The inference of gene trees with species trees

2013/11/04 by Gergely J. Szöllősi, Gergely J. Szöllosi, Szöllosi, Gergely J. +7 · 4 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #q-bio.PE

paper · pdf · doi:10.48550/arxiv.1311.0651

Review article in relation to the "Mathematical and Computational Evolutionary Biology" conference, Montpellier, 2013

arxiv created 2013/11/04 · openalex publication_date 2013/11/04 · arxiv updated 2013/11/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

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 co-exist 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. In this article we review the various models that have been used to describe the relationship between 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 better 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.

Citations

• The zebrafish reference genome sequence and its relationship to the human genome
• A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
• Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
• Gene Trees in Species Trees
• MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
• Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference

Cited by

• Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species
• Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data
• STRIDE: Species Tree Root Inference from Gene Duplication Events
• Whole-genome based phylogeny and comparative genomics of Sporidiobolales and related taxa of Basidiomycetes

Related

• Reconciliation of Gene and Species Trees With Polytomies
• Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species
• The Theory of Gene Family Histories
• Efficient Exploration of the Space of Reconciled Gene Trees
• An Evolving View of Species Tree Inference