The Inference of Gene Trees with Species Trees

Abstract

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.

Pitfalls in supermatrix phylogenomics

“…Clearly, the first approach will be limited by computational burden and a risk of over-parameterization. In contrast, it is unclear whether it is better to continue improving the current strategies based on a "static" supermatrix, or to further develop methods that simultaneously perform alignment and phylogenetic inference of a supermatrix (Hein 1990;Liu et al 2012) or to develop methods that simultaneously infer single-gene trees and the species tree using reconciliation (to handle incomplete lineage sorting, duplication or horizontal gene transfer; reviewed in Szollosi et al 2015). Careful (empirical) studies comparing the advantages of these different approaches are needed.…”

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

“…Studies have proposed various optimizing criteria, from minimizing the total Robinson-Foulds distance of the supertree (Bansal et al, 2010) to the Subtree Prune-and-Regraft distance (Whidden et al, 2014), and robustness to LGT Las compared betLeen tree-building approaches (e.g., supertrees versus supermatrix; Lapierre et al, 2014). HoLever, most of the methods dealing Lith LGT do not model coalescent process, except that a revieL paper by Szollosi et al (2015) discussed a potential model by extending and combining current methods (Szollosi et al, 2015). In this study, Le modelled ILS and LGT simultaneously, and it should be noted that Le tested CLASSIPHY's performance in a very difficult simulated scenario-high levels ILS.…”

Horizontal Gene Transfer and the History of Life

“…However, none of these approaches account for the fact that individual genes have complex and, most certainly, different histories, but rather simply combine phylogenetic markers, constraining them to a shared story, and as a result are bound to produce indecisive representations of the history of life. Reconstructing the history of life based on molecular data will require the development of more principled methodologies that explicitly deal with the complex processes of gene evolution (Boussau and Daubin 2010;Szölló´si et al 2015).…”

“…Hence, to reconstruct the history of species based on molecular data it is necessary, in addition to modeling sequence evolution, to be able to model the relationships between a gene tree and a species tree. This is currently an active avenue of research, although a complete model accounting for all mechanisms is still lacking (Szölló´si et al 2015). Most relevant to the inference of the tree of life, probabilistic models combining the likelihood of gene duplication, transfer, and loss scenarios and sequence evolution have been recently developed (Szölló´si et al 2013a;Sjöstrand et al 2014).…”