Abstract:
:Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree-species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Szöllõsi GJ,Rosikiewicz W,Boussau B,Tannier E,Daubin Vdoi
10.1093/sysbio/syt054subject
Has Abstractpub_date
2013-11-01 00:00:00pages
901-12issue
6eissn
1063-5157issn
1076-836Xpii
syt054journal_volume
62pub_type
杂志文章abstract::Even though relationships within Annelida are poorly understood, Eunicida is one of only a few major annelid lineages well supported by morphology. The seven recognized eunicid families possess sclerotized jaws that include mandibles and a maxillary apparatus. The maxillary apparatuses vary in shape and number of elem...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500354910
更新日期:2006-02-01 00:00:00
abstract::Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv084
更新日期:2016-03-01 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::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::Ants (Hymenoptera: Formicidae) are conspicuous organisms in most terrestrial ecosystems, often attaining high levels of abundance and diversity. In this study, we investigate the evolutionary history of a major clade of ants, the subfamily Dolichoderinae, whose species frequently achieve ecological dominance in ant co...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq012
更新日期:2010-05-01 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::Stochastic birth-death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this article, we first provide intuitive reasons for these known transfo...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syz039
更新日期:2019-09-01 00:00:00
abstract::We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an out-group. A Mar...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw063
更新日期:2017-05-01 00:00:00
abstract::We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the prob...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys030
更新日期:2012-10-01 00:00:00
abstract::Sequence divergence for segments of three mitochondrial DNA (mtDNA) genes encoding the 12S and 16S ribosomal RNA and cytochrome b was examined in newts belonging to the genus Euproctus (E. asper, E. montanus, E. platycephalus) and in three other species belonging to the same family (Salamandridae), Triturus carnifex, ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/46.1.126
更新日期:1997-03-01 00:00:00
abstract::How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids an...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500234625
更新日期:2005-10-01 00:00:00
abstract::Alignments of nucleotide or amino acid sequences may contain a variety of different signals, one of which is the historical signal that we often try to recover by phylogenetic analysis. Other signals, such as those arising due to compositional heterogeneities, among-lineage and among-site rate heterogeneities, invaria...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490503035
更新日期:2004-08-01 00:00:00
abstract::All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351599260319
更新日期:1999-06-01 00:00:00
abstract::Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the sam...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500481390
更新日期:2006-04-01 00:00:00
abstract::Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete tax...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa013
更新日期:2020-07-01 00:00:00
abstract::Siparunaceae comprise Glossocalyx with one species in West Africa and Siparuna with 65 species in the neotropics; all have unisexual flowers, and 15 species are monoecious, 50 dioecious. Parsimony and maximum likelihood analyses of combined nuclear ribosomal ITS and chloroplast trnL-trnF intergenic spacer sequences yi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351501753328820
更新日期:2001-09-01 00:00:00
abstract::Lice in the genus Pectinopygus parasitize a single order of birds (Pelecaniformes). To examine the degree of congruence between the phylogenies of 17 Pectinopygus species and their pelecaniform hosts, sequences from mitochondrial 12S rRNA, 16S rRNA, COI, and nuclear wingless and EF1-alpha genes (2290 nucleotides) and ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701311370
更新日期:2007-04-01 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::We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490503053
更新日期:2004-10-01 00:00:00
abstract::We collected ~29 kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 po...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys048
更新日期:2012-10-01 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::Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 spec...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490888840
更新日期:2004-12-01 00:00:00
abstract::Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recent...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syz030
更新日期:2020-01-01 00:00:00
abstract::Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflic...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa054
更新日期:2020-07-18 00:00:00
abstract::The genomics revolution offers great promise for resolving the phylogeny of living taxa, but does it offer any benefits for reconstructing relationships among extinct (fossil) taxa? Superficially, the answer would seem to be "no," given that molecular data cannot be obtained for most fossil taxa. However, because foss...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp012
更新日期:2009-02-01 00:00:00
abstract::Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv054
更新日期:2015-11-01 00:00:00
abstract::We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp020
更新日期:2009-04-01 00:00:00
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....
journal_title:Systematic biology
pub_type: 杂志文章,评审
doi:10.1093/sysbio/syu048
更新日期:2015-01-01 00:00:00
abstract::Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv058
更新日期:2016-01-01 00:00:00
abstract::Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated netw...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701424553
更新日期:2007-06-01 00:00:00