The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns
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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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The Royal Society
2022-12-01
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| Series: | Open Biology |
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsob.220223 |
| _version_ | 1827965700350672896 |
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| author | Gil Loewenthal Elya Wygoda Natan Nagar Lior Glick Itay Mayrose Tal Pupko |
| author_facet | Gil Loewenthal Elya Wygoda Natan Nagar Lior Glick Itay Mayrose Tal Pupko |
| author_sort | Gil Loewenthal |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-09T17:37:27Z |
| format | Article |
| id | doaj.art-895c3192c83149f99bb5781647946285 |
| institution | Directory Open Access Journal |
| issn | 2046-2441 |
| language | English |
| last_indexed | 2024-04-09T17:37:27Z |
| publishDate | 2022-12-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Open Biology |
| spelling | doaj.art-895c3192c83149f99bb57816479462852023-04-17T10:57:29ZengThe Royal SocietyOpen Biology2046-24412022-12-01121210.1098/rsob.220223The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human intronsGil Loewenthal0Elya Wygoda1Natan Nagar2Lior Glick3Itay Mayrose4Tal Pupko5The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 69978, IsraelThe Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 69978, IsraelThe Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 69978, IsraelSchool of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, IsraelSchool of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, IsraelThe Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 69978, IsraelInsertions 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.https://royalsocietypublishing.org/doi/10.1098/rsob.220223indelintrondeletion biasc-value paradoxgenome evolutionborder-induced selection |
| spellingShingle | Gil Loewenthal Elya Wygoda Natan Nagar Lior Glick Itay Mayrose Tal Pupko The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns Open Biology indel intron deletion bias c-value paradox genome evolution border-induced selection |
| title | The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns |
| title_full | The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns |
| title_fullStr | The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns |
| title_full_unstemmed | The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns |
| title_short | The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns |
| title_sort | evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias a model and its application to human introns |
| topic | indel intron deletion bias c-value paradox genome evolution border-induced selection |
| url | https://royalsocietypublishing.org/doi/10.1098/rsob.220223 |
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