TY - JOUR T1 - Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved A1 - Gemmell, Patrick A1 - Hein, Jotun A1 - Katzourakis, Aris Y1 - 2016/06/13 N2 - Author Summary Animal genomes contain ancient pathogens known as endogenous retroviruses (ERVs). Though the widespread abundance of ERVs is due to their ability to self replicate, some ERVs are known to have become important to host processes including placentation, and in the case of HERV-H, the functioning of human stem cells. In our study we place the insertion and deletion activity of primate ERV families in direct quantitative comparison. In particular, we show that ERV deletion is an age dependent process, so that as an ERV ages it becomes less likely to be deleted at any given instant. We also find that ERVs from the HERV-H family are unusually slowly deleted, an interesting result that suggests that the exaptation of HERV-H may have involved internal regions of the virus and not just its terminal promoters. Assuming the behaviour of primate ERVs is not unusual, our study suggests that future bioinformatics screening for ERVs with slow deletion dynamics could help identify large-scale exaptations in distant species. Furthermore, as we demonstrate that ERVs are deleted rapidly, we think that such screening could be performed using ratios of conserved to deleted elements and could therefore be applied to single genomes. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 12 IS - 6 UR - https://doi.org/10.1371/journal.pcbi.1004964 SP - e1004964 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1004964 ER -