Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split.

Patrick Gemmell,Jotun Hein,Aris Katzourakis

doi:10.1186/s12977-015-0172-6

Abstract

BackgroundEndogenous retroviruses (ERVs) are often viewed as selfish DNA that do not contribute to host phenotype. Yet ERVs have also been co-opted to play important roles in the maintenance of stem cell identity and placentation, amongst other things. This has led to debate over whether the typical ERV confers a cost or benefit upon the host. We studied the divergence of orthologous ERVs since the chimp-human split with the aim of assessing whether ERVs exert detectable fitness effects.ResultsERVs have evolved faster than other selfish DNA in human and chimpanzee. The divergence of ERVs relative to neighbouring selfish DNA is positively correlated with the length of the long terminal repeat of an ERV and with the percentage of neighbouring DNA that is not selfish. ERVs from the HERV-H family have diverged particularly quickly and in a manner that correlates with their level of transcription in human stem cells. A substitution into a highly transcribed HERV-H has a selective coefficient of the order of 10−4. This is large enough to suggest these substitutions are not dominated by drift.ConclusionsERVs differ from other selfish DNA in the extent to which they diverge and appear to have measurable effects on hosts, even after fixation. The effects are strongest for HERV-H and suggest that the HERV-H transcriptome has recently evolved under the influence of directional selection. As there are many HERV-H loci distributed across the ape lineage, our results suggest that in future this family can be used to model the evolutionary consequences of ERV exaptation in primates and other mammals.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-015-0172-6) contains supplementary material, which is available to authorized users.

Highlights

Endogenous retroviruses (ERVs) are often viewed as selfish DNA that do not contribute to host phenotype
The effects are strongest for HERV-H and suggest that the HERV-H transcriptome has recently evolved under the influence of directional selection
HERV-H loci distributed across the ape lineage, our results suggest that in future this family can be used to model the evolutionary consequences of ERV exaptation in primates and other mammals

Summary

Introduction

Endogenous retroviruses (ERVs) are often viewed as selfish DNA that do not contribute to host phenotype. ERVs have been co-opted to play important roles in the maintenance of stem cell identity and placentation, amongst other things. This has led to debate over whether the typical ERV confers a cost or benefit upon the host. As an obligate part of their lifecycle, retroviruses integrate their genomes into their host’s nuclear DNA. This integrated retroviral genome is referred to as a provirus. Sometimes integration occurs in a germ line cell, and if the integration is not too damaging to the host, it becomes possible for proviral DNA to be passed in a vertical (Mendelian) way from parent to offspring. Some ERVs reach high frequencies or fixation in a host population and it is possible to detect the traces of ancient viral infections, often in fragmented form, by examining modern genomes.

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