Nucleotide Substitution Models and Evolutionary Distances

Xia, Xuhua

doi:10.1007/978-3-319-90684-3_12

Cited by 6 publications

(4 citation statements)

References 849 publications

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“…For the DistPlot method, simultaneous estimated TN93 distances [ 29 ] were computed with a sliding window of 500 nt. The simultaneous estimation is more robust and accurate than the commonly used independent estimation [ 29 , 115 ]. The use of the TN93 distance instead of the more general GTR distance is because the window size of 500 nt often does not include all six different nucleotide replacements (two transitions and four transversions) needed for parameter estimation in the GTR model.…”

Section: Methodsmentioning

confidence: 99%

Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis

Xia

2023

Antibiotics

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Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.

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Section: Methodsmentioning

confidence: 99%

Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis

Xia

2023

Antibiotics

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“…Sejam as duas seqüências em cada nó pertencentes às espécies de humanos e de chimpanzés de acordo com a Figura 3.7. Para o modelo JC, as probabilidades de substituição junto a cada sítio são dadas por (LEWIS, 2002;NEI & KUMAR, 2000):…”

Section: Verossimilhança De áRvores Com Dois Nós E Um Ramounclassified

“…De acordo com BRYANT (2003), o problema das técnicas de consenso não está na escolha de alguma das técnicas, mas na maneira como as árvores resultantes da aplicação de técnicas de consenso têm sido interpretadas.…”

Section: Considerações Sobre As Técnicas De Consensounclassified

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Uma abordagem multi-objetivo e multimodal para reconstrução de arvores filogeneticas

Silva¹,

Zuben²

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ResumoA reconstrução de árvores filogenéticas pode ser interpretada como um processo sistemático de proposição de uma descrição arbórea para as diferenças relativas que se observam em conjuntos de atributos genéticos homólogos de espécies sob comparação. A árvore filogenética resultante apresenta uma certa topologia, ou padrão de ancestralidade, e os comprimentos dos ramos desta árvore são indicativos do número de mudanças evolutivas desde a divergência do ancestral comum. Tanto a topologia quanto os comprimentos de ramos são hipóteses descritivas de eventos não-observáveis e condicionais, razão pela qual tendem a existir diversas hipóteses de alta qualidade para a reconstrução, assim como múltiplos critérios de desempenho. Esta tese (i) aborda árvores sem raiz; (ii) enfatiza os critérios de quadrados mínimos, evolução mínima e máxima verossimilhança; (iii) propõe uma extensão ao algoritmo Neighbor Joining que oferece múltiplas hipóteses de alta qualidade para a reconstrução; e (iv) descreve e utiliza uma nova ferramenta para otimização multiobjetivo no contexto de reconstrução filogenética. São considerados dados artificiais e dados reais na apresentação de resultados, os quais apontam vantagens e aspectos diferenciais das metodologias propostas.

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Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method

Xia

2018

Preprint

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I analyzed various site pattern combinations in a 4-OTU case to identify sources of starless bias and parameter-estimation bias in likelihood-based phylogenetic methods, and reported three significant contributions. First, the likelihood method is odd in that it may not generate a star tree with sequences that are equidistant from each other. This behaviour, dubbed starless bias, happens in a 4-OTU tree when there is an excess (i.e., more than expected from a star tree and a substitution model) of conflicting phylogenetic signals supporting the three resolved topologies equally. Special site pattern combinations leading to rejection of a star tree, when sequences are equidistant from each other, were identified. Second, fitting gamma distribution to model rate heterogeneity over sites is strongly confounded with tree topology, especially in conjunction with the starless bias. I present examples to show dramatic differences in the estimated shape parameter α between a star tree and a resolved tree. There may be no rate heterogeneity over sites (with the estimated α > 10000) when a star tree is imposed, but α < 1 (suggesting strong rate heterogeneity over sites) when an (incorrect) resolved tree is imposed.Thus, the dependence of "rate heterogeneity" on tree topology implies that "rate heterogeneity"is not a sequence-specific feature, cautioning against interpreting a small α to mean that some sites are under strong purifying selection and others not. Thirdly, because there is no existing (and working) likelihood method for evaluating a star tree with continuous gamma-distributed rate, I have implemented the method for JC69 in a self-contained R script for a four-OTU tree (star or resolved), in addition to another R script assuming a constant rate over sites. These R scripts should be useful for teaching and exploring likelihood methods in phylogenetics.

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Nucleotide Substitution Models and Evolutionary Distances

Cited by 6 publications

References 849 publications

Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis

Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis

Uma abordagem multi-objetivo e multimodal para reconstrução de arvores filogeneticas

Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method

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