Journal
SYSTEMATIC BIOLOGY
Volume 64, Issue 1, Pages E42-E62Publisher
OXFORD UNIV PRESS
DOI: 10.1093/sysbio/syu048
Keywords
Algorithm; amalgamation; Bayesian inference; birth-death model; coalescent; dynamic programming; gene duplication; gene loss; gene transfer; gene tree; hybridization; maximum likelihood; phylogenetics; species tree
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Funding
- French Agence Nationale de la Recherche (ANR) [ANR-10-BINF-01-01]
- Marie Curie Genestory [CIG 618438]
- Albert Szent-Gyorgyi Call-Home Researcher Scholarship [A1-SZGYA-FOK-13-0005]
- European Union
- State of Hungary
- European Social Fund [TAMOP 4.2.4.A/1-11-1-2012-0001]
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This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.
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