The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns

Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko

Research output: Contribution to journalArticlepeer-review

Abstract

Insertions and deletions (indels) of short DNA segments are common evolutionary events. Numerous studies showed that deletions occur more often than insertions in both prokaryotes and eukaryotes. It raises the question why neutral sequences are not eradicated from the genome. We suggest that this is due to a phenomenon we term border-induced selection. Accordingly, a neutral sequence is bordered between conserved regions. Deletions occurring near the borders occasionally protrude to the conserved region and are thereby subject to strong purifying selection. Thus, for short neutral sequences, an insertion bias is expected. Here, we develop a set of increasingly complex models of indel dynamics that incorporate border-induced selection. Furthermore, we show that short conserved sequences within the neutrally evolving sequence help explain: (i) the presence of very long sequences; (ii) the high variance of sequence lengths; and (iii) the possible emergence of multimodality in sequence length distributions. Finally, we fitted our models to the human intron length distribution, as introns are thought to be mostly neutral and bordered by conserved exons. We show that when accounting for the occurrence of short conserved sequences within introns, we reproduce the main features, including the presence of long introns and the multimodality of intron distribution.

Original languageEnglish
Pages (from-to)220223
Number of pages1
JournalOpen Biology
Volume12
Issue number12
DOIs
StatePublished - 1 Dec 2022

Keywords

  • border-induced selection
  • c-value paradox
  • deletion bias
  • genome evolution
  • indel
  • intron

Fingerprint

Dive into the research topics of 'The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns'. Together they form a unique fingerprint.

Cite this