Ecological and Evolutionary Processes Shaping Viral Genetic Diversity

被引:19
作者
Retel, Cas [1 ,2 ]
Maerkle, Hanna [3 ]
Becks, Lutz [4 ]
Feulner, Philine G. D. [1 ,2 ]
机构
[1] Swiss Fed Inst Aquat Sci & Technol, EAWAG, Ctr Ecol Evolut & Biogeochem, Dept Fish Ecol & Evolut, CH-6047 Kastanienbaum, Switzerland
[2] Univ Bern, Inst Ecol & Evolut, Div Aquat Ecol, CH-3012 Bern, Switzerland
[3] Tech Univ Munich, TUM Sch Life Sci Weihenstephan, Sect Populat Genet, D-85354 Freising Weihenstephan, Germany
[4] Limnol Inst Univ Konstanz Aquat Ecol & Evolut, D-78464 Constance, Germany
来源
VIRUSES-BASEL | 2019年 / 11卷 / 03期
基金
瑞士国家科学基金会;
关键词
genetic diversity; viral population genetics; host-virus coevolution; eco-evolutionary feedback; ANTAGONISTIC COEVOLUTION; BACKGROUND SELECTION; RAPID EVOLUTION; BENEFICIAL MUTATIONS; POPULATION-DYNAMICS; BALANCING SELECTION; NATURAL-SELECTION; LOCAL ADAPTATION; HOST-RESISTANCE; VIRUSES;
D O I
10.3390/v11030220
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host-virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.
引用
收藏
页数:16
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共 131 条
[1]  
Agrawal A, 2002, EVOL ECOL RES, V4, P79
[2]   Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists Discussion [J].
Aguileta, Gabriela ;
Refregier, Guislaine ;
Yockteng, Roxana ;
Fournier, Elisabeth ;
Giraud, Tatiana .
INFECTION GENETICS AND EVOLUTION, 2009, 9 (04) :656-670
[3]   Thinking too positive? Revisiting current methods of population genetic selection inference [J].
Bank, Claudia ;
Ewing, Gregory B. ;
Ferrer-Admettla, Anna ;
Foll, Matthieu ;
Jensen, Jeffrey D. .
TRENDS IN GENETICS, 2014, 30 (12) :540-546
[4]   The effect of hitch-hiking on neutral genealogies [J].
Barton, NH .
GENETICS RESEARCH, 1998, 72 (02) :123-133
[5]   The functional genomics of an eco-evolutionary feedback loop: linking gene expression, trait evolution, and community dynamics [J].
Becks, Lutz ;
Ellner, Stephen P. ;
Jones, Laura E. ;
Hairston, Nelson G., Jr. .
ECOLOGY LETTERS, 2012, 15 (05) :492-501
[6]   MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years? [J].
Bernatchez, L ;
Landry, C .
JOURNAL OF EVOLUTIONARY BIOLOGY, 2003, 16 (03) :363-377
[7]   Spatial Structure, Transmission Modes and the Evolution of Viral Exploitation Strategies [J].
Berngruber, Thomas W. ;
Lion, Sebastien ;
Gandon, Sylvain .
PLOS PATHOGENS, 2015, 11 (04)
[8]   Host-parasite fluctuating selection in the absence of specificity [J].
Best, Alex ;
Ashby, Ben ;
White, Andy ;
Bowers, Roger ;
Buckling, Angus ;
Koskella, Britt ;
Boots, Mike .
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2017, 284 (1866)
[9]   Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages [J].
Betts, Alex ;
Kaltz, Oliver ;
Hochberg, Michael E. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (30) :11109-11114
[10]   The Role of Human Transportation Networks in Mediating the Genetic Structure of Seasonal Influenza in the United States [J].
Bozick, Brooke A. ;
Real, Leslie A. .
PLOS PATHOGENS, 2015, 11 (06)