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.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Szöllősi GJ,Tannier E,Daubin V,Boussau Bdoi
10.1093/sysbio/syu048subject
Has Abstractpub_date
2015-01-01 00:00:00pages
e42-62issue
1eissn
1063-5157issn
1076-836Xpii
syu048journal_volume
64pub_type
杂志文章,评审abstract：:The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, rece...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150490423430
更新日期：2004-04-01 00:00:00
abstract：:We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the fami...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syz043
更新日期：2020-03-01 00:00:00
abstract：:The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character sta...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150600697465
更新日期：2006-06-01 00:00:00
abstract：:Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approa...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa069
更新日期：2020-09-03 00:00:00
abstract：:A controversial topic that underlies much of phylogenetic experimental design is the relative utility of increased taxonomic versus character sampling. Conclusions about the relative utility of adding characters or taxa to a current phylogenetic study have subtly hinged upon the appropriateness of the rate of evolutio...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syq025
更新日期：2010-07-01 00:00:00
abstract：:We found that trends in the rate of description of 580,000 marine and terrestrial species, in the taxonomically authoritative World Register of Marine Species and Catalogue of Life databases, were similar until the 1950s. Since then, the relative number of marine to terrestrial species described per year has increased...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syr080
更新日期：2012-10-01 00:00:00
abstract：:The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpi...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syw039
更新日期：2016-09-01 00:00:00
abstract：:Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus intera...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150590945359
更新日期：2005-06-01 00:00:00
abstract：:Understanding the origin of island endemics is a central task of historical biogeography. Recent methodological advances provide a rigorous framework to determine the relative contribution of different biogeographic processes (e.g., vicariance, land migration, long-distance dispersal) to the origin of island endemics....
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syq046
更新日期：2010-12-01 00:00:00
abstract：:As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceede...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syy026
更新日期：2018-11-01 00:00:00
abstract：:Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, t...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syt009
更新日期：2013-05-01 00:00:00
abstract：:Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150802580949
更新日期：2008-12-01 00:00:00
abstract：:We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is...
journal_title：Systematic biology
pub_type： 杂志文章,评审
doi：10.1093/sysbio/syt029
更新日期：2013-09-01 00:00:00
abstract：:Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuc...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa085
更新日期：2021-01-07 00:00:00
abstract：:In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic o...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/sys088
更新日期：2013-03-01 00:00:00
abstract：:We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of indiv...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150390197019
更新日期：2003-08-01 00:00:00
abstract：:Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predic...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa071
更新日期：2020-09-17 00:00:00
abstract：:The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150500541672
更新日期：2006-04-01 00:00:00
abstract：:We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syr101
更新日期：2012-03-01 00:00:00
abstract：:Historically, comparisons of host and parasite phylogenies have concentrated on cospeciation. However, many of these comparisons have demonstrated that the phylogenies of hosts and parasites are seldom completely congruent, suggesting that phenomena other than cospeciation play an important role in the evolution of ho...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150490265085
更新日期：2004-02-01 00:00:00
abstract：:Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence bet...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635159950127321
更新日期：2000-09-01 00:00:00
abstract：:Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov ch...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150600812544
更新日期：2006-08-01 00:00:00
abstract：:Horizontal gene transfer (HGT) is one of the main mechanisms driving the evolution of microorganisms. Its accurate identification is one of the major challenges posed by reticulate evolution. In this article, we describe a new polynomial-time algorithm for inferring HGT events and compare 3 existing and 1 new tree com...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syp103
更新日期：2010-03-01 00:00:00
abstract：:Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplas...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/106351500750049734
更新日期：2000-12-01 00:00:00
abstract：:The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2-dimensional plane, however the accuracy of the...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa061
更新日期：2020-07-29 00:00:00
abstract：:Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a h...
journal_title：Systematic biology
pub_type： 杂志文章
doi：
更新日期：2001-06-01 00:00:00
abstract：:Randomization tests allow the formulation and statistical testing of null hypotheses about the quality of entire data sets or the quality of fit between the data and particular phylogenetic hypotheses. Randomization tests of phylogenetic hypotheses based on the concepts of split support and split conflict are describe...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/106351598260662
更新日期：1998-12-01 00:00:00
abstract：:Matrix representation with parsimony (MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study,...
journal_title：Systematic biology
pub_type： 杂志文章
doi：
更新日期：2003-12-01 00:00:00
abstract：:Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for th...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syw004
更新日期：2016-09-01 00:00:00
abstract：:Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide da...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syw018
更新日期：2016-07-01 00:00:00
