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Purifying selection and drift, not life history or RNAi, determine transposable element evolution

Amir Szitenberg, Soyeon Cha, Charles H. Opperman, David M. Bird, Mark Blaxter, David H. Lunt
doi: https://doi.org/10.1101/034884
Amir Szitenberg
1Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK,
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  • For correspondence: a.szitenberg@hull.ac.uk
Soyeon Cha
2Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA,
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Charles H. Opperman
2Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA,
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David M. Bird
2Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA,
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Mark Blaxter
3Institute of Evolutionary biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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  • For correspondence: mark.blaxter@ed.ac.uk
David H. Lunt
1Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK,
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  • For correspondence: d.h.lunt@hull.uk
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Abstract

Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may occasionally play an adaptive role in their host’s genome, they are much more often deleterious, and purifying selection is thus an important factor controlling genomic TE loads. In contrast, life history and genomic characteristics such as mating system, parasitism, GC content, and RNAi pathways, have been suggested to account for the startling disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long term effects on TE evolution. Here we explicitly test the long term determinants of TE evolution by comparing 42 nematode genomes that span over 500 million years of diversification, and include numerous transitions between life history states and RNAi pathways. We have analysed the reconstructed TE loads of ancestors through the Nematoda phylogeny to account for correlation with GC content and transitions in TE evolutionary models. We also analysed the effect of transitions in life history characteristics and RNAi using ANOVA of phylogenetically independent contrasts. We show that purifying selection against TEs is the dominant force throughout the evolutionary history of Nematoda, as indicated by reconstructed ancestral TE loads, and that strong stochastic Ornstein-Uhlenbeck processes are the underlying models which best explain TE diversification among extant species. In contrast we found no evidence that life history or RNAi variations have a significant influence upon genomic TE load across extended periods of evolutionary history. We suggest that these are largely inconsequential to the large differences in TE content observed between genomes and only by these large-scale comparisons can we distinguish long term and persistent effects from transient effects or misleading random changes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 20, 2015.
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Purifying selection and drift, not life history or RNAi, determine transposable element evolution
Amir Szitenberg, Soyeon Cha, Charles H. Opperman, David M. Bird, Mark Blaxter, David H. Lunt
bioRxiv 034884; doi: https://doi.org/10.1101/034884
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Purifying selection and drift, not life history or RNAi, determine transposable element evolution
Amir Szitenberg, Soyeon Cha, Charles H. Opperman, David M. Bird, Mark Blaxter, David H. Lunt
bioRxiv 034884; doi: https://doi.org/10.1101/034884

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