Modelling prokaryote gene content
The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical ev...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2006-01-01
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| Series: | Evolutionary Bioinformatics |
| Subjects: | |
| Online Access: | http://la-press.com/article.php?article_id=144 |
| _version_ | 1818401810222678016 |
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| author | Edward Susko Andrew J. Roger Matthew Spencer |
| author_facet | Edward Susko Andrew J. Roger Matthew Spencer |
| author_sort | Edward Susko |
| collection | DOAJ |
| description | The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time) to blocks models (allowing gain and loss of multiple genes within a family). We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea) and Bacillus subtilis (gram positive bacteria). Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common). For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model. |
| first_indexed | 2024-12-14T07:58:23Z |
| format | Article |
| id | doaj.art-471d596983154bde954bb8b4fd7d74d4 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-14T07:58:23Z |
| publishDate | 2006-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-471d596983154bde954bb8b4fd7d74d42022-12-21T23:10:29ZengSAGE PublishingEvolutionary Bioinformatics1176-93432006-01-012157178Modelling prokaryote gene contentEdward SuskoAndrew J. RogerMatthew SpencerThe patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time) to blocks models (allowing gain and loss of multiple genes within a family). We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea) and Bacillus subtilis (gram positive bacteria). Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common). For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model.http://la-press.com/article.php?article_id=144gene contentlateral transferphylogeneticslikelihood |
| spellingShingle | Edward Susko Andrew J. Roger Matthew Spencer Modelling prokaryote gene content Evolutionary Bioinformatics gene content lateral transfer phylogenetics likelihood |
| title | Modelling prokaryote gene content |
| title_full | Modelling prokaryote gene content |
| title_fullStr | Modelling prokaryote gene content |
| title_full_unstemmed | Modelling prokaryote gene content |
| title_short | Modelling prokaryote gene content |
| title_sort | modelling prokaryote gene content |
| topic | gene content lateral transfer phylogenetics likelihood |
| url | http://la-press.com/article.php?article_id=144 |
| work_keys_str_mv | AT edwardsusko modellingprokaryotegenecontent AT andrewjroger modellingprokaryotegenecontent AT matthewspencer modellingprokaryotegenecontent |