Species tree-aware simultaneous reconstruction of gene and domain evolution

Abstract

Most genes are composed of multiple domains, with a common evolutionary history, that typically perform a specific function in the resulting protein. As witnessed by many studies of key gene families, it is important to understand how domains have been duplicated, lost, transferred between genes, and rearranged. Analogously to the case of evolutionary events affecting entire genes, these domain events have large consequences for phylogenetic reconstruction and, in addition, they create considerable obstacles for gene sequence alignment algorithms, a prerequisite for phylogenetic reconstruction.We introduce the DomainDLRS model, a hierarchical, generative probabilistic model containing three levels corresponding to species, genes, and domains, respectively. From a dated species tree, a gene tree is generated according to the DL model, which is a birth-death model generalized to occur in a dated tree. Then, from the dated gene tree, a pre-specified number of dated domain trees are generated using the DL model and the molecular clock is relaxed, effectively converting edge times to edge lengths. Finally, for each domain tree and its lengths, domain sequences are generated for the leaves based on a selected model of sequence evolution.For this model, we present a MCMC-based inference framework called Do-mainDLRS that takes a dated species tree together with a multiple sequence alignment for each domain family as input and outputs an estimated posterior distribution over reconciled gene and domain trees. By requiring aligned domains rather than genes, our framework evades the problem of aligning full-length genes that have been exposed to domain duplications, in particular non-tandem domain duplications. We show that DomainDLRS performs better than MrBayes on synthetic data and that it outperforms MrBayes on biological data. We analyse several zincfinger genes and show that most domain duplications have been tandem duplications, some involving two or more domains, but non-tandem duplications have also been common. 1The main evolutionary events that affects gene evolution include speciation, gene duplication, gene loss, incomplete lineage sorting, and lateral gene transfer. During the last 10-15 years, considerable attention has been given to how such events induce an interplay between gene and species evolution and, in particular, its consequences for phylogenetic reconstruction. This trend has inspired considerable method development culminating in probabilistic species tree-aware methods for gene tree reconstruction and methods for simultaneous reconstruction of gene trees and species trees [1,2,3]. Complicating the issue further, most genes are composed of multiple domains, each a segment of contiguous nucleotides with a common evolutionary history that typically performs a specific function in the resulting protein (although also structure-based definitions of domains are common). As shown by many studies of key gene families such as PRDM9, ZNF91, and Reelin [4,5,6], domains can be also be an appropriate organizat...

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

“…Species trees are important models that can be used to address many biological questions, for example how is biodiversity created/maintained and how do species adapt to their environments ( Cracraft et al , 2004 ). There is also a vast literature regarding gene tree reconciliation , where gene trees are compared to an established species tree in order to understand how genes evolved (for some of the recent literature on this question, see Delabre et al , 2020 ; Dondi et al , 2019 ; El-Mabrouk and Noutahi, 2019 ; Hasić and Tannier, 2019 ; Jacox et al , 2016 ; Kundu and Bansal, 2018 ; Lai et al , 2017 ; Muhammad et al , 2018 ). However, in most cases, species trees are not known in advance and instead must be estimated.…”

Phylogenetic reconciliation

“…Just like two-level reconciliation can be used to improve lower or upper phylogenies, or to help constructing them from aligned sequences, joint reconciliation models can be used in the same manner. In this vein a coupled gene/species DL, domain gene DL and gene sequence evolution model in a bayesian framework improves the reconstruction of gene trees [ 176 ] ( Fig 5I ).…”

Improved inference of tandem domain duplications

“…Evolutionary event histories are typically gleaned through the process of reconciliation ( Goodman et al , 1979 ; Li and Bansal, 2019 ; Muhammad et al , 2018 ). In these methods, a phylogeny of related domains is built, along with a phylogeny of the genes (and sometimes species; Bansal et al , 2012 ; Stolzer et al , 2015 ) from which they came.…”