Academic literature on the topic 'Phylogenomic trees'
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Journal articles on the topic "Phylogenomic trees"
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Lee, Michael D. "Applications and Considerations of GToTree: A User-Friendly Workflow for Phylogenomics." Evolutionary Bioinformatics 15 (January 2019): 117693431986224. http://dx.doi.org/10.1177/1176934319862245.
Full textAbstract:
Phylogenomics is the practice of attempting to infer evolutionary relationships at a genome-level. This is becoming a standard step in the characterization of newly recovered genomes and to direct/constrain further research; yet the process from start to finish of building a de novo phylogenomic tree that is specific to the organisms of interest can still be computationally intractable for many biologists. GToTree is a recently published user-friendly workflow for phylogenomics intended to give more researchers the capability to generate phylogenomic trees to help guide their work. This commentary describes two common applications where GToTree can be helpful and then discusses some things to consider when using the program.
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Ay, Hilal, Hayrettin Saygin, and Nevzat Sahin. "Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae." International Journal of Systematic and Evolutionary Microbiology 70, no. 4 (April 1, 2020): 2569–79. http://dx.doi.org/10.1099/ijsem.0.004073.
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In recent years, the results of genome-based phylogenetic analyses have contributed to microbial systematics by increasing the availability of sequenced microbial genomes. Therefore, phylogenomic analysis within large taxa in the phylum Actinobacteria has appeared as a useful tool to clarify the taxonomic positions of ambiguous groups. In this study, we provide a revision of the actinobacterial family Streptosporangiaceae using a large collection of genome data and phylogenomics approaches. The phylogenomic analyses included the publicly available genome data of the members of the family Streptosporangiaceae and the state-of-the-art tools are used to infer the taxonomic affiliation of these species within the family. By comparing genome-based and 16S rRNA gene-based trees, as well as pairwise genome comparisons, the recently described genera Spongiactinospora and Desertactinospora are combined in the genus Spongiactinospora . In conclusion, a comprehensive phylogenomic revision of the family Streptosporangiaceae is proposed.
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Cheon, Seongmin, Jianzhi Zhang, and Chungoo Park. "Is Phylotranscriptomics as Reliable as Phylogenomics?" Molecular Biology and Evolution 37, no. 12 (July 13, 2020): 3672–83. http://dx.doi.org/10.1093/molbev/msaa181.
Full textAbstract:
Abstract Phylogenomics, the study of phylogenetic relationships among taxa based on their genome sequences, has emerged as the preferred phylogenetic method because of the wealth of phylogenetic information contained in genome sequences. Genome sequencing, however, can be prohibitively expensive, especially for taxa with huge genomes and when many taxa need sequencing. Consequently, the less costly phylotranscriptomics has seen an increased use in recent years. Phylotranscriptomics reconstructs phylogenies using DNA sequences derived from transcriptomes, which are often orders of magnitude smaller than genomes. However, in the absence of corresponding genome sequences, comparative analyses of transcriptomes can be challenging and it is unclear whether phylotranscriptomics is as reliable as phylogenomics. Here, we respectively compare the phylogenomic and phylotranscriptomic trees of 22 mammals and 15 plants that have both sequenced nuclear genomes and publicly available RNA sequencing data from multiple tissues. We found that phylotranscriptomic analysis can be sensitive to orthologous gene identification. When a rigorous method for identifying orthologs is employed, phylogenomic and phylotranscriptomic trees are virtually identical to each other, regardless of the tissue of origin of the transcriptomes and whether the same tissue is used across species. These findings validate phylotranscriptomics, brighten its prospect, and illustrate the criticality of reliable ortholog detection in such practices.
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Galtier, Nicolas, and Vincent Daubin. "Dealing with incongruence in phylogenomic analyses." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1512 (October 7, 2008): 4023–29. http://dx.doi.org/10.1098/rstb.2008.0144.
Full textAbstract:
Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent. We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.
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Shah, Toral, Fandey H. Mashimba, Haji O. Suleiman, Yahya S. Mbailwa, Julio V. Schneider, Georg Zizka, Vincent Savolainen, Isabel Larridon, and Iain Darbyshire. "Phylogenetics of Ochna (Ochnaceae) and a new infrageneric classification." Botanical Journal of the Linnean Society 198, no. 4 (December 3, 2021): 361–81. http://dx.doi.org/10.1093/botlinnean/boab071.
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Abstract Advances in high-throughput DNA sequencing are allowing faster and more affordable generation of molecular phylogenetic trees for many organisms. However, resolving relationships at species level is still challenging, particularly for taxonomically difficult groups. Until recently, the classification of Ochna had been based only on morphological data. Here, we present the first comprehensive phylogenomic study for the genus using targeted sequencing with a custom probe kit. We sampled c. 85% of species to evaluate the current infrageneric classification. Our results show that the data generated using the custom probe kit are effective in resolving relationships in the genus, revealing three sections consistent with the current classification and a new section consisting of species from Madagascar and the Mascarene Islands. Our results provide the first insights into the evolutionary relationships of several widespread and morphologically diverse species numerous poorly known and potentially new species to science. We demonstrate that for morphologically challenging groups such as Ochna, an integrated approach to classification is essential. Phylogenomic results are only informative when derived from accurately named samples. There is a symbiotic relationship between molecular phylogenomics and morphology-based taxonomy, with taxonomic expertise a requirement to accurately interpret the phylogenomic results.
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Vinh, Lê Sỹ. "Phylogenetic and Phylogenomic Analyses for Large Datasets." Journal of Research and Development on Information and Communication Technology 2019, no. 2 (December 31, 2019): 84–92. http://dx.doi.org/10.32913/mic-ict-research.v2019.n2.898.
Full textAbstract:
The phylogenetic tree is a main tool to study the evolutionary relationships among species. Computational methods for building phylogenetic trees from gene/protein sequences have been developed for decades and come of age. Efficient approaches, including distance-based methods, maximum likelihood methods, or classical maximum parsimony methods, are now able to analyze datasets with thousands of sequences. The advanced sequencing technologies have resulted in a huge amount of data including whole genomes. A number of methods have been proposed to analyze the wholegenome datasets, however, numerous challenges need to be addressed and solved to translate phylogenomic inferences into practices. In this paper, we will analyze widely-used methods to construct large phylogenetic trees, and available methods to build phylogenomic trees from whole-genome datasets. We will also give recommendations for best practices when performing phylogenetic and phylogenomic analyses. The paper will enable researchers to comprehend the state-ofthe-art methods and available software to efficiently study the evolutionary relationships among species from large datasets.
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Xiao, Guohua, Guirong Tang, and Chengshu Wang. "Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi." Journal of Fungi 6, no. 3 (August 13, 2020): 134. http://dx.doi.org/10.3390/jof6030134.
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Amid the genomic data explosion, phylogenomic analysis has resolved the tree of life of different organisms, including fungi. Genome-wide clustering has also been conducted based on gene content data that can lighten the issue of the unequal evolutionary rate of genes. In this study, using different fungal species as models, we performed phylogenomic and protein-content (PC)-based clustering analysis. The obtained sequence tree reflects the phylogenetic trajectory of examined fungal species. However, 15 PC-based trees constructed from the Pfam matrices of the whole genomes, four protein families, and ten subcellular locations largely failed to resolve the speciation relationship of cross-phylum fungal species. However, lifestyle and taxonomic associations were more or less evident between closely related fungal species from PC-based trees. Pairwise congruence tests indicated that a varied level of congruent or discordant relationships were observed between sequence- and PC-based trees, and among PC-based trees. It was intriguing to find that a few protein family and subcellular PC-based trees were more topologically similar to the phylogenomic tree than was the whole genome PC-based phylogeny. In particular, a most significant level of congruence was observed between sequence- and cell wall PC-based trees. Cophylogenetic analysis conducted in this study may benefit the prediction of the magnitude of evolutionary conservation, interactive associations, or networking between different family or subcellular proteins.
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Jiang, Xiaodong, Scott V. Edwards, and Liang Liu. "The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets." Systematic Biology 69, no. 4 (February 3, 2020): 795–812. http://dx.doi.org/10.1093/sysbio/syaa008.
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Abstract A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically congruent gene trees suggest that a poor fit of substitution models, rejected by 44% of loci, and concatenation models, rejected by 38% of loci, is widespread. Logistic regression shows that the proportions of GC content and informative sites are both negatively correlated with the fit of substitution models across loci. Moreover, a substantial violation of the concatenation assumption of congruent gene trees is consistently observed across six major groups (birds, mammals, fish, insects, reptiles, and others, including other invertebrates). In contrast, among those loci adequately described by a given substitution model, the proportion of loci rejecting the MSC model is 11%, significantly lower than those rejecting the substitution and concatenation models. Although conducted on reduced data sets due to computational constraints, Bayesian model validation and comparison both strongly favor the MSC over concatenation across all data sets; the concatenation assumption of congruent gene trees rarely holds for phylogenomic data sets with more than 10 loci. Thus, for large phylogenomic data sets, model comparisons are expected to consistently and more strongly favor the coalescent model over the concatenation model. We also found that loci rejecting the MSC have little effect on species tree estimation. Our study reveals the value of model validation and comparison in phylogenomic data analysis, as well as the need for further improvements of multilocus models and computational tools for phylogenetic inference. [Bayes factor; Bayesian model validation; coalescent prior; congruent gene trees; independent prior; Metazoa; posterior predictive simulation.]
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Lee, Michael D. "GToTree: a user-friendly workflow for phylogenomics." Bioinformatics 35, no. 20 (March 13, 2019): 4162–64. http://dx.doi.org/10.1093/bioinformatics/btz188.
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Abstract Summary Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists’ work. Accordingly, there are several tools available for the major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required—such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.—can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees. Availability and implementation GToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python. Supplementary information Supplementary data are available at Bioinformatics online.
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Zhang, Chao, Celine Scornavacca, Erin K. Molloy, and Siavash Mirarab. "ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy." Molecular Biology and Evolution 37, no. 11 (September 4, 2020): 3292–307. http://dx.doi.org/10.1093/molbev/msaa139.
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Abstract Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees. However, most of these methods, including the widely used ASTRAL, can only handle single-copy gene trees and do not attempt to model gene duplication and gene loss. As a result, most phylogenomic studies have focused on single-copy genes and have discarded large parts of the data. Here, we first propose a measure of quartet similarity between single-copy and multicopy trees that accounts for orthology and paralogy. We then introduce a method called ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs) to find the species tree that optimizes our quartet similarity measure using dynamic programing. By studying its performance on an extensive collection of simulated data sets and on real data sets, we show that ASTRAL-Pro is more accurate than alternative methods.
Dissertations / Theses on the topic "Phylogenomic trees"
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Kang, Qiwen. "UNSUPERVISED LEARNING IN PHYLOGENOMIC ANALYSIS OVER THE SPACE OF PHYLOGENETIC TREES." UKnowledge, 2019. https://uknowledge.uky.edu/statistics_etds/39.
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A phylogenetic tree is a tree to represent an evolutionary history between species or other entities. Phylogenomics is a new field intersecting phylogenetics and genomics and it is well-known that we need statistical learning methods to handle and analyze a large amount of data which can be generated relatively cheaply with new technologies. Based on the existing Markov models, we introduce a new method, CURatio, to identify outliers in a given gene data set. This method, intrinsically an unsupervised method, can find outliers from thousands or even more genes. This ability to analyze large amounts of genes (even with missing information) makes it unique in many parametric methods. At the same time, the exploration of statistical analysis in high-dimensional space of phylogenetic trees has never stopped, many tree metrics are proposed to statistical methodology. Tropical metric is one of them. We implement a MCMC sampling method to estimate the principal components in a tree space with the tropical metric for achieving dimension reduction and visualizing the result in a 2-D tropical triangle.
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Capella, Gutiérrez Salvador Jesús 1985. "Analysis of multiple protein sequence alignments and phylogenetic trees in the context of phylogenomics studies." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/97289.
Full textAbstract:
Phylogenomics is a biological discipline which can be understood as the intersection
of the fields of genomics and evolution. Its main focuses are the
analyses of genomes through the evolutionary lens and the understanding of
how different organisms relate to each other. Moreover, phylogenomics allows
to make accurate functional annotations of newly sequenced genomes.
This discipline has grown in response to the deluge of data coming from different
genome projects. To achieve their objectives, phylogenomics heavily
depends on the accuracy of different methods to generate precise phylogenetic
trees. Phylogenetic trees are the basic tool of this field and serve to
represent how sequences or species relate to each other through common
ancestry. During my thesis, I have centered my efforts in improving an automated
pipeline to generate accurate phylogenetic trees and its posterior
publication through a public database. Among the efforts to improve the
pipeline, I have specially focused on the problem of multiple sequence alignment
post-processing, which has been shown to be central to the reliability
of subsequent analyses. Subsequently I have applied this pipeline, and a
battery of other phylogenomics tools, to the study of the phylogenetic position
of Microsporidia, a group of fast-evolving intracellular parasites. Due
to their special genomic features, Microsporidia evolution constitutes one of
the classical examples of challenging problems for phylogenomics. Finally,
I have also used the pipeline as a part of a newly designed method for selecting
robust combinations of phylogenetic gene markers. I have used this
method for selecting optimal gene sets to assess the phylogenetic relationships
within fungi and cyanobacteria, showing that the potential of these
genes as phylogenetic markers goes well beyond the species used for their
selection.Filogenómica es una disciplina biológica que puede ser entendida como la intersección entre los campos de la genómica y la evolución. Su área de estudio es el análisis evolutivo de los genomas y como se relacionan las distintas especies entre sí. Además, la filogenómica tiene como objetivo anotar funcionalmente, con gran precisi ón, genomas recién secuenciados. De hecho, esta disciplina ha crecido rápidamente en los úultimos años como respuesta a la avalancha de datos provenientes de distintos proyectos genómicos. Para alcanzar sus objetivos, la filogenómica depende, en gran medida, de los distintos métodos usados para generar árboles filogenéticos. Los árboles filogenéticos son las herramientas básicas de la filogenómica y sirven para representar como secuencias y especies se relacionan entre sí por ascendencia. Durante el desarrollo de mi tesis, he centrado mis esfuerzos en mejorar una pipeline (conjunto de programas ejecutados de forma controlada) automática que permite generar árboles filogenéticos con gran precisión, y como ofrecer estos datos a la comunidad científica a través de una base de datos. Entre los esfuerzos realizados para mejorar la pipeline, me he centrado especialmente en el post-procesamiento previo a cualquier análisis de alineamientos múltiples de secuencias, ya que la calidad del alineamiento determina la de los estudios posteriores. En un contexto más biológico, he usado esta pipeline junto con otras herramientas filogenómicas en el estudio de la posición filogenética de Microsporidia. Dadas sus características genómicas especiales, la evolución de Microsporidia constituye uno de los problemas clásicos y difíciles de resolver en filogenómica. Finalmente, he usado también la pipeline como parte de un nuevo método para seleccionar combinaciones óptimas de genes con potencial como marcadores filogenéticos. De hecho, he usado este método para identificar conjuntos de marcadores filogenéticos que permiten reconstruir con alto grado de precisión las relaciones evolutivas en Cyanobacterias y en Hongos. Lo más interesante de este método es que eval úa la fiabilidad de los marcadores en especies no usadas para su selección.
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Martijn, Joran. "Exploration of microbial diversity and evolution through cultivation independent phylogenomics." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-327310.
Full textAbstract:
Our understanding of microbial evolution is largely dependent on available genomic data of diverse organisms. Yet, genome-sequencing efforts have mostly ignored the diverse uncultivable majority in favor of cultivable and sociologically relevant organisms. In this thesis, I have applied and developed cultivation independent methods to explore microbial diversity and obtain genomic data in an unbiased manner. The obtained genomes were then used to study the evolution of mitochondria, Rickettsiales and Haloarchaea. Metagenomic binning of oceanic samples recovered draft genomes for thirteen novel Alphaproteobacteria-related lineages. Phylogenomics analyses utilizing the improved taxon sample suggested that mitochondria are not related to Rickettsiales but rather evolved from a proteobacterial lineage closely related to all sampled alphaproteobacteria. Single-cell genomics and metagenomics of lake and oceanic samples, respectively, identified previously unobserved Rickettsiales-related lineages. They branched early relative to characterized Rickettsiales and encoded flagellar genes, a feature once thought absent in this order. Flagella are most likely an ancestral feature, and were independently lost during Rickettsiales diversification. In addition, preliminary analyses suggest that ATP/ADP translocase, the marker for energy parasitism, was acquired after the acquisition of type IV secretion systems during the emergence of the Rickettsiales. Further exploration of the oceanic samples yielded the first draft genomes of Marine Group IV archaea, the closest known relatives of the Haloarchaea. The halophilic and generally aerobic Haloarchaea are thought to have evolved from an anaerobic methanogenic ancestor. The MG-IV genomes allowed us to study this enigmatic evolutionary transition. Preliminary ancestral reconstruction analyses suggest a gradual loss of methanogenesis and adaptation to an aerobic lifestyle, respectively. The thesis further presents a new amplicon sequencing method that captures near full-length 16S and 23S rRNA genes of environmental prokaryotes. The method exploits PacBio's long read technology and the frequent proximity of these genes in prokaryotic genomes. Compared to traditional partial 16S amplicon sequencing, our method classifies environmental lineages that are distantly related to reference taxa more confidently. In conclusion, this thesis provides new insights into the origins of mitochondria, Rickettsiales and Haloarchaea and illustrates the power of cultivation independent methods with respect to the study of microbial evolution.
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He, Ding. "Inferring Ancestry : Mitochondrial Origins and Other Deep Branches in the Eukaryote Tree of Life." Doctoral thesis, Uppsala universitet, Systematisk biologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-231670.
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There are ~12 supergroups of complex-celled organisms (eukaryotes), but relationships among them (including the root) remain elusive. For Paper I, I developed a dataset of 37 eukaryotic proteins of bacterial origin (euBac), representing the conservative protein core of the proto-mitochondrion. This gives a relatively short distance between ingroup (eukaryotes) and outgroup (mitochondrial progenitor), which is important for accurate rooting. The resulting phylogeny reconstructs three eukaryote megagroups and places one, Discoba (Excavata), as sister group to the other two (neozoa). This rejects the reigning “Unikont-Bikont” root and highlights the evolutionary importance of Excavata. For Paper II, I developed a 150-gene dataset to test relationships in supergroup SAR (Stramenopila, Alveolata, Rhizaria). Analyses of all 150-genes give different trees with different methods, but also reveal artifactual signal due to extremely long rhizarian branches and illegitimate sequences due to horizontal gene transfer (HGT) or contamination. Removing these artifacts leads to strong consistent support for Rhizaria+Alveolata. This breaks up the core of the chromalveolate hypothesis (Stramenopila+Alveolata), adding support to theories of multiple secondary endosymbiosis of chloroplasts. For Paper III, I studied the evolution of cox15, which encodes the essential mitochondrial protein Heme A synthase (HAS). HAS is nuclear encoded (nc-cox15) in all aerobic eukaryotes except Andalucia godoyi (Jakobida, Excavata), which encodes it in mitochondrial DNA (mtDNA) (mt-cox15). Thus the jakobid gene was postulated to represent the ancestral gene, which gave rise to nc-cox15 by endosymbiotic gene transfer. However, our phylogenetic and structure analyses demonstrate an independent origin of mt-cox15, providing the first strong evidence of bacteria to mtDNA HGT. Rickettsiales or SAR11 often appear as sister group to modern mitochondria. However these bacteria and mitochondria also have independently evolved AT-rich genomes. For Paper IV, I assembled a dataset of 55 mitochondrial proteins of clear α-proteobacterial origin (including 30 euBacs). Phylogenies from these data support mitochondria+Rickettsiales but disagree on the placement of SAR11. Reducing amino-acid compositional heterogeneity (resulting from AT-bias) stabilizes SAR11 but moves mitochondria to the base of α-proteobacteria. Signal heterogeneity supporting other alternative hypotheses is also detected using real and simulated data. This suggests a complex scenario for the origin of mitochondria.
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Ullah, Ikram. "Probabilistic Models for Species Tree Inference and Orthology Analysis." Doctoral thesis, KTH, Beräkningsbiologi, CB, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-168146.
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A phylogenetic tree is used to model gene evolution and species evolution using molecular sequence data. For artifactual and biological reasons, a gene tree may differ from a species tree, a phenomenon known as gene tree-species tree incongruence. Assuming the presence of one or more evolutionary events, e.g., gene duplication, gene loss, and lateral gene transfer (LGT), the incongruence may be explained using a reconciliation of a gene tree inside a species tree. Such information has biological utilities, e.g., inference of orthologous relationship between genes. In this thesis, we present probabilistic models and methods for orthology analysis and species tree inference, while accounting for evolutionary factors such as gene duplication, gene loss, and sequence evolution. Furthermore, we use a probabilistic LGT-aware model for inferring gene trees having temporal information for duplication and LGT events. In the first project, we present a Bayesian method, called DLRSOrthology, for estimating orthology probabilities using the DLRS model: a probabilistic model integrating gene evolution, a relaxed molecular clock for substitution rates, and sequence evolution. We devise a dynamic programming algorithm for efficiently summing orthology probabilities over all reconciliations of a gene tree inside a species tree. Furthermore, we present heuristics based on receiver operating characteristics (ROC) curve to estimate suitable thresholds for deciding orthology events. Our method, as demonstrated by synthetic and biological results, outperforms existing probabilistic approaches in accuracy and is robust to incomplete taxon sampling artifacts. In the second project, we present a probabilistic method, based on a mixture model, for species tree inference. The method employs a two-phase approach, where in the first phase, a structural expectation maximization algorithm, based on a mixture model, is used to reconstruct a maximum likelihood set of candidate species trees. In the second phase, in order to select the best species tree, each of the candidate species tree is evaluated using PrIME-DLRS: a method based on the DLRS model. The method is accurate, efficient, and scalable when compared to a recent probabilistic species tree inference method called PHYLDOG. We observe that, in most cases, the analysis constituted only by the first phase may also be used for selecting the target species tree, yielding a fast and accurate method for larger datasets. Finally, we devise a probabilistic method based on the DLTRS model: an extension of the DLRS model to include LGT events, for sampling reconciliations of a gene tree inside a species tree. The method enables us to estimate gene trees having temporal information for duplication and LGT events. To the best of our knowledge, this is the first probabilistic method that takes gene sequence data directly into account for sampling reconciliations that contains information about LGT events. Based on the synthetic data analysis, we believe that the method has the potential to identify LGT highways.QC 20150529
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Muhammad, Sayyed Auwn. "Probabilistic Modelling of Domain and Gene Evolution." Doctoral thesis, KTH, Beräkningsvetenskap och beräkningsteknik (CST), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-191352.
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Phylogenetic inference relies heavily on statistical models that have been extended and refined over the past years into complex hierarchical models to capture the intricacies of evolutionary processes. The wealth of information in the form of fully sequenced genomes has led to the development of methods that are used to reconstruct the gene and species evolutionary histories in greater and more accurate detail. However, genes are composed of evolutionary conserved sequence segments called domains, and domains can also be affected by duplications, losses, and bifurcations implied by gene or species evolution. This thesis proposes an extension of evolutionary models, such as duplication-loss, rate, and substitution, that have previously been used to model gene evolution, to model the domain evolution. In this thesis, I am proposing DomainDLRS: a comprehensive, hierarchical Bayesian method, based on the DLRS model by Åkerborg et al., 2009, that models domain evolution as occurring inside the gene and species tree. The method incorporates a birth-death process to model the domain duplications and losses along with a domain sequence evolution model with a relaxed molecular clock assumption. The method employs a variant of Markov Chain Monte Carlo technique called, Grouped Independence Metropolis-Hastings for the estimation of posterior distribution over domain and gene trees. By using this method, we performed analyses of Zinc-Finger and PRDM9 gene families, which provides an interesting insight of domain evolution. Finally, a synteny-aware approach for gene homology inference, called GenFamClust, is proposed that uses similarity and gene neighbourhood conservation to improve the homology inference. We evaluated the accuracy of our method on synthetic and two biological datasets consisting of Eukaryotes and Fungal species. Our results show that the use of synteny with similarity is providing a significant improvement in homology inference.QC 20160904
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Galindo, González Luis Javier. "Deep eukaryotic phylogenomics : the holomycota branch Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): an early Branching Microsporidium A new fungal clade helps reconstructing the tree of Fungi and the evolution of the flagellum in Holomycota Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS050.
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La plupart de la diversité biologique est en réalité microbienne. L'arbre phylogénétique des eucaryotes comprend plusieurs grands supergroupes monophylétiques, dont les Opisthokonta. Ce groupe comprend deux branches, les Holozoa, qui inclut les animaux, et les Holomycota, qui regroupe les champignons et leurs parents unicellulaires. Bien que les champignons multicellulaires soient bien connus, nos connaissances sur la diversité des champignons unicellulaires et de leurs parents phylogénétiques restent limitées. Cette fraction unicellulaire comprend plusieurs lignées zoosporiques (par exemple chytrids) au sein des champignons, mais aussi une variété de lignées liées aux champignons classiques : les nucleariids, les rozellids, les aphelids et les microsporidies. Cependant, les relations phylogénétiques de ces lignées entre elles et avec les champignons restent à établir solidement. Les arbres phylogénétiques des gènes d'ARNr 18S environnementaux montrent une grande diversité d'Holomycota unicellulaires dans la plupart des écosystèmes terrestres. Cependant, le signal phylogénétique de ce gène est limité et ne permet pas de résoudre la plupart des relations phylogénétiques profondes. Au cours des dernières années, les techniques à haut débit ont permis de séquencer des centaines de nouveaux génomes et transcriptomes. Cela a permis de réaliser des études phylogénomiques multi-gènes, qui augmentent le signal disponible pour résoudre les relations évolutives. Néanmoins, la plupart de ces génomes correspondent à des espèces fongiques faciles à cultiver, souvent avec un intérêt particulier pour l'homme. Actuellement, les approches de type « omique » à partir des cellules uniques se révèlent comme potentiellement utiles pour étudier les eucaryotes unicellulaires non cultivés, en permettant de reconstruire des analyses phylogénétiques robustes d'une grande diversité environnementale à l'aide de données génomiques et transcriptomiques. Au cours de mon travail de doctorat, j'ai appliqué des approches de « cellule unique » pour obtenir des informations phylogénétiques à partir de lignées Holomycota divergentes, clarifier les relations phylogénétiques entre les champignons et ses proches parents et inférer l'évolution de leurs traits. Plus précisément, j'ai utilisé cette approche pour :1) Générer des données génomiques et transcriptomiques pour les nucleariids et mieux reconstruire les relations internes dans le clade et les caractères présents dans leur ancêtre. Nos résultats confirment que les genres de protistes à thèque Pompholyxophrys et Lithocolla sont en effet des nucleariids et branchent avec Nuclearia, Parvularia et Fonticula. La reconstruction d'une phylogénie robuste de ce groupe nous a permis d’inférer les traits (par exemple pas de flagelle) ancestraux du groupe. 2) Séquencer et analyser de manière comparative le génome de Metchnikovella incurvata, pour confirmer sa position relativement basale dans Microsporidia et déterminer les synapomorphies du clade. L'analyse phylogénomique du metchnikovellid Metchnikovella incurvata a confirmé que des Metchnikovellidae branchent à la base des Core-Microsporidia. Nous avons également confirmé que leur profil métabolique était plus similaire à celui des Core-microsporidia, tous deux ayant réduit de manière similaire leurs gènes / fonctions. 3) Générer des données génomiques pour Amoeboradix gromovi et Sanchytrium tribonematis, qui forment le clade des sanchytrides, une nouvelle lignée de champignons zoosporiques identifiée récemment, et résoudre leur position phylogénétique. L'étude des deux génomes de sanchytrids a clarifié leur placement au sein des Fungi en tant que nouvelle groupe frère des Blastocladiomycota. Des analyses génomiques comparatives montrent que leur métabolisme est réduit par rapport aux lignées apparentées. En particulier, le système flagellaire est fortement réduit par rapport à d'autres Holomycota, avec 4 événements indépendants de perte de flagelle dans le cladeDespite the astonishing diversity of plants, animals and macroscopic fungi, most eukaryotic diversity is actually microbial. The eukaryotic tree comprises several large monophyletic supergroups. One of these groups is the Opisthokonta, which encompasses two branches, Holozoa, including animals, and Holomycota, grouping Fungi and their unicellular relatives. While multicellular fungi are well known, knowledge on the diversity of unicellular Fungi and their phylogenetic relatives is still poor. This unicellular fraction includes several zoosporic lineages (e.g. Chytridiomycota and Blastocladiomycota) within Fungi, but also a variety of lineages related to the classical core Fungi: nucleariids, rozellids, aphelids and Microsporidia. However, the phylogenetic relationships of these lineages among them and with classical Fungi remain to be solidly established. Molecular phylogenetic trees of 18S rRNA genes retrieved from environmental studies have showed a wide diversity of unicellular holomycotans in almost all environments on Earth. However, the phylogenetic signal of this gene is limited and does not allow robustly resolving most deep phylogenetic relationships. During past years, high-throughput techniques have allowed sequencing hundreds of new genomes and transcriptomes. This has made possible to carry out multi-gene phylogenomic studies, which increase the available signal to resolve evolutionary relationships. Nevertheless, most sequenced genomes correspond to easy-to-culture fungal species, often with particular interest for humans (e.g. parasites, plant symbionts, yeast). Recently, single-cell omics has become a potential useful approach to study uncultured unicellular eukaryotes, making it possible to reconstruct robust phylogenetic analyses of a wide environmental diversity using genomic and transcriptomic data. During my PhD work, I have applied single-cell techniques to get phylogenetic information from divergent holomycotan lineages, clarify phylogenetic relationships among fungi and their close relatives and infer trait evolution. More specifically, I have used this approach to: 1) Generate genomic and transcriptomic data for nucleariids and better reconstruct inner relationships in the clade and the characters present in the nucleariid ancestor. Our results confirm that the cover-bearing unicellular genera Pompholyxophrys and Lithocolla are indeed nucleariids and branch together with Nuclearia, Parvularia and Fonticula. The reconstruction of a robust phylogeny for the group allowed us to infer the traits (e.g. no flagellum, glycocalyx, no cover) already present in their ancestor. 2) Sequence and comparatively analyze the genome of Metchnikovella incurvata, to confirm its relatively basal position within Microsporidia, and determine synapomorphies for the clade. Phylogenomic analysis of the metchnikovellid Metchnikovella incurvata confirmed that Metchnikovellidae branch at the base of Core-Microsporidia. We also confirmed their metabolic profile to be more similar to Core-microsporidia, being both similarly reduced in genes/functions. 3) Generate genomic data for Amoeboradix gromovi and Sanchytrium tribonematis, which form the newly described zoosporic fungal clade of sanchytrids, and resolve their phylogenetic position. The study of the two sanchytrid genomes clarified their placement within Fungi as a new clade sister to Blastocladiomycota. Comparative genomics showed that their metabolic composition was reduced in comparison with related lineages. This reduction was especially important in their flagellar toolkit when compared with other Holomycota, confirming 4 independent flagellum loss events in the clade
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Tucker, Derek B. "Molecular Studies of South American Teiid Lizards (Teiidae: Squamata) from Deep Time to Shallow Divergences." BYU ScholarsArchive, 2016. https://scholarsarchive.byu.edu/etd/6419.
Full textAbstract:
I focus on phylogenetic relationships of teiid lizards beginning with generic and species relationship within the family, followed by a detailed biogeographical examination of the Caribbean genus Pholidoscelis, and end by studying species boundaries and phylogeographic patterns of the widespread Giant Ameiva Ameiva ameiva. Genomic data (488,656 bp of aligned nuclear DNA) recovered a well-supported phylogeny for Teiidae, showing monophyly for 18 genera including those recently described using morphology and smaller molecular datasets. All three methods of phylogenetic estimation (two species tree, one concatenation) recovered identical topologies except for some relationships within the subfamily Tupinambinae (i.e. position of Salvator and Dracaena) and species relationships within Pholidoscelis, but these were unsupported in all analyses. Phylogenetic reconstruction focused on Caribbean Pholidoscelis recovered novel relationships not reported in previous studies that were based on significantly smaller datasets. Using fossil data, I improve upon divergence time estimates and hypotheses for the biogeographic history of the genus. It is proposed that Pholidoscelis colonized the Caribbean islands through the Lesser Antilles based on biogeographic analysis, the directionality of ocean currents, and evidence that most Caribbean taxa originally colonized from South America. Genetic relationships among populations within the Ameiva ameiva species complex have been poorly understood as a result of its continental-scale distribution and an absence of molecular data for the group. Mitochondrial ND2 data for 357 samples from 233 localities show that A. ameiva may consist of up to six species, with pairwise genetic distances among these six groups ranging from 4.7–12.8%. An examination of morphological characters supports the molecular findings with prediction accuracy of the six clades reaching 72.5% using the seven most diagnostic predictors.
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Mir, arabbaygi Siavash. "Novel scalable approaches for multiple sequence alignment and phylogenomic reconstruction." Thesis, 2015. http://hdl.handle.net/2152/31377.
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The amount of biological sequence data is increasing rapidly, a promising development that would transform biology if we can develop methods that can analyze large-scale data efficiently and accurately. A fundamental question in evolutionary biology is building the tree of life: a reconstruction of relationships between organisms in evolutionary time. Reconstructing phylogenetic trees from molecular data is an optimization problem that involves many steps. In this dissertation, we argue that to answer long-standing phylogenetic questions with large-scale data, several challenges need to be addressed in various steps of the pipeline. One challenges is aligning large number of sequences so that evolutionarily related positions in all sequences are put in the same column. Constructing alignments is necessary for phylogenetic reconstruction, but also for many other types of evolutionary analyses. In response to this challenge, we introduce PASTA, a scalable and accurate algorithm that can align datasets with up to a million sequences. A second challenge is related to the interesting fact that various parts of the genome can have different evolutionary histories. Reconstructing a species tree from genome-scale data needs to account for these differences. A main approach for species tree reconstruction is to first reconstruct a set of ``gene trees'' from different parts of the genome, and to then summarize these gene trees into a single species tree. We argue that this approach can suffer from two challenges: reconstruction of individual gene trees from limited data can be plagued by estimation error, which translates to errors in the species tree, and also, methods that summarize gene trees are not scalable or accurate enough under some conditions. To address the first challenge, we introduce statistical binning, a method that re-estimates gene trees by grouping them into bins. We show that binning improves gene tree accuracy, and consequently the species tree accuracy. To address the second challenge, we introduce ASTRAL, a new summary method that can run on a thousand genes and a thousand species in a day and has outstanding accuracy. We show that the development of these methods has enabled biological analyses that were otherwise not possible.
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Schreiber, Fabian. "The quest for orthologs, the tree of basal animals, and taxonomic profiles of metagenomes." Doctoral thesis, 2010. http://hdl.handle.net/11858/00-1735-0000-0006-B517-8.
Full textBook chapters on the topic "Phylogenomic trees"
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Liu, Liang, Christian Anderson, Dennis Pearl, and Scott V. Edwards. "Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model." In Methods in Molecular Biology, 211–39. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9074-0_7.
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Spatafora, Joseph W., and Barbara Robbertse. "Phylogenetics and Phylogenomics of the Fungal Tree of Life." In Cellular and Molecular Biology of Filamentous Fungi, 36–49. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555816636.ch4.
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Zhu, Qiyun, and Siavash Mirarab. "Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies." In Methods in Molecular Biology, 137–65. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2691-7_7.
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Mahbub, Sazan, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M. Sohel Rahman, and Md Shamsuzzoha Bayzid. "QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data." In Lecture Notes in Computer Science, 159–76. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-04749-7_10.
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Braun, Edward L., Joel Cracraft, and Peter Houde. "Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era." In Avian Genomics in Ecology and Evolution, 151–210. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-16477-5_6.
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Nahum, Laila A., and Sergio L. Pereira. "Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence." In Applications of Computational Intelligence in Biology, 259–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78534-7_11.
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DeSalle, Rob, Michael Tessler, and Jeffrey Rosenfeld. "Incongruence of Gene Trees." In Phylogenomics, 199–211. CRC Press, 2020. http://dx.doi.org/10.1201/9780429397547-19.
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DeSalle, Rob, Michael Tessler, and Jeffrey Rosenfeld. "Evolutionary Principles: Populations and Trees." In Phylogenomics, 33–46. CRC Press, 2020. http://dx.doi.org/10.1201/9780429397547-4.
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DeSalle, Rob, Michael Tessler, and Jeffrey Rosenfeld. "Introduction to Tree Building." In Phylogenomics, 133–46. CRC Press, 2020. http://dx.doi.org/10.1201/9780429397547-13.
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DeSalle, Rob, Michael Tessler, and Jeffrey Rosenfeld. "Phylogenomics and the Tree of Life." In Phylogenomics, 311–29. CRC Press, 2020. http://dx.doi.org/10.1201/9780429397547-28.
Full textConference papers on the topic "Phylogenomic trees"
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Sjölander, Kimmen. "THE PHYLOFACTS PHYLOGENOMIC ENCYCLOPEDIAS: STRUCTURAL PHYLOGENOMIC ANALYSIS ACROSS THE TREE OF LIFE." In Proceedings of the CSB 2007 Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781860948732_0004.
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PAGE, R. D. M., and J. A. COTTON. "VERTEBRATE PHYLOGENOMICS: RECONCILED TREES AND GENE DUPLICATIONS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0050.
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Percy, Diana. "Psylloidea phylogenomics: Resolving the psyllid tree." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.94959.
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Kheng, Goh Yong, Lim Foo Weng, and Leo Yean Ling. "Building phylogenomic tree with N-gram contrast value vector." In INTERNATIONAL CONFERENCE ON MATHEMATICAL SCIENCES AND STATISTICS 2013 (ICMSS2013): Proceedings of the International Conference on Mathematical Sciences and Statistics 2013. AIP, 2013. http://dx.doi.org/10.1063/1.4823910.
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Ocaña, Kary, Micaella Coelho, Guilherme Freire, and Carla Osthoff. "High-Performance Computing of BEAST/BEAGLE in Bayesian Phylogenetics using SDumont Hybrid Resources." In Brazilian e-Science Workshop. Sociedade Brasileira de Computação - SBC, 2020. http://dx.doi.org/10.5753/bresci.2020.11190.
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Bayesian phylogenetic algorithms are computationally intensive. BEAST 1.10 inferences made use of the BEAGLE 3 high-performance library for efficient likelihood computations. The strategy allows phylogenetic inference and dating in current knowledge for SARS-CoV-2 transmission. Follow-up simulations on hybrid resources of Santos Dumont supercomputer using four phylogenomic data sets, we characterize the scaling performance behavior of BEAST 1.10. Our results provide insight into the species tree and MCMC chain length estimation, identifying preferable requirements to improve the use of high-performance computing resources. Ongoing steps involve analyzes of SARS-CoV-2 using BEAST 1.8 in multi-GPUs.