The inference of gene trees with species trees.
The inference of gene trees with species trees.
复制标题
DOI：
10.1093/sysbio/syu048
复制
发表时间：
2015-01
影响因子：
6.5
通讯作者：
Boussau B
中科院分区：
文献类型：
--
作者：
Szöllősi GJ;Tannier E;Daubin V;Boussau B
本文综述了描述基因树和物种树之间关系的各种模型。分子遗传学主要集中在改进基于序列比对的基因树重建模型。然而，大多数遗传学家试图揭示物种的历史。虽然基因和物种的历史紧密相连，但它们很少是相同的，因为基因复制，丢失或水平转移，因为等位基因可以在种群中共存，可能跨越几个物种形成事件。因此，建立描述基因树和物种树之间关系的模型可以在已知物种树时改进基因树的重建，反之亦然。已经提出了几种方法来解决这个问题的一个方向或其他，但在一般情况下，既不基因树，也不物种树是已知的。只有少数研究试图联合推断基因树和物种树。这些模型解释了基因复制和丢失、转移或不完整的谱系分选。他们中的一些人认为几种类型的事件在一起，但目前还没有存在，认为完整的剧目，产生基因树沿着物种树。模拟以及基因组数据的实证研究表明，基因树物种树模型与序列进化模型相结合，提高了基因树重建。反过来，这些更好的基因树为研究基因组进化或重建祖先染色体和祖先基因序列提供了更可靠的基础。我们预测，基因树物种树的方法，可以处理基因组数据集将有助于推进我们对基因组进化的理解。
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.
登录
查看更多内容
横向遗传转移事件的系统发育鉴定。
影响因子：
3.4
作者：
Beiko RG;Hamilton N
通讯作者：
Hamilton N
影响因子：
3
作者：
Chaudhary R;Bansal MS;Wehe A;Fernández-Baca D;Eulenstein O
通讯作者：
Eulenstein O
影响因子：
5.8
作者：
Bansal, Mukul S.;Banay, Guy;Shamir, Ron
通讯作者：
Shamir, Ron
DOI：
10.1093/bioinformatics/bts374
发表时间：
2012-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Bérard S;Gallien C;Boussau B;Szöllősi GJ;Daubin V;Tannier E
通讯作者：
Tannier E
DOI：
10.1073/pnas.1116871109
发表时间：
2012-03-27
影响因子：
11.1
作者：
Abby, Sophie S.;Tannier, Eric;Daubin, Vincent
通讯作者：
Daubin, Vincent