. Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment. Sci Total Environ 2022; 820:153286. [PMID: 35074363 DOI: 10.1016/j.scitotenv.2022.153286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Very little is known about how microbiome interactions shape the horizontal transfer of antibiotic resistance genes in aquacultural environment. To this end, we first conducted 16S rRNA gene amplicon sequencing to monitor the dynamics of bacterial community compositions in one shrimp farm from 2019 to 2020. Next, co-occurrence analysis was then conducted to reveal the interactions network between Vibrio spp. and other species. Subsequently, 21 V. parahaemolyticus isolates and 15 related bacterial species were selected for whole-genome sequencing (WGS). The 16S rDNA amplicon sequencing results identified a remarkable increase of Vibrio and Providencia in September-2019 and a significant rise of Enterobacter and Shewanella in Septtember-2020. Co-occurrence analysis revealed that Vibrio spp. positively interacted with the above species, leading to the sequencing of their isolates to further understand the sharing of the resistant genomic islands (GIs). Subsequent pan-genomic analysis of V. parahaemolyticus genomes identified 278 horizontally transferred genes in 10 GIs, most of which were associated with antibiotic resistance, virulence, and fitness of metabolism. Most of the GIs have also been identified in Providencia, and Enterobacter, suggesting that exchange of genetic traits might occur in V. parahaemolyticus and other cooperative species in a specific niche. No genetic exchange was found between the species with negative relationships. The knowledge generated from this study would greatly improve our capacity to predict and mitigate the emergence of new resistant population and provide practical guidance on the microbial management during the aquacultural activities.
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Affiliation(s)
- Songzhe Fu
- College of Marine Science and Environment, Dalian Ocean University, Dalian, China.
| | - Qingyao Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian, China; Key Laboratory of Environment Controlled Aquaculture, Dalian Ocean University, Ministry of Education, 116023 Dalian, China
| | - Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian, China; Key Laboratory of Environment Controlled Aquaculture, Dalian Ocean University, Ministry of Education, 116023 Dalian, China
| | - Yixiang Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Fenglan He
- The Collaboration Unit for Field Epidemiology of State Key Laboratory for Infectious Disease Prevention and Control, Nanchang Center for Disease Control and Prevention, Nanchang, China
| | - Qian Yang
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium.
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Zhu H, Huang ZY, Jiang S, Pan L, Xi YL. Rapid adaptation of Brachionus dorcas (Rotifera) to tetracycline antibiotic stress. Aquat Toxicol 2022; 245:106126. [PMID: 35228124 DOI: 10.1016/j.aquatox.2022.106126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 01/25/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Although natural populations can rapidly adapt to selection pressures, the fitness consequences of selection are controversial. In this study, a selection experiment was conducted with replicate populations of Brachionus dorcas that were exposed to two sublethal concentrations (26.8 and 78.3 mg/L) of oxytetracycline (OTC), followed by two common garden experiments (population growth and life table experiments). During the 102-day (approximately 36 asexual generations) selection experiment, a markedly increased growth rate but a significantly decreased mictic ratio over time in the populations exposed to OTC when compared to the control populations suggested that the former adapted to the selection pressures and that a trade-off exists between asexual and sexual reproduction. The high and stable population growth rates after 90 days of OTC selection illustrate an example of evolutionary rescue. After 102 days of selection, OTC-selected populations showed higher population growth rates than the control populations when exposed to OTC, indicating significantly increased tolerance. OTC-selected populations showed a lower average growth rate, longer average generation time and life expectancy at hatching, and higher average net reproduction rate and proportion of mictic offspring than the control populations in the absence of OTC, which indicate that OTC selection results in two fitness costs and three fitness gains and that the effect of OTC selection on fitness differs with the measured fitness variables. Both the evolutionary potential of populations under the stress of higher concentrations of OTC and the fitness costs and gains of selection in the absence of OTC indicate that past exposures to pollutants cannot be neglected when evaluating the effects of current stressors on natural populations.
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Affiliation(s)
- Han Zhu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, Anhui Province, China
| | - Zhi-Yu Huang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, Anhui Province, China
| | - Shan Jiang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, Anhui Province, China
| | - Ling Pan
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, Anhui Province, China
| | - Yi-Long Xi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, Anhui Province, China.
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de Lourdes do Carmo Guimarães Diniz J, von Groll A, Unis G, Dalla-Costa ER, Rosa Rossetti ML, Vianna JS, Ramos DF, Reis AJ, Bartolomeu Halicki PC, Rheingantz Scaini JL, Castillos de Ibrahim das Neves Y, Phelan J, Gomes AR, Campino S, Machado KDS, Werhli AV, Pain A, Clark TG, Perdigão J, Viveiros M, Portugal I, Almeida Silva PE. Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates. Tuberculosis (Edinb) 2021; 131:102137. [PMID: 34673379 DOI: 10.1016/j.tube.2021.102137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 11/21/2022]
Abstract
Treatment of drug-resistant tuberculosis requires extended use of more toxic and less effective drugs and may result in retreatment cases due to failure, abandonment or disease recurrence. It is therefore important to understand the evolutionary process of drug resistance in Mycobacterium tuberculosis. We here in describe the microevolution of drug resistance in serial isolates from six previously treated patients. Drug resistance was initially investigated through phenotypic methods, followed by genotypic approaches. The use of whole-genome sequencing allowed the identification of mutations in the katG, rpsL and rpoB genes associated with drug resistance, including the detection of rare mutations in katG and mixed populations of strains. Molecular docking simulation studies of the impact of observed mutations on isoniazid binding were also performed. Whole-genome sequencing detected 266 single nucleotide polymorphisms between two isolates obtained from one patient, suggesting a case of exogenous reinfection. In conclusion, sequencing technologies can detect rare mutations related to drug resistance, identify subpopulations of resistant strains, and identify diverse populations of strains due to exogenous reinfection, thus improving tuberculosis control by guiding early implementation of appropriate clinical and therapeutic interventions.
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Shapiro JA. Why the third way of evolution is necessary. Theor Biol Forum 2021; 114:13-26. [PMID: 36382546 DOI: 10.19272/202111402002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Third Way of Evolution was founded in 2014 to make the public aware that contemporary evolution science is not limited to the neo-Darwinian Modern Synthesis of the past century. This was important to do because evolution was challenged as incapable of explaining biological complexity by the Intelligent Design movement. Expounding biological theories like the Modern Synthesis is always subject to limited empirical evidence, fundamental concepts that inevitably change over time, and conceptual preferences that often prove to be misleading. The Modern Synthesis was based on Darwin's preference for the phyletic gradualism necessary to elevate Natural Selection as the sole force determining the direction of evolutionary change. In contradiction to this principle, agricultural crop breeding, direct observation in nature, and genomics have shown that genome change following symbiogenetic cell fusions or interspecific hybridization, not selection, are empirically the most effective methods for originating novel life forms and new species. By asserting that the accumulation of random "slight" variations was the basic mode of both short-term and long-term evolutionary change, the Modern Synthesis also ignored the distinction between (1) microevolutionary change within species by localized mutations and (2) macroevolutionary origination of new species and taxa by genome restructuring. In so doing, the Modern Synthesis failed to recognize the evolutionary importance of cellular capacities to generate large-scale genome changes. By focusing on individual protein-coding genes as the fundamental units of genetic information, the Modern Synthesis did not successfully incorporate either the full non-coding informa tion content in genomes or the major evolutionary potential of mobile DNA elements to generate multisite intragenomic networks necessary for the development of complex organisms. When all of the phenomena overlooked by the Modern Synthesis are taken into consideration, it is not difficult to answer Intelligent Design arguments and show that science is making real progress in understanding the evolution of biological complexity.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, CGIS W123B, 979 E. 57th Street, University of Chicago, Chicago 60637 IL, USA -
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11
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Yang X, Xia Z, Liao Y, Zhang D, Li H, Zheng H, Ao J, Yang R, Zhang M. Proteomic analysis of serial isolates of Trichosporon asahii identifies host-specific adaptations using the TMT/MRM approach. J Proteomics 2021; 245:104309. [PMID: 34153541 DOI: 10.1016/j.jprot.2021.104309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022]
Abstract
The opportunistic fungal pathogen Trichosporon asahii (T. asahii) is an important causal agent of mortality in immunocompromised patients and associated with frequent relapses, even with sufficient antifungal treatment. Investigating the proteomes of initial and recurrent isolates may help to identify within-host adaptive changes. In this study, using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) technology, we analyzed the proteomes of two T. asahii strains that were isolated 15 years apart from the same patient who suffered initial and recurrent episodes of systemic disseminated trichosporonosis. A total of 597 differentially expressed proteins were identified. Functional analysis showed that the increased proteins were primarily concentrated on peptide/protein/energy/drug metabolism and translation. Most of the results were determined to be consistent with the findings of phenotypic assays, such as tests for drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays. Moreover, we performed multiple reaction monitoring (MRM) mass spectrometry to verify 27 candidate proteins, and the results of this experiment were also highly consistent with the results of the TMT analysis. Therefore, to the best of our knowledge, these data provide the first molecular evidence of how the T. asahii proteome changes related to host-specific adaptation during human infection. SIGNIFICANCE: Systemic infection with Trichosporon asahii (T. asahii) has recently been recognized as an important causal agent of mortality in immunocompromised patients. Although triazole treatment usually works efficiently in the early phase of infection, many patients relapse. Hence, comparative analyses of the proteomics of initial and recurrent isolates may reveal evidence of adaptive changes within the host. Our study demonstrates that the recurrent strain has undergone proteomic changes using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Moreover, the results of phenotypic assays, including drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays, were highly consistent with the proteomic changes, and multiple reaction monitoring (MRM) verification also showed similar trends to the TMT results. In summary, our study is the first to investigate the adaptation of T. asahii under pressure from antifungal chemotherapy and host immune responses.
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Tian JY, Yang YG, Chen S, Teng Y, Li XZ. Genetic diversity and molecular epidemiology of Candida albicans from vulvovaginal candidiasis patients. Infect Genet Evol 2021; 92:104893. [PMID: 33964472 DOI: 10.1016/j.meegid.2021.104893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 04/10/2021] [Accepted: 05/03/2021] [Indexed: 01/11/2023]
Abstract
Candida albicans (C. albicans) is a common cause of vulvovaginal candidiasis (VVC). In this paper, the genetic diversity and molecular epidemiology of 173C. albicans strains were investigated by multilocus sequence typing (MLST). A total of 52 diploid sequence types (DSTs) were recognized, and 27 (51.9%) of which have not been reported in the MLST database. Genotyping was performed on the multiple isolates collected from patients with recurrent VVC (RVVC, referring to VVC which attacks more than 4 times in one year) in different acute infectious phases. The results showed that 59.1% (26/44) of the patients suffered a relapse, with DST 79 (65.4%) as the dominant genotype. The etiology of the remaining 40.9% (18/44) of patients was reinfection, and the main genotypes included DST 79 (33.3%), DST 124 (8.6%) and DST 1895 (8.6%). DST 79 (45%) and DST 1395 (7.5%) were the main isolates of VVC patients, while DST 79 (24.1%), DST 727 (6.9%), DST 732 (6.9%) and DST 1867 (6.9%) were the main types of healthy volunteers. The results of the genotypes between RVVC patients and other groups were statistically different. Furthermore, cluster analysis was carried out on 1468 isolates, among which 1337 were downloaded from the MLST database, 130 were divided into 8 Clades in the present study and the remaining one was taken as a singleton. 92.3% isolates from relapse patients, 58.3% isolates from re-infected patients, 77.5% isolates from VVC patients and 51.7% isolates from volunteers were distributed in Clade 1. The analysis of the genotypes of multiple isolates from RVVC patients further demonstrated that point mutation and loss of heterozygosity contributed to the microevolution of C. albicans.
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Chambers KR, Van de Wouw AP, Gardiner DM, Elliott CE, Idnurm A. A conserved Zn 2Cys 6 transcription factor, identified in a spontaneous mutant from in vitro passaging, is involved in pathogenicity of the blackleg fungus Leptosphaeria maculans. Fungal Biol 2021; 125:541-550. [PMID: 34140150 DOI: 10.1016/j.funbio.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022]
Abstract
Continuous passaging in vitro can lead to the accumulation of changes in DNA sequence that potentially affect the properties of microbes, making them different from the original isolates. The identification of such genetic alterations is rare in fungi. A set of insertional mutants in the plant pathogenic fungus Leptosphaeria maculans, all derived from the same transformation experiment, had independent Agrobacterium T-DNA insertions and reduced pathogenicity on canola (Brassica napus). None of the insertions co-segregated in progeny from crosses with the reduction in pathogenicity. Genome sequences of three strains were analysed, and a mutation identified in a gene (ptf1, for pathogenicity-associated transcription factor 1) encoding a putative Zn2(II)Cys6 transcription factor. Homologs are found in other ascomycetes, and are required for pathogenicity by Fusarium graminearum, Fusarium oxysporum and Magnaporthe oryzae. The mutation in the L. maculans ptf1 gene co-segregates in progeny from crosses with the reduction in pathogenicity, a strain with an independent mutant allele isolated using CRISPR-Cas9 editing has reduced pathogenicity, and addition of wild type copies of the gene restores pathogenicity. Thus, this work defines a base pair substitution that occurred during in vitro passaging of a fungus that contributed to an attenuation of pathogenicity.
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Affiliation(s)
- Kylie R Chambers
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia; Department of Primary Industries and Regional Development, Northam, WA, 6401, Australia
| | | | - Donald M Gardiner
- CSIRO Agriculture and Food, St Lucia, Brisbane, QLD, 4067, Australia
| | - Candace E Elliott
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia.
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Roy C, Mandal SM, Mondal SK, Mukherjee S, Mapder T, Ghosh W, Chakraborty R. Trends of mutation accumulation across global SARS-CoV-2 genomes: Implications for the evolution of the novel coronavirus. Genomics 2020; 112:5331-5342. [PMID: 33161087 PMCID: PMC7644180 DOI: 10.1016/j.ygeno.2020.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022]
Abstract
To understand SARS-CoV-2 microevolution, this study explored the genome-wide frequency, gene-wise distribution, and molecular nature of all point-mutations detected across its 71,703 RNA-genomes deposited in GISAID till 21 August 2020. Globally, nsp1/nsp2 and orf7a/orf3a were the most mutation-ridden non-structural and structural genes respectively. Phylogeny of 4618 spatiotemporally-representative genomes revealed that entities belonging to the early lineages are mostly spread over Asian countries, including India, whereas the recently-derived lineages are more globally distributed. Of the total 20,163 instances of polymorphism detected across global genomes, 12,594 and 7569 involved transitions and transversions, predominated by cytidine-to-uridine and guanosine-to-uridine conversions, respectively. Positive selection of nonsynonymous mutations (dN/dS >1) in most of the structural, but not the non-structural, genes indicated that SARS-CoV-2 has already harmonized its replication/transcription machineries with the host metabolism, while it is still redefining virulence/transmissibility strategies at the molecular level. Mechanistic bases and evolutionary/pathogenicity-related implications are discussed for the predominant mutation-types.
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Affiliation(s)
- Chayan Roy
- College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Suresh K Mondal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Shriparna Mukherjee
- Department of Botany, Prasannadeb Women's College, Jalpaiguri, West Bengal, India
| | - Tarunendu Mapder
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, West Bengal, India.
| | - Ranadhir Chakraborty
- Department of Biotechnology, University of North Bengal, Raja Rammohanpur, Darjeeling 734013, West Bengal, India.
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15
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Rybak AV, Belykh ES, Maystrenko TA, Shadrin DM, Pylina YI, Chadin IF, Velegzhaninov IO. Genetic analysis in earthworm population from area contaminated with radionuclides and heavy metals. Sci Total Environ 2020; 723:137920. [PMID: 32213403 DOI: 10.1016/j.scitotenv.2020.137920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/12/2020] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
This study assessed the effects of environmental contamination by naturally occurring radionuclides and heavy metals on the genetic structure of a population of the earthworm Aporrectodea caliginosa. A. caliginosa were collected from four sites and characterized by amplified fragment length polymorphism (AFLP) analyses. No differences in genetic structure and diversity were found between sites that differed greatly in soil contamination levels of radionuclides and metals. However, when the genetic structure of the A. caliginosa population was analyzed without considering information about the sampling site, a complex intraspecific genetic structure was identified. At least three highly divergent lineages were found, in unequal proportions, of each genetically isolated group from each study site. No associations were found between the distribution of the detected genetic clusters and the geographical origin of the samples. Thus, no noticeable adaptive changes or signs of directional selection were detected, despite the long history of genotoxic waste disposal at the sampling site. These results suggest a combined effect of three factors on the genetic structure and diversity of A. caliginosa in soils: the complexity of the contaminant composition, the heterogeneous spatial distribution of the pollutants, and the complexity of the intraspecific genetic structures of A. caliginosa.
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Affiliation(s)
- Anna V Rybak
- Institute of Biology of Komi Science Centre of Ural Branch of RAS, Syktyvkar 167982, Russia
| | - Elena S Belykh
- Institute of Biology of Komi Science Centre of Ural Branch of RAS, Syktyvkar 167982, Russia
| | - Tatiana A Maystrenko
- Institute of Biology of Komi Science Centre of Ural Branch of RAS, Syktyvkar 167982, Russia.
| | - Dmitry M Shadrin
- Institute of Biology of Komi Science Centre of Ural Branch of RAS, Syktyvkar 167982, Russia
| | - Yana I Pylina
- Institute of Biology of Komi Science Centre of Ural Branch of RAS, Syktyvkar 167982, Russia
| | - Ivan F Chadin
- Institute of Biology of Komi Science Centre of Ural Branch of RAS, Syktyvkar 167982, Russia.
| | - Ilya O Velegzhaninov
- Institute of Biology of Komi Science Centre of Ural Branch of RAS, Syktyvkar 167982, Russia; Polytechnical Institute of Vyatka State University, Kirov 610020, Russia.
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16
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Boyce KJ, Cao C, Xue C, Idnurm A. A spontaneous mutation in DNA polymerase POL3 during in vitro passaging causes a hypermutator phenotype in Cryptococcus species. DNA Repair (Amst) 2019; 86:102751. [PMID: 31838381 DOI: 10.1016/j.dnarep.2019.102751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/08/2019] [Accepted: 11/19/2019] [Indexed: 10/25/2022]
Abstract
Passaging of microbes in vitro can lead to the selection of microevolved derivatives with differing properties to their original parent strains. One well characterised instance is the phenotypic differences observed between the series of strains derived from the type strain of the human pathogenic fungus Cryptococcus neoformans. A second case was reported in the close relative Cryptococcus deneoformans, in which a well-studied isolate ATCC 24067 (52D) altered its phenotypic characteristics after in vitro passaging in different laboratories. One of these derivatives, ATCC 24067A, has decreased virulence and also exhibits a hypermutator phenotype, in which the mutation rate is increased compared to wild type. In this study, the molecular basis behind the changes in the lineage of ATCC 24067 was determined by next-generation sequencing of the parent and passaged strain genomes. This analysis resulted in the identification of a point mutation that causes a D270G amino acid substitution within the exonuclease proofreading domain of the DNA polymerase delta subunit encoded by POL3. Complementation with POL3 confirmed that this mutation is responsible for the hypermutator phenotype of this strain. Regeneration of the mutation in C. neoformans, to eliminate the additional mutations present in the ATCC 24067A genetic background, demonstrated that the hypermutator phenotype of the pol3D270G mutant causes rapid microevolution in vitro but does not result in decreased virulence. These findings indicate that mutator strains can emerge in these pathogenic fungi without conferring a fitness cost, but the subsequent rapid accumulation of mutations can be deleterious.
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Affiliation(s)
- Kylie J Boyce
- School of Science, Engineering and Health, RMIT University, Victoria, Australia.
| | - Chengjun Cao
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Victoria, Australia.
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17
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Duchen P, Hautphenne S, Lehmann L, Salamin N. Linking micro and macroevolution in the presence of migration. J Theor Biol 2019; 486:110087. [PMID: 31758967 DOI: 10.1016/j.jtbi.2019.110087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/06/2019] [Accepted: 11/18/2019] [Indexed: 01/26/2023]
Abstract
Understanding macroevolutionary patterns is central to evolutionary biology. This involves the process of divergence within a species, which starts at the microevolutionary level, for instance, when two subpopulations evolve towards different phenotypic optima. The speed at which these optima are reached is controlled by the degree of stabilising selection, which pushes the mean trait towards different optima in the different subpopulations, and ongoing migration that pulls the mean phenotype away from that optimum. Traditionally, macro phenotypic evolution is modelled by directional selection processes, but these models usually ignore the role of migration within species. Here, our goal is to reconcile the processes of micro and macroevolution by modelling migration as part of the speciation process. More precisely, we introduce an Ornstein-Uhlenbeck (OU) model where migration happens between two subpopulations within a branch of a phylogeny and this migration decreases over time as it happens during speciation. We then use this model to study the evolution of trait means along a phylogeny, as well as the way phenotypic disparity between species changes with successive epochs. We show that ignoring the effect of migration in sampled time-series data biases significantly the estimation of the selective forces acting upon it. We also show that migration decreases the expected phenotypic disparity between species and we analyse the effect of migration in the particular case of niche filling. We further introduce a method to jointly estimate selection and migration from time-series data. Our model extends traditional quantitative genetics results of selection and migration from a microevolutionary time frame to multiple speciation events at a macroevolutionary scale. Our results further support that not accounting for gene flow has important consequences in inferences at both the micro and macroevolutionary scale.
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Affiliation(s)
- Pablo Duchen
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
| | - Sophie Hautphenne
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia; Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Lehmann
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
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18
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Multini LC, Wilke ABB, Marrelli MT. Urbanization as a driver for temporal wing-shape variation in Anopheles cruzii (Diptera: Culicidae). Acta Trop 2019; 190:30-36. [PMID: 30359567 DOI: 10.1016/j.actatropica.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/27/2018] [Accepted: 10/18/2018] [Indexed: 12/18/2022]
Abstract
Anopheles cruzii is the main vector of human and simian malaria in the Brazilian Atlantic Forest. This biome, which is an important hotspot of malaria transmission, has suffered fragmentation and deforestation as a result of urban expansion. Fragmentation and deforestation occur continually in the south of the city of São Paulo, Brazil, and findings of An. cruzii in the peridomicile have consequently become more frequent in this part of the city. Although An. cruzii is of considerable epidemiological importance, the impact of urbanization on the microevolution of this species in this malaria-endemic region has not been investigated to date. In this study, we investigated temporal variation in wing shape and size in An. cruzii populations collected in sylvatic, peri-urban and urban areas over a three-year period. Our results show a slight but significant phenotypic variation in all three populations over the study period. Time was a more powerful driver for wing variation than geographic distance. Temporal wing-shape variation appears to be positively associated with urbanization, suggesting that anthropogenic changes in the environment may be a strong driver for wing-shape variation in An. cruzii. Further studies using genetic markers are needed to assess genetic differentiation in these populations.
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Abstract
How to define a partition of individuals into species is a long-standing question called the species problem in systematics. Here, we focus on this problem in the thought experiment where individuals reproduce clonally and both the differentiation process and the population genealogies are explicitly known. We specify three desirable properties of species partitions: (A) Heterotypy between species, (B) Homotypy within species and (M) Genealogical monophyly of each species. We then ask: How and when is it possible to delineate species in a way satisfying these properties? We point out that the three desirable properties cannot in general be satisfied simultaneously, but that any two of them can. We mathematically prove the existence of the finest partition satisfying (A) and (M) and the coarsest partition satisfying (B) and (M). For each of them, we propose a simple algorithm to build the associated phylogeny out of the genealogy. The ways we propose to phrase the species problem shed new light on the interaction between the genealogical and phylogenetic scales in modeling work. The two definitions centered on the monophyly property can readily be used at a higher taxonomic level as well, e.g., to cluster species into monophyletic genera.
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20
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Honda T, Iijima H, Tsuboi J, Uchida K. A review of urban wildlife management from the animal personality perspective: The case of urban deer. Sci Total Environ 2018; 644:576-582. [PMID: 29990907 DOI: 10.1016/j.scitotenv.2018.06.335] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
Wildlife living around urbanized areas is often a cause of crucial issues such as zoonosis and wildlife-vehicle collisions. Despite this, residents hold positive views on the presence of urban wildlife primarily due to aesthetic reasons. This accepting attitude towards our coexistence with urban wildlife has made it difficult for wildlife managers to come to a consensus concerning the importance of human-urban wildlife conflicts. Although countermeasures such as lethal force and/or fencing are commonly used to control human-wildlife conflicts, these approaches are rarely applied in the case of urban wildlife. It is essential to recognize the gap between the current state of urban wildlife management and advanced scientific knowledge of urban wildlife behavior in order to mitigate urban deer conflicts. Fortunately, behavioral ecologists have been attempting to apply the perspective of individual differences, such as animal personality, to wildlife management. Studies have shown how the personalities of wildlife contribute to their adaptation to urban habitats. In order to prevent human-urban wildlife conflicts, recognizing the personalities of wildlife and selective culling of bold individuals should be conducted for deliberate selection for shyness when developing wildlife management plans. Making wildlife shy away from humans is essential to urban wildlife management. The aim of this study is to review observed measures against human-urban wildlife conflicts in Japan and to propose a new direction for innovative and effective approaches that takes animals personality into account to mitigate urban-wildlife conflicts. For this review we will target deer as a model species because deer are among the most serious of problem-causing urban wildlife.
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Affiliation(s)
- T Honda
- Yamanashi Prefecture Agricultural Research Center, 1100 Shimoimai, Kai, Japan.
| | - H Iijima
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Japan
| | - J Tsuboi
- National Research Institute of Fisheries Science, Fisheries Research and Education Agency, 2482-3, Chugushi, Nikko, Japan
| | - K Uchida
- Graduate School of Environmental Science, Hokkaido University, N10W5 Sapporo, Hokkaido, Japan
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21
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Rybak AV, Belykh ES, Maystrenko TA, Velegzhaninov IO. Microsatellite polymorphism of Trifolium pratense population at the conditions of radioactive and chemical contamination of soil (Komi republic, Russia). Environ Sci Pollut Res Int 2018; 25:34701-34710. [PMID: 30324368 DOI: 10.1007/s11356-018-3375-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
There is no clear understanding of microevolutionary changes in natural populations of plants and animals due to anthropogenic contamination of the environment with toxicants and mutagens. But such data are necessary to forecast long-term effects of human activity. In this research, we studied genetic polymorphism in T. pratense sampled from seven sites varying in radioactive and chemical soil contamination in the vicinity of Vodny settlement (Komi, Russia). Analysis of five SSR loci was shown to be similar in a whole (N), mean (Na) and effective (Ne) numbers of alleles, heterozygosity indexes (Ho and He), and the Shannon index (I). Difference in the private allele numbers was registered: the most contaminated site has 5 and others from 0 up 2 private alleles. No difference was found in the genetic structure of T. pratense population growing at the conditions of radioactive and chemical contamination. The Bayesian analysis provided evidence of a single cluster (K = 1) due to a similar genetic structure of samples, while AMOVA results demonstrated a high variability within individuals (75%) and a low variability (1%) among groups of T. pratense from sites that differ in the contamination level. Thus, the long-term radioactive and heavy metal contamination of soil did not result in significant microevolutionary changes in T. pratense population.
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Affiliation(s)
- Anna V Rybak
- Institute of Biology of Komi Scientific Centre of Ural Branch of Russian Academy of Sciences, Kommunisticheskaya 28, Syktyvkar, Russian Federation, 167982
| | - Elena S Belykh
- Institute of Biology of Komi Scientific Centre of Ural Branch of Russian Academy of Sciences, Kommunisticheskaya 28, Syktyvkar, Russian Federation, 167982.
| | - Tatiana A Maystrenko
- Institute of Biology of Komi Scientific Centre of Ural Branch of Russian Academy of Sciences, Kommunisticheskaya 28, Syktyvkar, Russian Federation, 167982
| | - Ilya O Velegzhaninov
- Institute of Biology of Komi Scientific Centre of Ural Branch of Russian Academy of Sciences, Kommunisticheskaya 28, Syktyvkar, Russian Federation, 167982
- Polytechnical Institute of Vyatka State University, Kirov, Russian Federation
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22
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Stritzler M, Berini C, Jozefkowicz C, Soto G, Ayub N. Understanding the intracellular-to-extracellular localization switch of polyhydroxybutyrate polymerase in pseudomonas backgrounds as a microevolutionary process. J Theor Biol 2018; 456:29-33. [PMID: 30063924 DOI: 10.1016/j.jtbi.2018.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/19/2018] [Accepted: 07/27/2018] [Indexed: 11/28/2022]
Abstract
After gene duplication, paralogous genes evolve independently, and consequently, the new proteins encoded by these duplicated genes are exposed to changes in their subcellular location. Although there are increasing evidence that phylogenetically related proteins play different functions in different subcellular compartments, the number of evolutionary steps required for the emergence of a novel protein with a novel subcellular localization remains unclear. Regarding this intriguing topic, here we examine in depth our previous reports describing both intracellular and extracellular polyhydroxybutyrate polymerases (PhaC) in the Pseudomonadales group. The recapitulation of the intracellular-to-extracellular localization switch of PhaC in these strains shows a gradual evolution from a simple cytosolic PhaC form to a complex extracellular PhaC form specifically secreted via the type 1 secretion system. This gradual evolution includes several adaptive and pre-adaptive changes at the genomic, genetic and enzymatic levels, which are intimately related to the lifestyle of organisms during the evolution of protein localization. We conclude that the protein localization switch can be an extremely complex process in nature.
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Affiliation(s)
- Margarita Stritzler
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Carolina Berini
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CABA, Argentina
| | - Cintia Jozefkowicz
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Gabriela Soto
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Nicolás Ayub
- Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina.
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Ji Z, Liu T, Zhang J, Yan H, Wang E, Cui Q, Chen W, Chen W. Genetic divergence among Bradyrhizobium strains nodulating wild and cultivated Kummerowia spp. in China. Syst Appl Microbiol 2018; 42:223-231. [PMID: 30343835 DOI: 10.1016/j.syapm.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Abstract
Distribution of rhizobial species is affected by geographical isolation and selected by leguminous hosts, however, little is known about the molecular evolution of rhizobia nodulating the same legume in different eco-environments. In present study, the microevolution of Bradyrhizobium associated with the leguminous grass Kummerowia grown in exurban areas and cultivated in urban areas in China was investigated. Total 14 genospecies, including seven new groups, were identified based on a concatenated sequence analysis of taxonomic markers (SMc00019, truA and thrA) for 94 representative strains. Results demonstrated that lower levels of nucleotide diversity were found in the strains isolated from urban areas compared with those isolated from exurban areas, based on the evolutional analyses of three housekeeping genes (atpD, glnII and recA), two symbiosis-related genes (nodC and nifH), and the taxonomic markers. Moreover, compared with urban areas, gene exchange and recombination occurred more frequently among the genospecies isolated from exurban areas, regardless of the geographical distribution. Finally, the evolutionary lineage of Bradyrhizobium strains isolated from urban areas was independent of that of the strains isolated from exurban areas. In summary, the evolutionary history of Kummerowia bradyrhizobia may have been gradually segregated to different evolutionary lineages, irrespective of distinct biogeography.
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Affiliation(s)
- Zhaojun Ji
- College of Life Science and Horqin Plant Stress Biology Research Institute, Inner Mongolia University for the Nationalities, Tongliao 028042, Inner Mongolia, China; State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Tianyan Liu
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Jixing Zhang
- College of Life Science and Horqin Plant Stress Biology Research Institute, Inner Mongolia University for the Nationalities, Tongliao 028042, Inner Mongolia, China
| | - Hui Yan
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Qingguo Cui
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wenxin Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China.
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24
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Abstract
BACKGROUND Macroevolutionary modeling of species diversification plays important roles in inferring large-scale biodiversity patterns. It allows estimation of speciation and extinction rates and statistically testing their relationships with different ecological factors. However, macroevolutionary patterns are ultimately generated by microevolutionary processes acting at population levels, especially when speciation and extinction are considered protracted instead of point events. Neglecting the connection between micro- and macroevolution may hinder our ability to fully understand the underlying mechanisms that drive the observed patterns. RESULTS In this simulation study, we used the protracted speciation framework to demonstrate that distinct microevolutionary scenarios can generate very similar biodiversity patterns (e.g., latitudinal diversity gradient). We also showed that current macroevolutionary models may not be able to distinguish these different scenarios. CONCLUSIONS Given the compounded nature of speciation and extinction rates, one needs to be cautious when inferring causal relationships between ecological factors and macroevolutioanry rates. Future studies that incorporate microevolutionary processes into current modeling approaches are in need.
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Affiliation(s)
- Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA. .,Museum of Natural History, University of Colorado Boulder, Boulder, USA. .,Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA.
| | - Jen-Pen Huang
- Integrative Research Center, The Field Museum, Chicago, USA.,Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
| | - Jeet Sukumaran
- Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
| | - L Lacey Knowles
- Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
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25
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Eichhorn I, Heidemanns K, Ulrich RG, Schmidt H, Semmler T, Fruth A, Bethe A, Goulding D, Pickard D, Karch H, Wieler LH. Lysogenic conversion of atypical enteropathogenic Escherichia coli (aEPEC) from human, murine, and bovine origin with bacteriophage Φ3538 Δstx 2::cat proves their enterohemorrhagic E. coli (EHEC) progeny. Int J Med Microbiol 2018; 308:890-898. [PMID: 29937391 DOI: 10.1016/j.ijmm.2018.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/04/2018] [Accepted: 06/16/2018] [Indexed: 10/28/2022] Open
Abstract
Bacteriophages play an important role in the evolution of bacterial pathogens. A phage-mediated transfer of stx-genes to atypical enteropathogenic E. coli (aEPEC) which are prevalent in different hosts, would convert them to enterohemorrhagic E. coli (EHEC). We decided to confirm this hypothesis experimentally to provide conclusive evidence that aEPEC isolated from different mammalian hosts are indeed progenitors of typical EHEC which gain the ability to produce Shiga-Toxin by lysogeny with stx-converting bacteriophages, utilizing the model phage Φ3538 Δstx2::cat. We applied a modified in vitro plaque-assay, using a high titer of a bacteriophage carrying a deletion in the stx2 gene (Φ3538 Δstx2::cat) to increase the detection of lysogenic conversion events. Three wild-type aEPEC strains were chosen as acceptor strains: the murine aEPEC-strain IMT14505 (sequence type (ST)28, serotype Ont:H6), isolated from a striped field mouse (Apodemus agrarius) in the surrounding of a cattle shed, and the human aEPEC-strain 910#00 (ST28, Ont:H6). The close genomic relationship of both strains implies a high zoonotic potential. A third strain, the bovine aEPEC IMT19981, was of serotype O26:H11 and ST21 (STC29). All three aEPEC were successfully lysogenized with phage Φ3538 Δstx2::cat. Integration of the bacteriophage DNA into the aEPEC host genomes was confirmed by amplification of chloramphenicol transferase (cat) marker gene and by Southern-Blot hybridization. Analysis of the whole genome sequence of each of the three lysogens showed that the bacteriophage was integrated into the known tRNA integration site argW, which is highly variable among E. coli. In conclusion, the successful lysogenic conversion of aEPEC with a stx-phage in vitro underlines the important role of aEPEC as progenitors of EHEC. Given the high prevalence and the wide host range of aEPEC acceptors, their high risk of zoonotic transmission should be recognized in infection control measures.
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Affiliation(s)
- Inga Eichhorn
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Katrin Heidemanns
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, University of Hohenheim, Hohenheim, Germany
| | | | | | - Astrid Bethe
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - David Goulding
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Helge Karch
- Institute for Hygiene, University Münster, Münster, Germany
| | - Lothar H Wieler
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany; Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany.
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26
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Abstract
Morphological homeostasis limits the extent to which genetic and/or environmental variation is translated into phenotypic variation, providing generation-to-generation fitness advantage under a stabilizing selection regime. Depending on its lability, morphological homeostasis might also have a longer-term impact on evolution by restricting the variation-and thus the response to directional selection-of a trait. The fossil record offers an inviting opportunity to investigate whether and how morphological homeostasis constrained trait evolution in lineages or clades on long timescales (thousands to millions of years) that are not accessible to neontological studies. Fossils can also reveal insight into the nature of primitive developmental systems that might not be predictable from the study of modern organisms. The ability to study morphological homeostasis in fossils is strongly limited by taphonomic processes that can destroy, blur, or distort the original biological signal: genetic data are unavailable; phenotypic data can be modified by tectonic or compaction-related deformation; time-averaging limits temporal resolution; and environmental variation is hard to study and impossible to control. As a result of these processes, neither allelic sensitivity (and thus genetic canalization) nor macroenvironmental sensitivity (and thus environmental canalization) can be unambiguously assessed in the fossil record. However, homeorhesis-robustness against microenvironmental variation (developmental noise)-can be assessed in ancient developmental systems by measuring the level of fluctuating asymmetry (FA) in a nominally symmetric trait. This requires the analysis of multiple, minimally time-averaged samples of exquisite preservational quality. Studies of FA in fossils stand to make valuable contributions to our understanding of the deep-time significance of homeorhesis. Few empirical studies have been conducted to date, and future paleontological research focusing on how homeorhesis relates to evolutionary rate (including stasis), species survivorship, and purported macroevolutionary trends in evolvability would reap high reward.
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Affiliation(s)
- Mark Webster
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL, 60637, USA.
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27
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Canales-Aguirre CB, Ferrada-Fuentes S, Galleguillos R, Oyarzun FX, Hernández CE. Population genetic structure of Patagonian toothfish ( Dissostichus eleginoides) in the Southeast Pacific and Southwest Atlantic Ocean. PeerJ 2018; 6:e4173. [PMID: 29362690 PMCID: PMC5774298 DOI: 10.7717/peerj.4173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 11/29/2017] [Indexed: 11/20/2022] Open
Abstract
Previous studies of population genetic structure in Dissostichus eleginoides have shown that oceanographic and geographic discontinuities drive in this species population differentiation. Studies have focused on the genetics of D. eleginoides in the Southern Ocean; however, there is little knowledge of their genetic variation along the South American continental shelf. In this study, we used a panel of six microsatellites to test whether D. eleginoides shows population genetic structuring in this region. We hypothesized that this species would show zero or very limited genetic structuring due to the habitat continuity along the South American shelf from Peru in the Pacific Ocean to the Falkland Islands in the Atlantic Ocean. We used Bayesian and traditional analyses to evaluate population genetic structure, and we estimated the number of putative migrants and effective population size. Consistent with our predictions, our results showed no significant genetic structuring among populations of the South American continental shelf but supported two significant and well-defined genetic clusters of D. eleginoides between regions (South American continental shelf and South Georgia clusters). Genetic connectivity between these two clusters was 11.3% of putative migrants from the South American cluster to the South Georgia Island and 0.7% in the opposite direction. Effective population size was higher in locations from the South American continental shelf as compared with the South Georgia Island. Overall, our results support that the continuity of the deep-sea habitat along the continental shelf and the biological features of the study species are plausible drivers of intraspecific population genetic structuring across the distribution of D. eleginoides on the South American continental shelf.
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Affiliation(s)
- Cristian B Canales-Aguirre
- Centro i˜mar, Universidad de Los Lagos, Camino Chinquihue Km 6, Puerto Montt, Chile.,Laboratorio de Genética y Acuicultura, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Laboratorio de Ecología Evolutiva y Filoinformática, Departamento de Zoología, Universidad de Concepción, Concepción, Chile.,Núcleo Milenio INVASAL, Concepción, Chile
| | - Sandra Ferrada-Fuentes
- Laboratorio de Genética y Acuicultura, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Programa de Doctorado en Sistemática y Biodiversidad, Universidad de Concepción, Concepción, Chile
| | - Ricardo Galleguillos
- Laboratorio de Genética y Acuicultura, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Fernanda X Oyarzun
- Centro i˜mar, Universidad de Los Lagos, Camino Chinquihue Km 6, Puerto Montt, Chile.,Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Cristián E Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática, Departamento de Zoología, Universidad de Concepción, Concepción, Chile
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28
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Jozefkowicz C, Brambilla S, Frare R, Stritzler M, Puente M, Piccinetti C, Soto G, Ayub N. Microevolution Rather than Large Genome Divergence Determines the Effectiveness of Legume-Rhizobia Symbiotic Interaction Under Field Conditions. J Mol Evol 2017; 85:79-83. [PMID: 28828631 DOI: 10.1007/s00239-017-9808-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/12/2017] [Indexed: 11/24/2022]
Abstract
Despite the vast screening for natural nitrogen-fixing isolates by public and private consortia, no significant progresses in the production of improved nitrogen-fixing inoculants for alfalfa production have been made in the last years. Here, we present a comprehensive characterization of the nitrogen-fixing strain Ensifer meliloti B399 (originally named Rhizobium meliloti 102F34), probably the inoculant most widely used in alfalfa production since the 1960s. Complete nucleotide sequence and genome analysis of strain B399 showed that the three replicons present in this commercial strain and the model bacterium Ensifer meliloti 1021 are extremely similar to each other in terms of nucleotide identity and synteny conservation. In contrast to that observed in B399-treated plants, inoculation of plants with strain 1021 did not improve nitrogen content in different alfalfa cultivars under field conditions, suggesting that a small genomic divergence can drastically impact on the symbiotic phenotype. Therefore, in addition to the traditional screening of natural nitrogen-fixing isolates, the genome engineering of model strains could be an attractive strategy to improve nitrogen fixation in legume crops.
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Affiliation(s)
- Cintia Jozefkowicz
- Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Buenos Aires, Argentina.,Instituto de Genética Ewald A. Favret (INTA), De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Silvina Brambilla
- Instituto de Genética Ewald A. Favret (INTA), De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Romina Frare
- Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Buenos Aires, Argentina.,Instituto de Genética Ewald A. Favret (INTA), De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Margarita Stritzler
- Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Buenos Aires, Argentina.,Instituto de Genética Ewald A. Favret (INTA), De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Mariana Puente
- Instituto de Microbiología y Zoología Agrícola (INTA), Buenos Aires, Argentina
| | - Carlos Piccinetti
- Instituto de Microbiología y Zoología Agrícola (INTA), Buenos Aires, Argentina
| | - Gabriela Soto
- Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Buenos Aires, Argentina.,Instituto de Genética Ewald A. Favret (INTA), De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina
| | - Nicolás Ayub
- Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Buenos Aires, Argentina. .,Instituto de Genética Ewald A. Favret (INTA), De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina.
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29
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Sidorenko J, Jatsenko T, Kivisaar M. Ongoing evolution of Pseudomonas aeruginosa PAO1 sublines complicates studies of DNA damage repair and tolerance. Mutat Res 2017; 797-799:26-37. [PMID: 28340408 DOI: 10.1016/j.mrfmmm.2017.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 12/23/2016] [Accepted: 03/07/2017] [Indexed: 06/06/2023]
Abstract
Sublines of the major P. aeruginosa reference strain PAO1 are derivatives of the original PAO1 isolate, which are maintained in laboratories worldwide. These sublines display substantial genomic and phenotypic variation due to ongoing microevolution. Here, we examined four sublines, MPAO1, PAO1-L, PAO1-DSM and PAO1-UT, originated from different laboratories, and six DNA polymerase-deficient mutants from the P. aeruginosa MPAO1 transposon library for their employment in elucidation of DNA damage repair and tolerance mechanisms in P. aeruginosa. We found that PAO1 subline PAO1-UT carries a large deletion encompassing the DNA damage inducible imuA-imuB-imuC cassette (PA0669-PA0671), which is implied in mutagenesis in several species. Furthermore, the genetic changes leading to variation in the functionality of the MexEF-OprN efflux system contributed largely to the phenotypic discordance between P. aeruginosa PAO1 sublines. Specifically, we identified multiple mutations in the mexT gene, which encodes a transcriptional regulator of the mexEF-oprN genes, mutations in the mexF, and complete absence of these genes. Of the four tested sublines, MPAO1 was the only subline with the functional MexEF-OprN multidrug efflux system. Active efflux through MexEF-OprN rendered MPAO1 highly resistant to chloramphenicol and ciprofloxacin. Moreover, the functions of specialized DNA polymerase IV and nucleotide excision repair (NER) in 4-NQO-induced DNA damage tolerance appeared to be masked in MPAO1, while were easily detectable in other sublines. Finally, the frequencies of spontaneous and MMS-induced Rifr mutations were also significantly lower in MPAO1 in comparison to the PAO1 sublines with impaired MexEF-OprN efflux system. The MexEF-OprN-attributed differences were also observed between MPAO1 and MPAO1-derived transposon mutants from the two-allele transposon mutant collection. Thus, the accumulating mutations and discordant phenotypes of the PAO1 derivatives challenge the reproducibility and comparability of the results obtained with different PAO1 sublines and also limit the usage of the MPAO1 transposon library in DNA damage tolerance and mutagenesis studies.
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Affiliation(s)
- Julia Sidorenko
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia.
| | - Tatjana Jatsenko
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia
| | - Maia Kivisaar
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010, Tartu, Estonia.
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30
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Abstract
The Basques live at the Western extremity of the Pyrenees. According to linguistic and genetic data they could be considered as one of the most ancient European populations. Numerous studies have evidenced particular patterns in the frequency of several genetic polymorphisms in this relatively unmixed human group. We discuss herein the puzzling distribution of the two major hemochromatosis HFE mutations associated with hereditary hemochromatosis. Thus, one can observe a low frequency of C282Y and, in contrast, one of the highest European frequencies of H63D. Genetic drift (enhanced by the long history and the small size of this population), long persistence of Paleolithic iron-rich diet, lower exposure to major infectious threats and limited mixing with both Celts and Vikings (who demonstrate the highest prevalence of C282Y) could be the underlying factors explaining these particular genetic features. Historical and environmental data represent key elements for understanding the role of the different evolutionary forces which shape the genetic profile of human populations.
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Affiliation(s)
- F Bauduer
- UMR 5199 PACEA, University of Bordeaux, Pessac, France; Department of Hematology, Centre Hospitalier de la Côte Basque, Bayonne, France.
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31
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Liu Z, Ji Z, Wang G, Chao T, Hou L, Wang J. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. BMC Genomics 2016; 17:863. [PMID: 27809776 PMCID: PMC5094087 DOI: 10.1186/s12864-016-3212-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
Background Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits. Results This research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds. Conclusions Our results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3212-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhaohua Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China.
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32
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Ssengooba W, de Jong BC, Joloba ML, Cobelens FG, Meehan CJ. Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients. BMC Infect Dis 2016; 16:371. [PMID: 27495002 PMCID: PMC4974755 DOI: 10.1186/s12879-016-1737-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 07/28/2016] [Indexed: 03/14/2023] Open
Abstract
Background In the context of advanced immunosuppression, M. tuberculosis is known to cause detectable mycobacteremia. However, little is known about the intra-patient mycobacterial microevolution and the direction of seeding between the sputum and blood compartments. Methods From a diagnostic study of HIV-infected TB patients, 51 pairs of concurrent blood and sputum M. tuberculosis isolates from the same patient were available. In a previous analysis, we identified a subset with genotypic concordance, based on spoligotyping and 24 locus MIRU-VNTR. These paired isolates with identical genotypes were analyzed by whole genome sequencing and phylogenetic analysis. Results Of the 25 concordant pairs (49 % of the 51 paired isolates), 15 (60 %) remained viable for extraction of high quality DNA for whole genome sequencing. Two patient pairs were excluded due to poor quality sequence reads. The median CD4 cell count was 32 (IQR; 16–101)/mm3 and ten (77 %) patients were on ART. No drug resistance mutations were identified in any of the sequences analyzed. Three (23.1 %) of 13 patients had SNPs separating paired isolates from blood and sputum compartments, indicating evidence of microevolution. Using a phylogenetic approach to identify the ancestral compartment, in two (15 %) patients the blood isolate was ancestral to the sputum isolate, in one (8 %) it was the opposite, and ten (77 %) of the pairs were identical. Conclusions Among HIV-infected patients with poor cellular immunity, infection with multiple strains of M. tuberculosis was found in half of the patients. In those patients with identical strains, whole genome sequencing indicated that M. tuberculosis intra-patient microevolution does occur in a few patients, yet did not reveal a consistent direction of spread between sputum and blood. This suggests that these compartments are highly connected and potentially seed each other repeatedly. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1737-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda. .,Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium. .,Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
| | - Bouke C de Jong
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases, New York University, New York, NY, USA
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Frank G Cobelens
- Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Conor J Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
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33
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Safarchi A, Octavia S, Wu SZ, Kaur S, Sintchenko V, Gilbert GL, Wood N, McIntyre P, Marshall H, Keil AD, Lan R. Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic. J Infect 2016; 72:468-77. [PMID: 26826518 DOI: 10.1016/j.jinf.2016.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/15/2015] [Accepted: 01/14/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Despite high pertussis vaccination coverage, Australia experienced a prolonged epidemic in 2008-2012. The predominant Bordetella pertussis genotype harboured pertussis toxin promoter allele, ptxP3, and pertactin gene allele, prn2. The emergence and expansion of prn non-expressing isolates (Prn negative), were also observed. We aimed to investigate the microevolution and genomic diversity of epidemic B. pertussis isolates. METHODS We sequenced 22 B. pertussis isolates collected in 2008-2012 from two states of Australia which are geographically widely separated. Ten of the 22 were Prn negative isolates with three different modes of silencing of prn (prn::IS481F, prn::IS481R and prn::IS1002). Five pre-epidemic isolates were also sequenced for comparison. RESULTS Five single nucleotide polymorphisms were common in the epidemic isolates and differentiated them from pre-epidemic isolates. The Australian epidemic isolates can be divided into five lineages (EL1-EL5) with EL1 containing only Prn negative isolates. Comparison with global isolates showed that three lineages remained geographically and temporally distinct whereas two lineages mixed with isolates from 2012 UK outbreak. CONCLUSION Our results suggest significant diversification and the microevolution of B. pertussis within the 2008-2012 Australian epidemic.
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Affiliation(s)
- Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sunny Z Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
| | - Gwendolyn L Gilbert
- Centre for Infectious Diseases and Microbiology - Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
| | - Nicholas Wood
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Peter McIntyre
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Discipline of Paediatrics and Child Health, University of Sydney, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia; Department of Microbiology and Infectious Diseases, The Children's Hospital at Westmead, New South Wales, Australia
| | - Helen Marshall
- Vaccinology and Immunology Research Trials Unit, Women's and Children's Hospital and School of Medicine and Robinson Research Institute, University of Adelaide, South Australia, Australia
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Haap T, Schwarz S, Köhler HR. Metallothionein and Hsp70 trade-off against one another in Daphnia magna cross-tolerance to cadmium and heat stress. Aquat Toxicol 2016; 170:112-119. [PMID: 26655655 DOI: 10.1016/j.aquatox.2015.11.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 11/04/2015] [Accepted: 11/10/2015] [Indexed: 05/29/2023]
Abstract
The association between the insensitivity of adapted ecotypes of invertebrates to environmental stress, such as heavy metal pollution, and overall low Hsp levels characterizing these organisms has been attracting attention in various studies. The present study seeks to induce and examine this phenomenon in Daphnia magna by multigenerational acclimation to cadmium in a controlled laboratory setting. In this experiment, interclonal variation was examined: two clones of D. magna that have previously been characterized to diverge regarding their cadmium resistance and levels of the stress protein Hsp70, were continuously exposed to a sublethal concentration of Cd over four generations to study the effects of acclimation on Hsp70, metallothionein (MT), reproduction and cross-tolerance to heat stress. The two clones differed in all the measured parameters in a characteristic way, clone T displaying Cd and heat resistance, lower Hsp70 levels and offspring numbers on the one hand and higher MT expression on the other hand, clone S the opposite for all these parameters. We observed only slight acclimation-induced changes in constitutive Hsp70 levels and reproductive output. The differences in MT expression between clones as well as between acclimated organisms and controls give evidence for MT accounting for the higher Cd tolerance of clone T. Overall high Hsp70 levels of clone S did not confer cross tolerance to heat stress, contrary to common expectations. Our results suggest a trade-off between the efforts to limit the proteotoxic symptoms of Cd toxicity by Hsp70 induction and those to sequester and detoxify Cd by means of MT.
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Affiliation(s)
- Timo Haap
- Animal Physiological Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany.
| | - Simon Schwarz
- Animal Physiological Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
| | - Heinz-R Köhler
- Animal Physiological Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076 Tübingen, Germany
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Ormerod KL, George NM, Fraser JA, Wainwright C, Hugenholtz P. Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PeerJ 2015; 3:e1223. [PMID: 26401445 PMCID: PMC4579023 DOI: 10.7717/peerj.1223] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/10/2015] [Indexed: 12/16/2022] Open
Abstract
The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer) in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis.
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Affiliation(s)
- Kate L. Ormerod
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Narelle M. George
- Health Support Queensland, Department of Health, Queensland Government, Herston, Queensland, Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Claire Wainwright
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Department of Respiratory and Sleep Medicine, Lady Cilento Children’s Hospital, South Brisbane, Queensland, Australia
- Queensland Children’s Medical Research Insitute, Herston, Queensland, Australia
| | - Philip Hugenholtz
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
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Pergams ORW, Byrn D, Lee KLY, Jackson R. Rapid morphological change in black rats (Rattus rattus) after an island introduction. PeerJ 2015; 3:e812. [PMID: 25780765 PMCID: PMC4358651 DOI: 10.7717/peerj.812] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/11/2015] [Indexed: 11/20/2022] Open
Abstract
Rapid morphological change has been shown in rodent populations on islands, including endemic deer mice (Peromyscus maniculatus subspp.) on the California Channel Islands. Surprisingly, most of these changes were towards a smaller size. Black rats were introduced to Anacapa Island in the mid-1800s (probably in 1853) and eradicated in 2001-2002. To assess possible changes in these rats since their introduction, eleven cranial and four standard external measurements were taken from 59 Rattus rattus specimens collected from 1940-2000. All rat cranial traits changed 3.06-10.43% (724-2567 d, 0.06-0.42 h), and all became larger. When considered in haldanes, these changes are among the fastest on record in any organism, and far exceed changes found in other island rodents. These changes were confirmed by MANOVA (Wilk's λ < 0.0005, F d.f.15 = 2974.386, P < 0.0005), and all 11 cranial traits significantly fit linear regressions. We speculate that concurrent changes in mice may have been due in part to competition with and/or predation by rats. Future research might evaluate whether the vector of mouse evolution on Anacapa is again changing after rat eradication.
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Affiliation(s)
- Oliver R W Pergams
- Department of Biology, Olive-Harvey College, One of the City Colleges of Chicago , Chicago, IL , USA ; Department of Biological Sciences, University of Illinois at Chicago , Chicago, IL , USA
| | - David Byrn
- Department of Biology, Olive-Harvey College, One of the City Colleges of Chicago , Chicago, IL , USA
| | - Kashawneda L Y Lee
- Department of Biology, Olive-Harvey College, One of the City Colleges of Chicago , Chicago, IL , USA
| | - Racheal Jackson
- Department of Biology, Olive-Harvey College, One of the City Colleges of Chicago , Chicago, IL , USA
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Navarro Y, Romero B, Copano MF, Bouza E, Domínguez L, de Juan L, García-de-Viedma D. Multiple sampling and discriminatory fingerprinting reveals clonally complex and compartmentalized infections by M. bovis in cattle. Vet Microbiol 2014; 175:99-104. [PMID: 25439651 DOI: 10.1016/j.vetmic.2014.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/27/2014] [Accepted: 11/02/2014] [Indexed: 10/24/2022]
Abstract
The combination of new genotyping tools and a more exhaustive sampling policy in the analysis of infection by Mycobacterium tuberculosis has shown that infection by this pathogen is more complex than initially expected. Mixed infections, coexistence of clonal variants from a parental strain, and compartmentalized infections are all different modalities of this clonal complexity. Until recently, genotyping of Mycobacterium bovis in animal populations was based on spoligotyping and analysis of a single isolate per infection; therefore, clonal complexity is probably underdetected. We used multiple sampling combined with highly discriminatory MIRU-VNTR to study compartmentalized infections by M. bovis in a low-tuberculosis prevalence setting. We spoligotyped the M. bovis isolates from two or more anatomic locations sampled from 55 animals on 39 independent farms. Compartmentalized infections, with two different strains infecting independent lymph nodes in the same animal, were found in six cases (10.9%). MIRU-VNTR analysis confirmed that the compartmentalization was strict and that only one strain was present in each infected node. MIRU-VNTR analysis of additional infected animals on one of the farms confirmed that the compartmentalized infection was a consequence of superinfection, since the two strains were independently infecting other animals. This same analysis revealed the emergence of a microevolved clonal variant in one of the lymph nodes of the compartmentalized animal. Clonal complexity must also be taken into consideration in M. bovis infection, even in low-prevalence settings, and analyses must be adapted to detect it and increase the accuracy of molecular epidemiology studies.
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Affiliation(s)
- Yurena Navarro
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Beatriz Romero
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain
| | | | - Emilio Bouza
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucas Domínguez
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Lucía de Juan
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Darío García-de-Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain.
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Gómez GF, Márquez EJ, Gutiérrez LA, Conn JE, Correa MM. Geometric morphometric analysis of Colombian Anopheles albimanus (Diptera: Culicidae) reveals significant effect of environmental factors on wing traits and presence of a metapopulation. Acta Trop 2014; 135:75-85. [PMID: 24704285 DOI: 10.1016/j.actatropica.2014.03.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 01/24/2023]
Abstract
Anopheles albimanus is a major malaria mosquito vector in Colombia. In the present study, wing variability (size and shape) in An. albimanus populations from Colombian Maracaibo and Chocó bio-geographical eco-regions and the relationship of these phenotypic traits with environmental factors were evaluated. Microsatellite and morphometric data facilitated a comparison of the genetic and phenetic structure of this species. Wing size was influenced by elevation and relative humidity, whereas wing shape was affected by these two variables and also by rainfall, latitude, temperature and eco-region. Significant differences in mean shape between populations and eco-regions were detected, but they were smaller than those at the intra-population level. Correct assignment based on wing shape was low at the population level (<58%) and only slightly higher (>70%) at the eco-regional level, supporting the low population structure inferred from microsatellite data. Wing size was similar among populations with no significant differences between eco-regions. Population relationships in the genetic tree did not agree with those from the morphometric data; however, both datasets consistently reinforced a panmictic population of An. albimanus. Overall, site-specific population differentiation is not strongly supported by wing traits or genotypic data. We hypothesize that the metapopulation structure of An. albimanus throughout these Colombian eco-regions is favoring plasticity in wing traits, a relevant characteristic of species living under variable environmental conditions and colonizing new habitats.
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Affiliation(s)
- Giovan F Gómez
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Edna J Márquez
- Facultad de Ciencias, Universidad Nacional de Colombia, Medellín, Colombia.
| | - Lina A Gutiérrez
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Jan E Conn
- Wadsworth Center, New York State Department of Health, Slingerlands, 12159 NY, USA; Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, 12222 NY, USA.
| | - Margarita M Correa
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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Pérez-Lago L, Navarro Y, Herranz M, Bouza E, García-de-Viedma D. Differences in gene expression between clonal variants of Mycobacterium tuberculosis emerging as a result of microevolution. Int J Med Microbiol 2013; 303:674-7. [PMID: 24189285 DOI: 10.1016/j.ijmm.2013.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/20/2013] [Accepted: 09/28/2013] [Indexed: 01/22/2023] Open
Abstract
Clonal variants of Mycobacterium tuberculosis can emerge as a result of microevolution in a single host or after sequential infection of different hosts. The significance of subtle genotypic variations is still unknown. In three of the four loci analyzed from clonal variants differing in only one MIRU-VNTR locus, we found that the expression of the adjacent genes was modulated differently. These data highlight the potential advantages that acquisition of subtle variability may have in M. tuberculosis.
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Tan XE, Neoh HM, Hussin S, Zin NM. Clonal distribution and possible microevolution of methicillin-resistant Staphylococcus aureus strains in a teaching hospital in Malaysia. Asian Pac J Trop Biomed 2013; 3:224-8. [PMID: 23620843 PMCID: PMC3631755 DOI: 10.1016/s2221-1691(13)60055-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 02/27/2013] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE To genotypically characterize methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from medical and surgical wards in Universiti Kebangsaan Malaysia Medical Centre (UKMMC) in 2009. METHODS MRSA strains were collected and molecularly typed by pulsed-field gel electrophoresis (PFGE). RESULTS PFGE typing on 180 MRSA isolated in UKMMC identified 5 pulsotypes (A-E) and 6 singletons, where pulsotypes B and C were suspected to be divergent clones originating from a single ancestor. This study also showed that most MRSA strains were isolated from swab (119 isolates), followed by blood (22 isolates), tracheal aspirate (11 isolates) and sputum (10 isolates). On the other hand, urine and bone isolates were less, which were 4 and 1 isolates, respectively. The distribution of different pulsotypes of MRSA among wards suggested that MRSA was communicated in surgical and medical wards in UKMMC, with pulsotype B MRSA as the dominant strain. Besides, it was found that most deceased patients were infected by pulsotype B MRSA, however, no particular pulsotype could be associated with patient age, underlying disease, or ward of admittance. CONCLUSIONS Five pulsotypes of MRSA and 6 singletons were identified, with pulsotype B MRSA as the endemic strains circulating in these wards, which is useful in establishment of preventive measures against MRSA transmission.
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Affiliation(s)
- Xin Ee Tan
- Department of Biomedical Science, Faculty of Allied Health Sciences, Malaysia
| | - Hui-min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Malaysia
| | - Salasawati Hussin
- Department of Medical Microbiology and Immunology, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur,Malaysia
| | - Noraziah Mohamad Zin
- Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, 50300 Kuala Lumpur, Malaysia
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