Jun 13, 2012

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

Bioinformatics
Mukul S BansalManolis Kellis

Abstract

Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction. We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accu...Continue Reading

  • References30
  • Citations44

References

Mentioned in this Paper

Genes, Reiterated
Gene Deletion
Reconcile
Phylogeny
Computer Programs and Programming
Gene Transfer, Horizontal
Genomics
Gene Duplication Abnormality
Gene Family
Recombination, Interspecies

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