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Academic literature on the topic 'Phylogentic'

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Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Phylogentic"

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Journal, Baghdad Science. "phylogentic study of cephalopharyngeal selerites." Baghdad Science Journal 3, no. 1 (March 5, 2006): 62–72. http://dx.doi.org/10.21123/bsj.3.1.62-72.

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Maharjan, Mahendra. "Characterization of Heat Shock Protein (HSP 70) Sequence in Leishmania donovani." Journal of Institute of Science and Technology 20, no. 1 (November 25, 2015): 82–86. http://dx.doi.org/10.3126/jist.v20i1.13914.

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Heat shock protein HSP70 is the highly conserved protein along the kinetoplastid phylogenetic spectrum. A full length hsp70 gene was amplified, cloned and sequenced. The protein sequence was aligned and phylogentic tree was constructed. The Leishmania donovani HSP70 protein sequence (653 amino acids) is slightly larger than the Human HSP70 protein sequence (641 amino acids) with 72% identity. The putative protein sequence is 98%, 97%, 96% and 92% identical to L. major, L. infantum, L. tarentolae and L. braziliensis respectively. Evolutionary relationship showed that kinetoplastid parasites are closely related to the human compared to prokaryotes, E. coli.Journal of Institute of Science and Technology, 2015, 20(1): 82-86
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Aravena-Román, M., T. J. J. Inglis, C. Siering, P. Schumann, and A. F. Yassin. "Canibacter oris gen. nov., sp. nov., isolated from an infected human wound." International Journal of Systematic and Evolutionary Microbiology 64, Pt_5 (May 1, 2014): 1635–40. http://dx.doi.org/10.1099/ijs.0.058859-0.

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A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order Micrococcales of the class Actinobacteria , displaying 91.6 % to 96 % sequence similarity with members of the family Microbacteriaceae . Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus Leucobacter . Chemical studies revealed the presence of a cell-wall murein based on l-lysine (type B1α), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T ( = DSM 27064T = CCUG 64069T).
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Titov, V. N. "Phylogentic theory of pathology. Common phylogenetic features in the pathogenesis of essential arterial hyperntesion and insulin resistance syndrome." Systemic Hypertension 11, no. 3 (September 15, 2014): 53–60. http://dx.doi.org/10.26442/sg29045.

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Our phylogenetic theory of pathology (algorrhythm of a disease development) is based on 1) a theory of biological functions and biological reactions in vivo; 2) regulation of biological functions, reactions, and metabolic processes at three phylogenetically different levels: а) autocrine (cell level); b) paracrine (in paracrine-regulated cell communities) and c) total organism level; 3) conceptions on formation of physiological and aphysiological processes («civilization» diseases) at various stages of phylogenesis. Universal pathogenesis of essential arterial hypertension and insulin resistance syndrome is based on functional discrepancy between phylogenetically early regulatory mechanisms at the level of paracrine cell communities and phylogenetically late regulation at the organism level. Pathogenic factors of this discrepancy are impaired biological functions of homeostasis, trophology, endoecology and adaptation. An increase in the content of unesterified fatty acids in the intercellular medium results from activation of lipolysis in paracrine community cells which cannot inhibit phylogenetically late insulin, but not in insulin-dependent adipocytes. The formation of pathogenesis of each metabolic pandemia occurs dynamically at different stages of phylogenesis.
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Jin-Chan, Wang, Qi Wei-Wei, Zhang Long-Xian, Ning Chang-Shen, Jian Fu-Chun, Zhao Jin-Feng, and Wang Ming. "Phylogenetic analysis ofCryptosporidiumisolates in Henan." Chinese Journal of Agricultural Biotechnology 4, no. 3 (December 2007): 247–52. http://dx.doi.org/10.1017/s1479236207001957.

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AbstractThe functional mitochondrial protein alternative oxidase (AOX) gene was used as a marker to analyse the phylogenetic relationship betweenCryptosporidiumisolates. This gene was characterized, and the phylogentic tree was established fromCryptosporidiumisolates and compared to those generated from 18S rRNA and heat-shock protein 70 (HSP70) gene sequences. The present trial aimed at finding out whether the AOX gene is suitable for phylogenetic analysis of theCryptosporidiumgenus. The results revealed that the genusCryptosporidiumcontained the phylogenetically distinct speciesC. parvum,C. hominis,C. suisandC. baileyi, which were consistent with the biological characterization and host specificity reported earlier.Cryptosporidiumspecies formed two clades: one includedC. hominis,C. suis,C. parvumcattle genotypes andC. parvummouse genotype; and the other comprisedC. meleagridisandC. baileyiisolates. WithinC. parvum, both the mouse genotype and the pig genotype I (also known asC. suis) isolates differed from cattle and human (also known asC. hominis) genotypes, based on the aligned nucleotide sequences. The sequence identity of the AOX gene was higher betweenC. meleagridisandC. baileyithan betweenC. meleagridisandC. parvum. The phylogenetic trees showed thatC. meleagridiswas closer toC. baileyithan toC. parvum. This result was inconsistent with the phylogenetic analysis deduced from 18S rRNA and HSP70 gene sequences, respectively. The present results suggest that the AOX gene is not only equally suitable for the phylogenetic analysis ofCryptosporidium, but also provides an outstanding and new approach in determiningCryptosporidiumheredity.
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Day, J. Michael. "The diversity of the orthoreoviruses: Molecular taxonomy and phylogentic divides." Infection, Genetics and Evolution 9, no. 4 (July 2009): 390–400. http://dx.doi.org/10.1016/j.meegid.2009.01.011.

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Les, Donald, Michael Moody, and Connie Soros. "A Reappraisal of Phylogentic Relationships in the Monocotyledon Family Hydrocharitaceae (Alismatidae)." Aliso 22, no. 1 (2006): 211–30. http://dx.doi.org/10.5642/aliso.20062201.18.

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ABDELMAKSOUD, HESHAM M., AYMAN M. MANDOUR, and AHMED S. GAMAL ELDIN. "MOLECULAR IDENTIFICATION AND PHYLOGENTIC ANALYSIS OF POTATO LEAF ROLL VIRUS IN EGYPT." Egyptian Journal of Agricultural Research 91, no. 4 (December 1, 2013): 1259–69. http://dx.doi.org/10.21608/ejar.2013.165097.

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Price, Peter W. "Phylogentic constraints, adaptive syndromes, and emergent properties: From individuals to population dynamics." Researches on Population Ecology 36, no. 1 (June 1994): 3–14. http://dx.doi.org/10.1007/bf02515079.

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Achatz, Tyler J., Eric E. Pulis, Ethan T. Woodyard, Thomas G. Rosser, Jakson R. Martens, Sara B. Weinstein, Alan Fecchio, Chris T. McAllister, Carlos Carrión Bonilla, and Vasyl V. Tkach. "Molecular phylogenetic analysis of Neodiplostomum and Fibricola (Digenea, Diplostomidae) does not support host-based systematics." Parasitology 149, no. 4 (January 19, 2022): 542–54. http://dx.doi.org/10.1017/s003118202100216x.

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AbstractFibricola and Neodiplostomum are diplostomid genera with very similar morphology that are currently separated based on their definitive hosts. Fibricola spp. are normally found in mammals, while Neodiplostomum spp. typically parasitize birds. Previously, no DNA sequence data was available for any member of Fibricola. We generated nuclear ribosomal and mtDNA sequences of Fibricola cratera (type-species), Fibricola lucidum and 6 species of Neodiplostomum. DNA sequences were used to examine phylogenetic interrelationships among Fibricola and Neodiplostomum and re-evaluate their systematics. Molecular phylogenies and morphological study suggest that Fibricola should be considered a junior synonym of Neodiplostomum. Therefore, we synonymize the two genera and transfer all members of Fibricola into Neodiplostomum. Specimens morphologically identified as Neodiplostomum cratera belonged to 3 distinct phylogenetic clades based on mitochondrial data. One of those clades also included sequences of specimens identified morphologically as Neodiplostomum lucidum. Further study is necessary to resolve the situation regarding the morphology of N. cratera. Our results demonstrated that some DNA sequences of N. americanum available in GenBank originate from misidentified Neodiplostomum banghami. Molecular phylogentic data revealed at least 2 independent host-switching events between avian and mammalian hosts in the evolutionary history of Neodiplostomum; however, the directionality of these host-switching events remains unclear.
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Dissertations / Theses on the topic "Phylogentic"

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Holmes, Jennifer K. "A Phylogentic Analysis of PLATZ Transcription Factors in Plants." University of Toledo / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=toledo149339721432989.

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CICCOLELLA, SIMONE. "Practical algorithms for Computational Phylogenetics." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/364980.

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In questo manoscritto vengono discussi le principali sfide computazionali nel campo della inferenza di filogenesi tumorale a vengono proposte diverse soluzione per i tre principali problemi di (i) ricostruzione dell'evoluzioni di un campione tumorale, (ii) clustering di dati SCS per una piu' pulita e veloce inferenza e (iii) il confronto di diverse filogenesi. Inoltre viene discusso come combinare le diverse soluzioni in una singola pipeline per una piu' rapida analisi.
In this manuscript we described the main computational challenges of the cancer phylogenetic field and we proposed different solutions for the three main problems of (i) the progression reconstruction of a tumor sample, (ii) the clustering of SCS data to allow for a cleaner and faster inference and (iii) the evaluation of different phylogenies. Furthermore we combined them into a usable pipeline to allow for a faster analysis.
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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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Jirásková, Kristýna. "Metody rekonstrukce fylogenetických superstromů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2012. http://www.nusl.cz/ntk/nusl-219518.

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The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.
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Kosíř, Kamil. "Metody rekonstrukce fylogenetických superstromů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2014. http://www.nusl.cz/ntk/nusl-220860.

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The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.
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Faller, Beáta. "Combinatorial and probabilistic methods in biodiversity theory." Thesis, University of Canterbury. Mathematics and Statistics, 2010. http://hdl.handle.net/10092/3985.

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Phylogenetic diversity (PD) is a measure of species biodiversity quantified by how much of an evolutionary tree is spanned by a subset of species. In this thesis, we study optimization problems that aim to find species sets with maximum PD in different scenarios, and examine random extinction models under various assumptions to predict the PD of species that will still be present in the future. Optimizing PD with Dependencies is a combinatorial optimization problem in which species form an ecological network. Here, we are interested in selecting species sets of a given size that are ecologically viable and that maximize PD. The NP-hardness of this problem is proved and it is established which special cases of the problem are computationally easy and which are computationally hard. It is also shown that it is NP-complete to decide whether the feasible solution obtained by the greedy algorithm is optimal. We formulate the optimization problem as an integer linear program and find exact solutions to the largest food web currently in the empirical literature. In addition, we give a generalization of PD that can be used for example when we do not know the true evolutionary history. Based on this measure, an optimization problem is formulated. We discuss the complexity and the approximability properties of this problem. In the generalized field of bullets model (g-FOB), species are assumed to become extinct with possibly different probabilities, and extinction events are independent. We show that under this model the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows. When extinction probabilities are influenced by some binary character on the tree, the state-based field of bullets model (s-FOB) represents a more realistic picture. We compare the expected loss of PD under this model to that under the associated g-FOB model and find that the former is always greater than or equal to the latter. It is natural to further generalize the s-FOB model to allow more than one binary character to affect the extinction probabilities. The expected future PD obtained for the resulting trait-dependent field of bullets model (t-FOB) is compared to that for the associated g-FOB model and our previous result is generalized.
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Powell, Robyn Faye. "Systematics, diversification and ecology of the Conophytum-clade (Ruschieae; Aizoaceae)." University of the Western Cape, 2016. http://hdl.handle.net/11394/5453.

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Philosophiae Doctor - PhD
The Ruschieae is the most diverse and speciose tribe within the large subfamily Ruschioideae (Aizoaceae), with approximately 71 genera and a distribution centred in the arid parts of the Greater Cape Floristic Region (GCFR) of South Africa. Recent phylogenetic analyses provided the first insights into generic relationships within the tribe, with a number of novel generic relationships discovered. The tribal phylogeny recovered 12 large clades, of which the Conophytum-clade was one the most morphologically diverse based on leaf and capsule characters. The Conophytum-clade is an early-diverging lineage of the Ruschieae and includes the following 10 genera: Cheiridopsis N.E.Br., Conophytum N.E.Br., Enarganthe N.E.Br., Ihlenfeldtia H.E.K.Hartmann, Jensenobotrya A.G.J.Herre, Namaquanthus L.Bolus, Octopoma N.E.Br., Odontophorus N.E.Br., Ruschianthus L.Bolus and Schlechteranthus Schwantes. The present study presents an expanded phylogenetic analysis of the Conophytum-clade, with the sampling of the majority of species in the genera and a representative sampling (56% of species) of the speciose genus Conophytum. Phylogenetic data for up to nine plastid gene regions (atpB–rbcL, matK, psbJ–petA, rpl16, rps16, trnD– trnT, trnL–F, trnQᶷᶷᶢ–rps16, trnS–trnG) were produced for each of the sampled species. The produced plastid data was analyses using maximum parsimony, maximum likelihood and Bayesian inference. The combined plastid phylogenetic analyses were used in combination with morphological, anatomical and palynological data to assess generic and subgeneric circumscriptions within the clade. Upon assessment of generic circumscriptions in the Conophytum-clade, the number of recognised genera in the clade decreased from ten to seven. Arenifera A.G.J.Herre, which had not been sampled in any phylogeny of the Ruschieae, and Octopoma were recovered as polyphyletic, with species placed in the Conophytum-clade, while the type species was placed in the xeromorphic clade of the tribal phylogeny. The species of Arenifera and Octopoma placed in the Conophytum-clade were subsequently included in Schlechteranthus upon assessment of generic circumscriptions between the taxa. Two morphological groupings were recognised within Schlechteranthus, one including the species of Schlechteranthus and the other including species previously recognised as Arenifera and Octopoma. These two morphological groupings were treated as subgenera, with the erection of the new subgenus Microphyllus R.F.Powell. A detailed taxonomic revision of subgenus Microphyllus is presented with a key to species, descriptions of the species (including a new species: S. parvus R.F.Powell & Klak), known geographical distributions and illustrations of the species. In addition to the changes mentioned above, the expanded sampling and phylogenetic analyses of the Conophytum-clade recovered Ihlenfeldtia and Odontophorus embedded in Cheiridopsis. The species of Ihlenfeldtia were recovered with species of heiridopsis subgenus Aequifoliae H.E.K.Hartmann, while the species of Odontophorus were recovered as polyphyletic within the Cheiridopsis subgenus Odontophoroides H.E.K.Hartmann clade. Cheiridopsis was subsequently expanded to include the species of Ihlenfeldtia and Odontophorus, with these species accommodated in the subgenera of Cheiridopsis. The phylogenetic placement and relationship of these species was supported by the shared capsule morphology. The expanded sampling of the clade did not resolve the phylogenetic relationship of the monotypic genera Enarganthe, Jensenobotrya, Namaquanthus and Ruschianthus, with these genera unresolved in the Conophytum-clade. These genera however, exhibit a unique combination of morphological characters, such as a glabrous leaf epidermis and variation in pollen exine and colpi structure, in contrast to the other genera of the clade. The assessment of the generic circumscription of these genera, based on the molecular, morphological, anatomical and palynological data suggested that the generic statuses of these monotypic genera should be maintained. The expanded phylogenetic sampling of the morphologically diverse and speciose genus Conophytum recovered the genus as monophyletic. This monophyly was supported by the unique floral type in Conophytum, with the fused petaloid staminodes forming a tube. None of the sectional classifications were recovered as monophyletic but the phylogenetic analyses did recover a few clades which more or less corresponded to the current sectional classification of the genus. A number of clades were also recovered which included species from a range of different sections. Diverse leaf and floral traits were shown to have evolved numerous times across the genus. This was particularly interesting with regards to the selected floral traits, as the phylogeny indicated a number of switches in floral morphologies across the genus. The floral diversity was assessed in complex species communities of Conophytum across the GCFR, where up to 11 species of Conophytum are found occurring sympatrically, and floral traits were shown to be different across the species within the communities. Pollination competition and adaptation were suggested as possible drivers of floral diversity in the genus, with differences in phenology, anthesis and floral morphology within the species complex communities. The unique floral type of Conophytum has enabled the species to develop a diverse range of specialised flowers, with a variety of structures, scents and colours, resulting in the diverse floral morphologies found across the genus. The complex Conophytum species communities included both closely as well as distantly related species, suggesting the soft papery capsules of Conophytum are wind dispersed. This adaptation to long distance seed dispersal resulted in a significantly higher phylogenetic diversity in Conophytum when compared to its sister genus, Cheiridopsis. A population genetics study of Conophytum also suggested that the capsules may be wind dispersed, with an indication of genetic connectivity between the geographically isolated populations of C. marginatum Lavis across the Bushmanland Inselberg Region. Although the capsules are dispersed by wind, the seeds are released from the hygrochastic capsules by runoff during rainfall events. The relationship between seed dispersal and runoff is evident from the genetic structure of populations of C. maughanii N.E.Br. and C. ratum S.A.Hammer that occur on the tops and the surrounding bases of the inselbergs, as the drainage pattern was found to directly influence population structure in these species. In addition, the AFLP analyses provided insight into the conservation of the flagship species C. ratum. The summit populations of this species were shown to sustain the populations at the base of the Gamsberg. This finding is especially important, as the distribution of the species is restricted to the Gamsberg inselberg, where mining has already commenced as of this year.
National Research Foundation (NRF)
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Spindler, Frederik. "The basal Sphenacodontia – systematic revision and evolutionary implications." Doctoral thesis, Technische Universitaet Bergakademie Freiberg Universitaetsbibliothek "Georgius Agricola", 2015. http://nbn-resolving.de/urn:nbn:de:bsz:105-qucosa-171748.

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The presented study comprises a complete morphological and phylotaxonomic revision of basal Sphenacodontia, designated as the paraphyletic ‘haptodontines’. Ianthodon from the Kasimovian is known from newly identified elements, including most of the skull and particular postcrania. This species is determined as the best model for the initial morphology of the Sphenacomorpha (Edaphosauridae and Sphenacodontia). Remarkably older sphenacodontian remains from the Moscovian indicate a derived, though fragmentarily known form, possibly basal Sphenacodontoidea. The genus Haptodus is conclusively revised, including the revalidation of the type species H. baylei from the Artinskian. Haptodus grandis is renamed as Hypselohaptodus, gen. nov. “Haptodus” garnettensis is not monophyletic with Haptodus, moreover the material assigned to it yielded a greater diversity. Thus, its renaming includes Eohaptodus garnettensis, gen. nov., Tenuacaptor reiszi, gen. et spec. nov., and Kenomagnathus scotti, gen. et spec. nov. Along with Ianthodon and the basal edaphosaurid Ianthasaurus, these taxa from a single assemblage are differentiated by dentition and skull proportions, providing a case study of annidation. Since Ianthodon can be excluded from Sphenacomorpha, the larger, stem-based taxon Haptodontiformes is introduced. More derived ‘haptodontines’ apparently form another radiation, named as Pantherapsida. This new taxon includes Cutleria, Tetraceratops, Hypselohaptodus, the Palaeohatteriidae (Pantelosaurus and Palaeohatteria), and the Sphenacodontoidea. The ‘pelycosaur’-therapsid transition is affirmed as a long-term development. An integrative evolutionary hypothesis of basal sphenacodontians is provided, within which the ghost lineage of Early Permian therapsids can be explained by biome shift.
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Hernandez, Rosales Maribel. "The Orthology Road." Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-127823.

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The evolution of biological species depends on changes in genes. Among these changes are the gradual accumulation of DNA mutations, insertions and deletions, duplication of genes, movements of genes within and between chromosomes, gene losses and gene transfer. As two populations of the same species evolve independently, they will eventually become reproductively isolated and become two distinct species. The evolutionary history of a set of related species through the repeated occurrence of this speciation process can be represented as a tree-like structure, called a phylogenetic tree or a species tree. Since duplicated genes in a single species also independently accumulate point mutations, insertions and deletions, they drift apart in composition in the same way as genes in two related species. The divergence of all the genes descended from a single gene in an ancestral species can also be represented as a tree, a gene tree that takes into account both speciation and duplication events. In order to reconstruct the evolutionary history from the study of extant species, we use sets of similar genes, with relatively high degree of DNA similarity and usually with some functional resemblance, that appear to have been derived from a common ancestor. The degree of similarity among different instances of the “same gene” in different species can be used to explore their evolutionary history via the reconstruction of gene family histories, namely gene trees. Orthology refers specifically to the relationship between two genes that arose by a speciation event, recent or remote, rather than duplication. Comparing orthologous genes is essential to the correct reconstruction of species trees, so that detecting and identifying orthologous genes is an important problem, and a longstanding challenge, in comparative and evolutionary genomics as well as phylogenetics. A variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has been shown that orthology can be estimated at acceptable levels of accuracy without having to infer gene trees and/or reconciling gene trees with species trees. Therefore, there is good reason to look at the connection of trees and orthology from a different angle: How much information about the gene tree, the species tree, and their reconciliation is already contained in the orthology relation among genes? Intriguingly, a solution to the first part of this question has already been given by Boecker and Dress [Boecker and Dress, 1998] in a different context. In particular, they completely characterized certain maps which they called symbolic ultrametrics. Semple and Steel [Semple and Steel, 2003] then presented an algorithm that can be used to reconstruct a phylogenetic tree from any given symbolic ultrametric. In this thesis we investigate a new characterization of orthology relations, based on symbolic ultramterics for recovering the gene tree. According to Fitch’s definition [Fitch, 2000], two genes are (co-)orthologous if their last common ancestor in the gene tree represents a speciation event. On the other hand, when their last common ancestor is a duplication event, the genes are paralogs. The orthology relation on a set of genes is therefore determined by the gene tree and an “event labeling” that identifies each interior vertex of that tree as either a duplication or a speciation event. In the context of analyzing orthology data, the problem of reconciling event-labeled gene trees with a species tree appears as a variant of the reconciliation problem where genes trees have no labels in their internal vertices. When reconciling a gene tree with a species tree, it can be assumed that the species tree is correct or, in the case of a unknown species tree, it can be inferred. Therefore it is crucial to know for a given gene tree whether there even exists a species tree. In this thesis we characterize event-labelled gene trees for which a species tree exists and species trees to which event-labelled gene trees can be mapped. Reconciliation methods are not always the best options for detecting orthology. A fundamental problem is that, aside from multicellular eukaryotes, evolution does not seem to have conformed to the descent-with-modification model that gives rise to tree-like phylogenies. Examples include many cases of prokaryotes and viruses whose evolution involved horizontal gene transfer. To treat the problem of distinguishing orthology and paralogy within a more general framework, graph-based methods have been proposed to detect and differentiate among evolutionary relationships of genes in those organisms. In this work we introduce a measure of orthology that can be used to test graph-based methods and reconciliation methods that detect orthology. Using these results a new algorithm BOTTOM-UP to determine whether a map from the set of vertices of a tree to a set of events is a symbolic ultrametric or not is devised. Additioanlly, a simulation environment designed to generate large gene families with complex duplication histories on which reconstruction algorithms can be tested and software tools can be benchmarked is presented.
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Guillory, Wilson. "Comprehensive phylogenomic reconstruction of Ameerega (Anura: Dendrobatidae) and introduction of a new method for phylogenetic niche modeling." OpenSIUC, 2020. https://opensiuc.lib.siu.edu/theses/2654.

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To understand present patterns of biodiversity, knowledge of a lineage’s past – both evolutionary and geographic – is required. Here I present the first comprehensive phylogenomic study of an Amazonian poison frog genus, Ameerega, as well as the introduction of a new method for characterizing ancestral distributions via phylogenetic niche modeling, which I use to investigate Ameerega’s biogeographic past. I sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. My phylogenetic inference diverged strongly from those of previous studies. I also introduce a new phylogenetic niche modeling method, which accounts for issues of bias in other methods by incorporating knowledge of evolutionary relationships into niche models. Given modern-day and paleoclimatic data, species occurrence data, and a time-calibrated phylogeny, my method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. I demonstrate my method on the Ameerega bassleri group. I also use simulations to show that my method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space.
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Books on the topic "Phylogentic"

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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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Wiley, E. O., and Bruce S. Lieberman. Phylogenetics. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118017883.

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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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Basic phylogenetic combinatorics. New York: Cambridge University Press, 2011.

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Inc, ebrary, ed. Phylogenetics: Theory and practice of phylogenetics systematics. 2nd ed. Hoboken, N.J: Wiley-Blackwell, 2011.

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Mendoza Straffon, Larissa, ed. Cultural Phylogenetics. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-25928-4.

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Bakker, Peter, Finn Borchsenius, Carsten Levisen, and Eeva Sippola, eds. Creole Studies – Phylogenetic Approaches. Amsterdam: John Benjamins Publishing Company, 2017. http://dx.doi.org/10.1075/z.211.

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Wägele, Johann Wolfgang. Foundations of phylogenetic systematics. München: Pfeil, 2005.

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1968-, Salemi Marco, Vandamme Anne-Mieke 1960-, and Lemey Philippe, eds. The phylogenetic handbook: A practical approach to phylogenetic analysis and hypothesis testing. 2nd ed. Cambridge, UK: Cambridge University Press, 2009.

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Book chapters on the topic "Phylogentic"

1

Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0265.

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Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.
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Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0015.

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Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.
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Quicke, Donald L. J., Buntika A. Butcher, and Rachel A. Kruft Welton. "Phylogenies and trees." In Practical R for biologists: an introduction, 275–83. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245349.0023.

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Abstract Several packages have been developed to allow R-users to work with phylogenetic trees, something that most biologists will need to do at some point in their careers. The most basic is the ape package, which stands for Analysis of Phylogenetics and Evolution. This chapter gives some of the basics of handling 'trees' in R and show things that can be calculated with them. Phytools, another package with extra capabilities, are also introduced in this chapter. Insects are given as examples.
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Quicke, Donald L. J., Buntika A. Butcher, and Rachel A. Kruft Welton. "Phylogenies and trees." In Practical R for biologists: an introduction, 275–83. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245349.0275.

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Abstract Several packages have been developed to allow R-users to work with phylogenetic trees, something that most biologists will need to do at some point in their careers. The most basic is the ape package, which stands for Analysis of Phylogenetics and Evolution. This chapter gives some of the basics of handling 'trees' in R and show things that can be calculated with them. Phytools, another package with extra capabilities, are also introduced in this chapter. Insects are given as examples.
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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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Rieppel, Olivier. "The Turn against Haeckel." In Phylogenetic Systematics, 67–106. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-3.

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Rieppel, Olivier. "The Rise of Holism in German Biology." In Phylogenetic Systematics, 107–47. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-4.

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Rieppel, Olivier. "The Rise of German (“Aryan”) Biology." In Phylogenetic Systematics, 149–85. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-5.

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Conference papers on the topic "Phylogentic"

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Melilli Serbin, Giulia, Eliana Regina Forni Martins, RAFAEL BARBOSA PINTO, Raquel Moura Machado, VIDAL MANSONO, and Ana Maria G. de Azevedo Tozzi. "CYTOGENETIC CHARACTERISTICS OF THE HYMENAEA CLADE (LEGUMINOSE, DETARIOIDEAE) REVEAL PHYLOGENTIC SIGNALS." In XXV Congresso de Iniciação Cientifica da Unicamp. Campinas - SP, Brazil: Galoa, 2017. http://dx.doi.org/10.19146/pibic-2017-79014.

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STANLEY, SCOTT, and BENJAMIN A. SALISBURY. "PHYLOGENETIC GENOMICS AND GENOMIC PHYLOGENETICS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0047.

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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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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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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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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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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 "Phylogentic"

1

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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