Journal
COMPUTATION
Volume 2, Issue 3, Pages 112-130Publisher
MDPI AG
DOI: 10.3390/computation2030112
Keywords
gene duplication; gene loss; phylogeny; gene tree/species tree reconciliation; stochastic models; birth/death processes
Categories
Funding
- NSF [DBI-0743374, DMS-1222940]
- Division Of Mathematical Sciences
- Direct For Mathematical & Physical Scien [1515691, 1222745] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1300426] Funding Source: National Science Foundation
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Characterizing the mechanisms of duplicate gene retention using phylogenetic methods requires models that are consistent with different biological processes. The interplay between complex biological processes and necessarily simpler statistical models leads to a complex modeling problem. A discussion of the relationship between biological processes, existing models for duplicate gene retention and data is presented. Existing models are then extended in deriving two new birth/death models for phylogenetic application in a gene tree/species tree reconciliation framework to enable probabilistic inference of the mechanisms from model parameterization. The goal of this work is to synthesize a detailed discussion of modeling duplicate genes to address biological questions, moving from previous work to future trajectories with the aim of generating better models and better inference.
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