A synergism between adaptive effects and evolvability drives whole genome duplication to fixation.
Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. Thi...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-04-01
|
| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC3990473?pdf=render |
| _version_ | 1819238288181952512 |
|---|---|
| author | Thomas D Cuypers Paulien Hogeweg |
| author_facet | Thomas D Cuypers Paulien Hogeweg |
| author_sort | Thomas D Cuypers |
| collection | DOAJ |
| description | Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. This pattern has been explained by a neutral process of subfunctionalization and more recently, dosage balance selection. However, much about the relationship between environmental change, WGD and adaptation remains unknown. Here, we study the duplicate retention pattern postWGD, by letting virtual cells adapt to environmental changes. The virtual cells have structured genomes that encode a regulatory network and simple metabolism. Populations are under selection for homeostasis and evolve by point mutations, small indels and WGD. After populations had initially adapted fully to fluctuating resource conditions re-adaptation to a broad range of novel environments was studied by tracking mutations in the line of descent. WGD was established in a minority (≈30%) of lineages, yet, these were significantly more successful at re-adaptation. Unexpectedly, WGD lineages conserved more seemingly redundant genes, yet had higher per gene mutation rates. While WGD duplicates of all functional classes were significantly over-retained compared to a model of neutral losses, duplicate retention was clearly biased towards highly connected TFs. Importantly, no subfunctionalization occurred in conserved pairs, strongly suggesting that dosage balance shaped retention. Meanwhile, singles diverged significantly. WGD, therefore, is a powerful mechanism to cope with environmental change, allowing conservation of a core machinery, while adapting the peripheral network to accommodate change. |
| first_indexed | 2024-12-23T13:33:50Z |
| format | Article |
| id | doaj.art-46f26b6c706a4de6805b82551bb8cf40 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-23T13:33:50Z |
| publishDate | 2014-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-46f26b6c706a4de6805b82551bb8cf402022-12-21T17:45:05ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582014-04-01104e100354710.1371/journal.pcbi.1003547A synergism between adaptive effects and evolvability drives whole genome duplication to fixation.Thomas D CuypersPaulien HogewegWhole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. This pattern has been explained by a neutral process of subfunctionalization and more recently, dosage balance selection. However, much about the relationship between environmental change, WGD and adaptation remains unknown. Here, we study the duplicate retention pattern postWGD, by letting virtual cells adapt to environmental changes. The virtual cells have structured genomes that encode a regulatory network and simple metabolism. Populations are under selection for homeostasis and evolve by point mutations, small indels and WGD. After populations had initially adapted fully to fluctuating resource conditions re-adaptation to a broad range of novel environments was studied by tracking mutations in the line of descent. WGD was established in a minority (≈30%) of lineages, yet, these were significantly more successful at re-adaptation. Unexpectedly, WGD lineages conserved more seemingly redundant genes, yet had higher per gene mutation rates. While WGD duplicates of all functional classes were significantly over-retained compared to a model of neutral losses, duplicate retention was clearly biased towards highly connected TFs. Importantly, no subfunctionalization occurred in conserved pairs, strongly suggesting that dosage balance shaped retention. Meanwhile, singles diverged significantly. WGD, therefore, is a powerful mechanism to cope with environmental change, allowing conservation of a core machinery, while adapting the peripheral network to accommodate change.http://europepmc.org/articles/PMC3990473?pdf=render |
| spellingShingle | Thomas D Cuypers Paulien Hogeweg A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. PLoS Computational Biology |
| title | A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. |
| title_full | A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. |
| title_fullStr | A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. |
| title_full_unstemmed | A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. |
| title_short | A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. |
| title_sort | synergism between adaptive effects and evolvability drives whole genome duplication to fixation |
| url | http://europepmc.org/articles/PMC3990473?pdf=render |
| work_keys_str_mv | AT thomasdcuypers asynergismbetweenadaptiveeffectsandevolvabilitydriveswholegenomeduplicationtofixation AT paulienhogeweg asynergismbetweenadaptiveeffectsandevolvabilitydriveswholegenomeduplicationtofixation AT thomasdcuypers synergismbetweenadaptiveeffectsandevolvabilitydriveswholegenomeduplicationtofixation AT paulienhogeweg synergismbetweenadaptiveeffectsandevolvabilitydriveswholegenomeduplicationtofixation |