Does phylogeny tree help in explain how gene families evolve?
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Phylogenetic trees are frequently used to represent the evolution of gene families. Gene family evolution is usually represented within a species tree, but recent models also consider the evolution of protein domains within gene trees. Various simulation frameworks have been developed to validate the accuracy of phylogenetic reconciliation methods, such as the Duplication-Transfer-Loss (DTL) reconciliation algorithm. These frameworks simulate gene family evolution, including horizontal gene transfers and the evolution of domain families. The accuracy of DTL reconciliation has been evaluated on simulated datasets, showing its robustness to the presence of replacing transfers. Additionally, the construction of gene trees can be improved by considering dependencies between gene families, such as information from species trees, extant synteny, and ancestral synteny. RefineTree is a software package that corrects gene trees using these dependencies, resulting in more plausible trees. Phylogenetic trees and correction methods contribute to understanding how gene families evolve.
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20 Mar 2020 | The paper does not directly mention how phylogenetic trees explain how gene families evolve. The paper focuses on developing a method for reconstructing ancestral states of various domains and proteins using transcriptomes. |
| Yes, the paper discusses how gene families evolve along the branches of a species tree, which is a representation of the phylogeny. | |
| Yes, the paper discusses using gene family trees to infer the evolution of gene families by incorporating information from species trees, extant synteny, and ancestral synteny. | |
| Yes, phylogeny reconstruction can help understand how gene families evolve and identify the chronology of duplications within a gene family of a single species. | |
| Yes, phylogenetic trees are frequently used to represent the evolution of gene families, as they show the relationships between different species, genes, and protein domains. |
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