Relevant bibliographies by topics / Phylogenesi

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Phylogenesi'

Author: Grafiati
Published: 10 March 2023

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Journal articles on the topic "Phylogenesi"

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Miyamoto, Michael M., and Walter M. Fitch. "Testing Species Phylogenies and Phylogenetic Methods with Congruence." Systematic Biology 44, no. 1 (March 1995): 64. http://dx.doi.org/10.2307/2413483.

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Borges, Rui, João Paulo Machado, Cidália Gomes, Ana Paula Rocha, and Agostinho Antunes. "Measuring phylogenetic signal between categorical traits and phylogenies." Bioinformatics 35, no. 11 (October 25, 2018): 1862–69. http://dx.doi.org/10.1093/bioinformatics/bty800.

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Abstract Motivation Determining whether a trait and phylogeny share some degree of phylogenetic signal is a flagship goal in evolutionary biology. Signatures of phylogenetic signal can assist the resolution of a broad range of evolutionary questions regarding the tempo and mode of phenotypic evolution. However, despite the considerable number of strategies to measure it, few and limited approaches exist for categorical traits. Here, we used the concept of Shannon entropy and propose the δ statistic for evaluating the degree of phylogenetic signal between a phylogeny and categorical traits. Results We validated δ as a measure of phylogenetic signal: the higher the δ-value the higher the degree of phylogenetic signal between a given tree and a trait. Based on simulated data we proposed a threshold-based classification test to pinpoint cases of phylogenetic signal. The assessment of the test’s specificity and sensitivity suggested that the δ approach should only be applied to 20 or more species. We have further tested the performance of δ in scenarios of branch length and topology uncertainty, unbiased and biased trait evolution and trait saturation. Our results showed that δ may be applied in a wide range of phylogenetic contexts. Finally, we investigated our method in 14 360 mammalian gene trees and found that olfactory receptor genes are significantly associated with the mammalian activity patterns, a result that is congruent with expectations and experiments from the literature. Our application shows that δ can successfully detect molecular signatures of phenotypic evolution. We conclude that δ represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories. Availability and implementation https://github.com/mrborges23/delta_statistic. Supplementary information Supplementary data are available at Bioinformatics online.
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Miyamoto, Michael M., and Walter M. Fitch. "Testing Species Phylogenies and Phylogenetic Methods with Congruence." Systematic Biology 44, no. 1 (March 1995): 64–76. http://dx.doi.org/10.1093/sysbio/44.1.64.

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Palmer, Marike, Stephanus N. Venter, Alistair R. McTaggart, Martin P. A. Coetzee, Stephanie Van Wyk, Juanita R. Avontuur, Chrizelle W. Beukes, et al. "The synergistic effect of concatenation in phylogenomics: the case in Pantoea." PeerJ 7 (April 16, 2019): e6698. http://dx.doi.org/10.7717/peerj.6698.

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With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.
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Kim, Junhyong. "Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators." Systematic Biology 47, no. 1 (March 1, 1998): 43–60. http://dx.doi.org/10.1080/106351598261021.

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Aris-Brosou, Stéphane, and Xuhua Xia. "Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods." International Journal of Plant Genomics 2008 (April 30, 2008): 1–16. http://dx.doi.org/10.1155/2008/683509.

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The reconstruction of phylogenies is becoming an increasingly simple activity. This is mainly due to two reasons: the democratization of computing power and the increased availability of sophisticated yet user-friendly software. This review describes some of the latest additions to the phylogenetic toolbox, along with some of their theoretical and practical limitations. It is shown that Bayesian methods are under heavy development as they offer the possibility to solve a number of long-standing issues and to integrate several steps of the phylogenetic analyses into a single framework. Specific topics include not only phylogenetic reconstruction, but also the comparison of phylogenies, the detection of adaptive evolution, and the estimation of divergence times between species.
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Hinchliff, Cody E., Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, et al. "Synthesis of phylogeny and taxonomy into a comprehensive tree of life." Proceedings of the National Academy of Sciences 112, no. 41 (September 18, 2015): 12764–69. http://dx.doi.org/10.1073/pnas.1423041112.

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Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.
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CRUICKSHANK, ROBERT H. "Exploring character conflict in molecular data." Zootaxa 2946, no. 1 (July 8, 2011): 45. http://dx.doi.org/10.11646/zootaxa.2946.1.10.

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Mooi & Gill (2010) have made a number of criticisms of statistical approaches to the phylogenetic analysis of molecular data as it is currently practiced. There are many different uses for molecular phylogenies, and for most of them statistical methods are entirely appropriate, but for taxonomic purposes the way that these methods have been used is questionable. In these cases it is necessary to introduce an extra step into the analysis – exploration of character conflict. Existing methods for exploring character conflict in molecular data such as spectral analysis, phylogenetic networks, likelihood mapping and sliding window analyses are briefly reviewed, but there is also a need for development of new tools to facilitate the analysis of large data sets. Incorporation of previous phylogenies as priors in Bayesian analyses could help to provide taxonomic stability, while still leaving room for new data to alter these conclusions if they contain sufficiently strong phylogenetic signal. Molecular phylogeneticists should make a clearer distinction between the different uses to which their phylogenies are put; methods suitable in one context may not be appropriate in others.
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DeBlasio, Dan F., and Jennifer H. Wisecaver. "SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees." PeerJ 4 (August 23, 2016): e2359. http://dx.doi.org/10.7717/peerj.2359.

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We present the phylogeny analysis softwareSICLE(SisterCladeExtractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome ofSalinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships toS. ruberacross the 4,589 gene phylogenies.S. rubergrouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association betweenS. ruberand Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates howSICLEmakes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation.SICLEis available for free for noncommercial use athttp://eebweb.arizona.edu/sicle/.
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Lloyd, Graeme T., and Graham J. Slater. "A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses." Systematic Biology 70, no. 5 (January 28, 2021): 922–39. http://dx.doi.org/10.1093/sysbio/syab002.

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Abstract Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins, and allies). Our trees extend sampling from the $\sim 90$ extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios, we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.[Extinction; macroevolution; matrix representation with parsimony; morphology; supertree.]
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Dissertations / Theses on the topic "Phylogenesi"

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Höhna, Sebastian. "Bayesian Phylogenetic Inference : Estimating Diversification Rates from Reconstructed Phylogenies." Doctoral thesis, Stockholms universitet, Matematiska institutionen, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-95361.

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Phylogenetics is the study of the evolutionary relationship between species. Inference of phylogeny relies heavily on statistical models that have been extended and refined tremendously over the past years into very complex hierarchical models. Paper I introduces probabilistic graphical models to statistical phylogenetics and elaborates on the potential advantages a unified graphical model representation could have for the community, e.g., by facilitating communication and improving reproducibility of statistical analyses of phylogeny and evolution. Once the phylogeny is reconstructed it is possible to infer the rates of diversification (speciation and extinction). In this thesis I extend the birth-death process model, so that it can be applied to incompletely sampled phylogenies, that is, phylogenies of only a subsample of the presently living species from one group. Previous work only considered the case when every species had the same probability to be included and here I examine two alternative sampling schemes: diversified taxon sampling and cluster sampling. Paper II introduces these sampling schemes under a constant rate birth-death process and gives the probability density for reconstructed phylogenies. These models are extended in Paper IV to time-dependent diversification rates, again, under different sampling schemes and applied to empirical phylogenies. Paper III focuses on fast and unbiased simulations of reconstructed phylogenies. The efficiency is achieved by deriving the analytical distribution and density function of the speciation times in the reconstructed phylogeny.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Accepted.

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Ross, Edith. "Inferring tumour evolution from single-cell and multi-sample data." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274604.

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Tumour development has long been recognised as an evolutionary process during which cells accumulate mutations and evolve into a mix of genetically distinct cell subpopulations. The resulting genetic intra-tumour heterogeneity poses a major challenge to cancer therapy, as it increases the chance of drug resistance. To study tumour evolution in more detail, reliable approaches to infer the life histories of tumours are needed. This dissertation focuses on computational methods for inferring trees of tumour evolution from single-cell and multi-sample sequencing data. Recent advances in single-cell sequencing technologies have promised to reveal tumour heterogeneity at a much higher resolution, but single-cell sequencing data is inherently noisy, making it unsuitable for analysis with classic phylogenetic methods. The first part of the dissertation describes OncoNEM, a novel probabilistic method to infer clonal lineage trees from noisy single nucleotide variants of single cells. Simulation studies are used to validate the method and to compare its performance to that of other methods. Finally, OncoNEM is applied in two case studies. In the second part of the dissertation, a comprehensive collection of existing multi-sample approaches is used to infer the phylogenies of metastatic breast cancers from ten patients. In particular, shallow whole-genome, whole exome and targeted deep sequencing data are analysed. The inference methods comprise copy number and point mutation based approaches, as well as a method that utilises a combination of the two. To improve the copy number based inference, a novel allele-specific multi-sample segmentation algorithm is presented. The results are compared across methods and data types to assess the reliability of the different methods. In summary, this thesis presents substantial methodological advances to understand tumour evolution from genomic profiles of single cells or related bulk samples.
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Hamberg, Erlend Heggheim. "Inferring Phylogenies Using Evolutionary Algorithms : A maximum likelihood approach for constructing phylogenetic trees from molecular data." Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for datateknikk og informasjonsvitenskap, 2011. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-13687.

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This thesis has evaluated the use of the computationally expensivemaximum-likelihood (ML) method coupled with an evolutionaryalgorithm (EA) for the problem of inferring evolutionaryrelationships among species (phylogenies) from molecular data. MLmethods allow using all the information from molecular data, suchas DNA sequences, and have several beneficial properties compared toother methods. Evolutionary algorithms is a class of optimizationalgorithms that often perform well in complex fitness landscapes.EAs are also proclaimed to be easy to parallelize, an aspect thatis increasingly more important.A parallel EA system has been implemented and tested on a clusterfor the task of phylogeny inference. The system shows promisingresults and is able to utilize processors of a massively parallelsystem in a transparent manner.
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Roeser-Mueller, Kerstin [Verfasser], Erhard [Akademischer Betreuer] Strohm, and Christoph [Akademischer Betreuer] Oberprieler. "Phylogenies and pheromones - Defensive symbionts, phylogenetic affiliations and olfactory communication in beewolves (Philanthini, Hymenoptera, Crabronidae) / Kerstin Roeser-Mueller. Betreuer: Erhard Strohm ; Christoph Oberprieler." Regensburg : Universitätsbibliothek Regensburg, 2012. http://d-nb.info/1033688363/34.

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Marchiselli, Simone. "Molecular phylogenesis of Mediterranean Octocorals." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amslaurea.unibo.it/4905/.

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In order to support the conservation of the Mediterranean octocorals improvements on information regarding their taxonomic units and phylogenetic relationships are strongly needed. In the present thesis work, phylogenetic analyses based on the mitochondrial mtMSH and 16S genes were performed including 15 Mediterranean octocorals species on the 56 recognized to date. Moreover, an extended datasets with Atlanto/Pacific congeners Octocorallia species was implemented to clarify their phylogenetic relationships and estimate the divergence times of the Mediterranean species. Results indicated that: 1) there are similarity and differences among molecular and morphological traits depending on the taxonomical level considered; 2) the molecular phylogeny of the Mediterranean octocorals retrace the previous relationships based on wide octocorals analyses; and 3) the divergence time among Mediterranean and Atlanto/Pacific species varies depending on analysed taxa. At higher taxonomic level, the Mediterranean trees supported the division of the Mediterranean Octocorallia into one major clade (Alcyoniina-Holaxonia) plus two unresolved branch including the single species available of Scleraxonia and Stolonifera respectively. This topology was better supported including the Atlanto/Pacific congeners species. The molecular evidence suggested that Alcyonium palmatum and Corallium rubrum species are the youngest with a divergence time estimated around 4 MYA. Particularly, C. rubrum results were in agreement with the hypothesis that recent orogenesis process of the Mediterranean Sea promoted the allopatric speciation of this specie. Increasing the sample design and implementing the emerging next-generation genomic-sequencing technologies, further studies would be able to improve the understanding of the Mediterranean octocorals phylogenetic relationships and evolution.
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Mecham, Jesse L. "Jumpstarting phylogenetic searches /." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1403.pdf.

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McHugh, Sean W. "Phylogenetic Niche Modeling." Thesis, Virginia Tech, 2021. http://hdl.handle.net/10919/104893.

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Projecting environmental niche models through time is a common goal when studying species response to climatic change. Species distribution models (SDMs) are commonly used to estimate a species' niche from observed patterns of occurrence and environmental predictors. However, a species niche is also shaped by non-environmental factors--including biotic interactions and dispersal barrier—truncating SDM estimates. Though truncated SDMs may accurately predict present-day species niche, projections through time are often biased by environmental condition change. Modeling niche in a phylogenetic framework leverages a clade's shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche implemented in R. Under our model, species SDM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving under multivariate Brownian motion random walk. Through simulation analyses, we demonstrated model accuracy and precision that improved as phylogeny size increased. We also demonstrated our model on a clade of eastern United States Plethodontid salamanders by accurately estimating species niche, even when no occurrence data is present. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and niche in data deficient species.
Master of Science
As many species face increasing pressure in a changing climate, it is crucial to understand the set of environmental conditions that shape species' ranges--known as the environmental niche--to guide conservation and land management practices. Species distribution models (SDMs) are common tools that are used to model species' environmental niche. These models treat a species' probability of occurrence as a function of environmental conditions. SDM niche estimates can predict a species' range given climate data, paleoclimate, or projections of future climate change to estimate species range shifts from the past to the future. However, SDM estimates are often biased by non-environmental factors shaping a species' range including competitive divergence or dispersal barriers. Biased SDM estimates can result in range predictions that get worse as we extrapolate beyond the observed climatic conditions. One way to overcome these biases is by leveraging the shared evolutionary history amongst related species to "fill in the gaps". Species that are more closely phylogenetically related often have more similar or "conserved" environmental niches. By estimating environmental niche over all species in a clade jointly, we can leverage niche conservatism to produce more biologically realistic estimates of niche. However, currently a methodological gap exists between SDMs estimates and macroevolutionary models, prohibiting them from being estimated jointly. We propose a novel model of evolutionary niche called PhyNE (Phylogenetic Niche Evolution), where biologically realistic environmental niches are fit across a set of species with occurrence data, while simultaneously fitting and leveraging a model of evolution across a portion of the tree of life. We evaluated model accuracy, bias, and precision through simulation analyses. Accuracy and precision increased with larger phylogeny size and effectively estimated model parameters. We then applied PhyNE to Plethodontid salamanders from Eastern North America. This ecologically-important and diverse group of lungless salamanders require cold and wet conditions and have distributions that are strongly affected by climatic conditions. Species within the family vary greatly in distribution, with some species being wide ranging generalists, while others are hyper-endemics that inhabit specific mountains in the Southern Appalachians with restricted thermal and hydric conditions. We fit PhyNE to occurrence data for these species and their associated average annual precipitation and temperature data. We identified no correlations between species environmental preference and specialization. Pattern of preference and specialization varied among Plethodontid species groups, with more aquatic species possessing a broader environmental niche, likely due to the aquatic microclimate facilitating occurrence in a wider range of conditions. We demonstrated the effectiveness of PhyNE's evolutionarily-informed estimates of environmental niche, even when species' occurrence data is limited or even absent. PhyNE establishes a proof-of-concept framework for a new class of approaches for studying niche evolution, including improved methods for estimating niche for data-deficient species, historical reconstructions, future predictions under climate change, and evaluation of niche evolutionary processes across the tree of life. Our approach establishes a framework for leveraging the rapidly growing availability of biodiversity data and molecular phylogenies to make robust eco-evolutionary predictions and assessments of species' niche and distributions in a rapidly changing world.
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Mecham, Jesse Lewis. "Jumpstarting Phylogenetic Searches." BYU ScholarsArchive, 2006. https://scholarsarchive.byu.edu/etd/483.

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Phylogenetic analysis is a central tool in studies of comparative genomics. When a new region of DNA is isolated and sequenced, researchers are often forced to throw away months of computation on an existing phylogeny of homologous sequences in order to incorporate this new sequence. The previously constructed trees are often discarded, and the researcher begins the search again from scratch. The jumpstarting algorithm uses trees from the prior search as a starting point for a new phylogenetic search. This technique drastically decreases search time for large data sets. This kind of analysis is necessary as researchers analyze tree of life size data sets.
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Krig, Kåre. "Methods for phylogenetic analysis." Thesis, Linköping University, Department of Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56814.

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In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix d.

In this thesis I present a few methods for constructing a phylogenetic tree from d. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When d does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data.

Finally I have tested the methods both on real measured data and constructed test cases.

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Pardi, Fabio. "Algorithms on phylogenetic trees." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611685.

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Books on the topic "Phylogenesi"

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The phylogenetic system: The systematization of organisms on the basis of their phylogenesis. Chichester [West Sussex]: Wiley, 1987.

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Foster, Alan Dean. Phylogenesis. New York: Del Rey, 1999.

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Forey, Peter L., and Norman MacLeod. Morphology, shape and phylogeny. London: Taylor & Francis, 2002.

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Boudreaux, H. Bruce. Arthropod phylogeny with special reference to insects. Malabar, Fla: R.E. Krieger Pub. Co., 1987.

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Architects, Foreign Office. Phylogenesis: Foa's ark. Barcelona: Actar, 2004.

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Architects, Foreign Office. Phylogenesis: Foa's ark. Barcelona: Actar, 2004.

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Bininda-Emonds, Olaf R. P., ed. Phylogenetic Supertrees. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-1-4020-2330-9.

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Scherson, Rosa A., and Daniel P. Faith, eds. Phylogenetic Diversity. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-93145-6.

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W, Warr Gregory, and Cohen Nicholas 1938-, eds. Phylogenesis of immune functions. Boca Raton, Fla: CRC Press, 1991.

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Lemey, Philippe, Marco Salemi, and Anne-Mieke Vandamme, eds. The Phylogenetic Handbook. Cambridge: Cambridge University Press, 2009. http://dx.doi.org/10.1017/cbo9780511819049.

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Book chapters on the topic "Phylogenesi"

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Meireles, José Eduardo, Brian O’Meara, and Jeannine Cavender-Bares. "Linking Leaf Spectra to the Plant Tree of Life." In Remote Sensing of Plant Biodiversity, 155–72. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-33157-3_7.

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AbstractEvolutionary trees recount the history of how biological diversity came to be and how evolution gave rise to the incredible variation in plant form and function that can be captured by spectral reflectance. Understanding plant spectra in light of evolution is thus important for assessing biodiversity and critical for explaining how spectral diversity is generated. Here, we focus on leaf spectra and how they are linked to the plant tree of life. We review what evolutionary trees (phylogenies) are and how to interpret them. We then describe how to model the evolution of quantitative traits, discuss which evolutionary processes are involved, and explain specific concepts and metrics, such as phylogenetic signal and evolutionary rates, and how they can be applied to reflectance spectra. Next, we describe a framework that links phylogenies and leaf spectra by coupling models of evolution and radiative transfer models. In doing so, we review some of the challenges of subjecting spectra to evolutionary analyses. We then discuss how spectra can help us to understand leaf evolution and to differentiate plant taxa at different phylogenetic scales from populations to lineages, advancing our potential to remotely detect biodiversity.
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Matzke, Nicholas J. "Science Without Species: Doing Science with Tree-Thinking." In Speciesism in Biology and Culture, 47–61. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-99031-2_3.

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AbstractThe focus of this volume is speciesism. While the concepts of species and speciation remain the focus of a great deal of research, it is worth exploring how in recent decades evolutionary biology has, in several ways, moved away from species as the key unit of analysis of biological questions. I begin by outlining how phylogenetic comparative methods have become essential methodological tools in statistical analyses of relationships between traits. Species are not statistically independent observations, because the reality is that they are related, genetically and statistically, on a phylogenetic tree. Phylogeny also plays a key role in modern analyses of spatial patterns in biodiversity, and in fact relying on phylogenetic biodiversity measures can avoid a number of problems created by attempting to impose a uniform species rank across different continents and clades. Similarly, a major challenge in modern studies of diversification and extinction concerns the units of analysis and how they are defined and recognized. Both “genus” and “species” are human-defined ranks imposed on the phylogenetic tree. The phylogenetic tree is the more fundamental reality that is produced by the macroevolutionary process, and it could include every level of gradation of genetic and morphological divergence. Once ranks are imposed upon it, a variety of methodological problems are created as scientists attempt to make these ranks standardized and comparable across different datasets and timescales. I outline how phylogenetic thinking might help provide a solution. I conclude with other examples where cutting-edge science is done with phylogenies without much need of the “species” rank—for example, in the battle against Covid-19.
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Zrzavý, Jan, Stanislav Mihulka, Hynek Burda, Sabine Begall, and David Storch. "Phylogenese." In Evolution, 155–214. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-39696-0_3.

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Zrzavý, J., D. Storch, S. Mihulka, Hynek Burda, and Sabine Begall. "Phylogenese." In Evolution, 146–205. Heidelberg: Spektrum Akademischer Verlag, 2009. http://dx.doi.org/10.1007/978-3-8274-2233-0_3.

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Scheunpflug, Annette. "Phylogenese." In Handbuch Pädagogische Anthropologie, 305–15. Wiesbaden: Springer Fachmedien Wiesbaden, 2013. http://dx.doi.org/10.1007/978-3-531-18970-3_27.

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Peter, Helga. "Phylogenese." In Springer Reference Medizin, 1. Berlin, Heidelberg: Springer Berlin Heidelberg, 2020. http://dx.doi.org/10.1007/978-3-642-54672-3_751-1.

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Toepfer, Georg. "Phylogenese." In Historisches Wörterbuch der Biologie, 34–87. Stuttgart: J.B. Metzler, 2011. http://dx.doi.org/10.1007/978-3-476-00461-1_3.

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Rieppel, Olivier. "The Evolutionary Turn in Comparative Anatomy." In Phylogenetic Systematics, 1–33. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-1.

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Rieppel, Olivier. "Epilogue." In Phylogenetic Systematics, 323–25. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-10.

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Rieppel, Olivier. "Of Parts and Wholes." In Phylogenetic Systematics, 35–66. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-2.

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Conference papers on the topic "Phylogenesi"

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Forghani, Majid Ali, Artyom L. Firstkov, Pavel Alexandrovich Vasev, and Edward S. Ramsay. "Visualization of the Evolutionary Trajectory: Application of Reduced Amino Acid Alphabets and Word2Vec Embedding." In 32nd International Conference on Computer Graphics and Vision. Keldysh Institute of Applied Mathematics, 2022. http://dx.doi.org/10.20948/graphicon-2022-275-287.

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Analysis of viral evolution is a key element of epidemiological surveillance and control. One of the fundamental tools which is widely used to illustrate evolutionary history is the phylogenetic tree. Recently, we have proposed an alternative visualization for the phylogenetic tree using the evolutionary trajectory of its taxa. An evolutionary trajectory is a path starting from a taxon and ending at the root of the tree. In this paper, we propose an embedding of tree nodes by encoding their genetic sequence using a reduced amino acid alphabet and employing the Word2Vec framework. The suggested visualization maintains the phylogenetic relationship between nodes, while their proximity in 3D space depends on three factors: the type of reduced amino acid alphabet; fixed-length genetic patterns used in Word2Vec; and the neighbor effect of adjacent signatures. The results of our experiments showed that the majority of evolutionary history can be described in the embedded space. Moreover, they suggest potential application of our approach as an explanatory tool in studying various aspects: evolutionary dynamics; evolutionary deviation of viral variants; and phylogenetic characteristics, such as formation of new clades. Besides the usual local analysis of point mutations, the developed framework enables studying these aspects based on a more comprehensive global context, including neighboring effects, genetic signatures.
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Forghani, Majid, Pavel Vasev, Edward Ramsay, and Alexander Bersenev. "Visualization of the Evolutionary Path: an Influenza Case Study." In 31th International Conference on Computer Graphics and Vision. Keldysh Institute of Applied Mathematics, 2021. http://dx.doi.org/10.20948/graphicon-2021-3027-358-368.

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Visualization of viral evolution is one of the essential tasks in bioinformatics, through which virologists characterize a virus. The fundamental visualization tool for such a task is constructing a dendrogram, also called the phylogenetic tree. In this paper, we propose the visualization and characterization of the evolutionary path, starting from the root to isolated virus in the leaf of the phylogenetic tree. The suggested approach constructs the sequences of inner nodes (ancestors) within the phylogenetic tree and uses one-hot-encoding to represent the genetic sequence in a binary format. By employing embedding methods, such as multi-dimensional scaling, we project the path into 2D and 3D spaces. The final visualization demonstrates the dynamic of viral evolution locally (for an individual strain) and globally (for all isolated viruses). The results suggest applications of our approach in: detecting earlier changes in the characteristics of strains; exploring emerging novel strains; modeling antigenic evolution; and study of evolution dynamics. All of these potential applications are critical in the fight against viruses.
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Jamil, H. M., G. A. Modica, and M. A. Teran. "Querying phylogenies visually." In Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001). IEEE, 2001. http://dx.doi.org/10.1109/bibe.2001.974405.

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Daskalakis, Constantinos, Elchanan Mossel, and Sébastien Roch. "Optimal phylogenetic reconstruction." In the thirty-eighth annual ACM symposium. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1132516.1132540.

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Christinat, Yann, and Bernard M. E. Moret. "Inferring Transcript Phylogenies." In 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2011. http://dx.doi.org/10.1109/bibm.2011.11.

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Snell, Q., M. Whiting, M. Clement, and D. McLaughlin. "Parallel Phylogenetic Inference." In ACM/IEEE SC 2000 Conference. IEEE, 2000. http://dx.doi.org/10.1109/sc.2000.10062.

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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.
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Bansal, Mukul S. "Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation." In 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2016. http://dx.doi.org/10.1109/iccabs.2016.7802785.

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Gerasimchuk, A. L., P. A. Bukhtiyarova, D. V. Antsiferov, and D. A. Ivasenko. "Diversity and activity of cultivated lipophilic bacteria from fat-containing industrial wastes." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.085.

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Pure cultures of lipophilic microorganisms of different phylogenetic groups were isolated from fat-containing industrial wastewaters. The strains of the genera Pseudomonas and Bacillus were the most active lipolytic microorganisms.
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Kiryushkin, A. S., E. D. Guseva, E. L. Ilina, and K. N. Demchenko. "Study of the DEEPER ROOTING 1 (DRO1) expression features in the cucumber (Cucumis sativus) root system architecture formation." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.121.

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Identification of the cucumber DRO clade in IGT protein family was performed using phylogenetic analysis. Relative expression to the exogenous auxin and promoter tissue activity of the DRO genes were studied.
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Reports on the topic "Phylogenesi"

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Nierzwicki-Bauer, S. A. Phylogenetic relationships among subsurface microorganisms. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/6106595.

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Nierzwicki-Bauer, S. A. Phylogenetic relationships among subsurface microorganisms. Progress report. Office of Scientific and Technical Information (OSTI), December 1991. http://dx.doi.org/10.2172/10106325.

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Bruice, Thomas C. DNG and RNG Phylogenetic Single Cell Probes. Fort Belvoir, VA: Defense Technical Information Center, February 1999. http://dx.doi.org/10.21236/ada360479.

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Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using rRNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, June 1989. http://dx.doi.org/10.21236/ada209595.

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Lapedes, A. S., B. G. Giraud, L. C. Liu, and G. D. Stormo. Correlated mutations in protein sequences: Phylogenetic and structural effects. Office of Scientific and Technical Information (OSTI), December 1998. http://dx.doi.org/10.2172/296863.

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Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using Tau RNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, February 1991. http://dx.doi.org/10.21236/ada254451.

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Nierzwicki-Bauer, S. A. Phylogenetic relationships among subsurface microorganisms. Project technical progress report. Office of Scientific and Technical Information (OSTI), August 1993. http://dx.doi.org/10.2172/10171574.

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Balkwill, D. L., and R. H. Reeves. Physiological and phylogenetic study of microbes from geochemically and hydrogeologically diverse subsurface environments. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/5026959.

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Gardner, S., and C. Jaing. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees. Office of Scientific and Technical Information (OSTI), March 2012. http://dx.doi.org/10.2172/1047247.

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Marsh, Terence L. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia... Office of Scientific and Technical Information (OSTI), May 2004. http://dx.doi.org/10.2172/824396.

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