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. 2014 Jun 12;9(6):e99480.
doi: 10.1371/journal.pone.0099480. eCollection 2014.

Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

Free PMC article

Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

Ryan M Ames et al. PLoS One. .
Free PMC article


The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Figure 1
Figure 1. The distribution of average family sizes in the Génolevures data.
Figure 2
Figure 2. The rate of family evolution in the Génolevures data estimated by DupliPHY-ML as the mean posterior rate with gamma-distributed rates across families.
Here a high estimated rate indicates a family that is evolving quickly and has undergone many duplication and loss events in its history. The average rate is 1.
Figure 3
Figure 3. The phylogeny for the Génolevures data.
Branch lengths represent the average number of gain and loss events per gene family as inferred by DupliPHY-ML. The branch on which the whole-genome duplication occurred is indicated with a star.
Figure 4
Figure 4. Functional enrichment of lineage specific expanding gene families for GO slim terms.
Each cell represents a GO slim term from the biological process, molecular function or cellular component ontology. The positioning of the cells is determined by a term overlap metric so that more similar terms are positioned close together. Cells are shaded if one or more expanding gene family shows enrichment for that term. The intensity of the shading represents the number of gene families showing enrichment for that term. The most intense colour shows formula image 10 families are enriched. Each panel represents a species from the Génolevures data set: Y. lipolytica (A), D. hansenii (B), E. gossypii (C), K. lactis (D), S. kluyveri (E), K. thermotolerans (F), Z. rouxii (G), S. cerevisiae (H) and C. glabrata (I). Lists of enriched terms in expanding families are available in File S3

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    1. Hahn M, Han M, Han S (2007) Gene family evolution across 12 Drosophila genomes. PLoS Genetics 3: e197–e209. - PMC - PubMed

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