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  Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Näpflin, K., O’Connor, E. A., Becks, L., Bensch, S., Ellis, V. A., Hafer-Hahmann, N., et al. (2019). Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ, 7: e8013. doi:10.7717/peerj.8013.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-688F-6 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-6890-3
Genre: Journal Article

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 Creators:
Näpflin, Kathrin, Author
O’Connor, Emily A., Author
Becks, Lutz1, Author              
Bensch, Staffan, Author
Ellis, Vincenzo A., Author
Hafer-Hahmann, Nina2, Author              
Harding, Karin C., Author
Lindén, Sara K., Author
Olsen, Morten T., Author
Roved, Jacob, Author
Sackton, Timothy B., Author
Shultz, Allison J., Author
Venkatakrishnan, Vignesh, Author
Videvall, Elin, Author
Westerdahl, Helena, Author
Winternitz, Jamie C.3, Author              
Edwards, Scott V., Author
Newton, Irene, Contributor
Affiliations:
1Emmy-Noether-Group Community Dynamics, Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2068285              
2Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445634              
3Emmy Noether Research Group Evolutionary Immunogenomics, Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2068286              

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Free keywords: Plasmodium, MHC, Immunotoxins, Mucus, Natural selection, GWAS, Infectious diseases, Anthropogenic stressors, Co-evolution, Epidemiological surveillance
 Abstract: Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.

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Language(s): eng - English
 Dates: 2019-05-152019-10-082019-11-052019
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.7717/peerj.8013
 Degree: -

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Title: PeerJ
  Other : PeerJ
Source Genre: Journal
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Publ. Info: London [u.a.] : PeerJ Inc.
Pages: - Volume / Issue: 7 Sequence Number: e8013 Start / End Page: - Identifier: ISSN: 2167-8359
CoNE: https://pure.mpg.de/cone/journals/resource/2167-8359