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30
Molecular phylogenetics, principles and practice.
- Nature Reviews Genetics
, 2012
"... Systematics The inference of phylogenetic relationships among species and the use of such information to classify species. Taxonomy The description, classification and naming of species. Coalescent The process of joining ancestral lineages when the genealogical relationships of a random sample of s ..."
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Systematics The inference of phylogenetic relationships among species and the use of such information to classify species. Taxonomy The description, classification and naming of species. Coalescent The process of joining ancestral lineages when the genealogical relationships of a random sample of sequences from a modern population are traced back. Abstract | Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use.
Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria. Mol Biol Evol
"... The emergence of photosynthetic eukaryotes has played a crucial role in evolution and has strongly modified earth’s ecology. Several phylogenetic analyses have established that primary plastids arose from a cyanobacterium through endosymbiosis. However, the question of which present-day cyanobacteri ..."
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The emergence of photosynthetic eukaryotes has played a crucial role in evolution and has strongly modified earth’s ecology. Several phylogenetic analyses have established that primary plastids arose from a cyanobacterium through endosymbiosis. However, the question of which present-day cyanobacterial lineage is most closely related to primary plastids has been unclear. Here, we have performed an extensive phylogenomic investigation on the origin of primary plastids based on the analysis of up to 191 protein markers and over 30,000 aligned amino acid sites from 22 primary photosynthetic eukaryotes and 61 cyanobacteria representing a wide taxonomic sampling of this phylum. By using a number of solutions to circumvent a large range of systematic errors, we have reconstructed a robust global phylogeny of cyanobacteria and studied the placement of primary plastids within it. Our results strongly support an early emergence of primary plastids within cyanobacteria, prior to the diversification of most present-day cyanobacterial lineages for which genomic data are available. Key words: primary plastids, cyanobacteria, phylogenomics, character state recoding, ancestral sequences.
Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals
, 2011
"... Abstract.—Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian or ..."
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Abstract.—Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years. [Laurasiatheria; phylogenomics; rapid divergence; placental mammals.] Mammalian phylogeny has recently received extensive
Aguileta G: Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple coinertia analysis
- Mol Biol Evol
"... Full genome data sets are currently being explored on a regular basis to infer phylogenetic trees, but there are often discordances among the trees produced by different genes. An important goal in phylogenomics is to identify which individual gene and species produce the same phylogenetic tree and ..."
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Full genome data sets are currently being explored on a regular basis to infer phylogenetic trees, but there are often discordances among the trees produced by different genes. An important goal in phylogenomics is to identify which individual gene and species produce the same phylogenetic tree and are thus likely to share the same evolutionary history. On the other hand, it is also essential to identify which genes and species produce discordant topologies and therefore evolve in a different way or represent noise in the data. The latter are outlier genes or species and they can provide a wealth of information on potentially interesting biological processes, such as incomplete lineage sorting, hybridization, and horizontal gene transfers. Here, we propose a new method to explore the genomic tree space and detect outlier genes and species based on multiple co-inertia analysis (MCOA), which efficiently captures and compares the similarities in the phylogenetic topologies produced by individual genes. Our method allows the rapid identification of outlier genes and species by extracting the similarities and discrepancies, in terms of the pairwise distances, between all the species in all the trees, simultaneously. This is achieved by using MCOA, which finds successive decomposition axes from individual ordinations (i.e., derived from distance matrices) that maximize a covariance function. The method is freely available as a set of R functions. The source code and tutorial can be found online at
Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus
, 2011
"... In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring ..."
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In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring the genetic and chromosomal changes involved in the evolution of dioecy, but is mainly based on data from a single locus (ITS). To establish the order of events more clearly, and inform outgroup choice, we therefore carried out (i) multi-nuclear-gene phylogenetic analyses of 14 Silene species (including 7 hermaphrodite or gynodioecious species), representing species from both Silene clades with dioecious members, plus a more distantly related outgroup, and (ii) a BayesTraits character analysis of the evolution of dioecy. We confirm two origins of dioecy within this genus in agreement with recent work on comparing sex chromosomes from both clades with dioecious species. We conclude that sex chromosomes evolved after the origin of Silene and within a clade that includes only S. latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of
Phylogenomic Analysis Using Bayesian Congruence Measuring
- In Proceedings of 2nd ISCA International Conference on Bioinformatics and Computational Biology (BICoB
, 2010
"... Phylogenomic analysis of large sets of molecu-lar characters, primarily DNA and proteins, provides great opportunities to estimate and understand impor-tant evolutionary processes. However, molecular phy-logenies inferred from individual loci often differ. This incongruence among phylogenies can be ..."
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Phylogenomic analysis of large sets of molecu-lar characters, primarily DNA and proteins, provides great opportunities to estimate and understand impor-tant evolutionary processes. However, molecular phy-logenies inferred from individual loci often differ. This incongruence among phylogenies can be the result of systematic error, but can also be the result of differ-ent evolutionary histories. We propose a new method, based on Bayesian hierarchical clustering and poste-rior probability, to measure congruence between genes and to identify sets of congruent loci within which the genes or proteins share identical evolutionary history. We demonstrate the method on a sequence data of 10 nuclear genes from 20 ray-finned fish (Actinopterygii) species. 1
DIVERSITY OF EUKARYOTES AND THEIR GENOMES
, 2011
"... This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact ..."
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This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact
