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| Format: | Recurso digital |
| Idioma: | anglès |
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2026
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| Accés en línia: | https://doi.org/10.5281/zenodo.20022042 |
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| _version_ | 1866901388693340160 |
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| author | molecular evolution science |
| author_facet | molecular evolution science |
| contents | Molecular phylogenetics has evolved from analyzing single conserved genes to leveraging genome-scale data, a transition defining the modern era of phylogenomics. This comprehensive guide explores the methodological frameworks and computational tools essential for reconstructing the Tree of Life. It begins by establishing fundamental terminology and tree interpretation, detailing the construction of rooted and unrooted trees using distance-based, maximum parsimony, maximum likelihood, and Bayesian inference methods. A critical component is the molecular clock hypothesis, which utilizes genetic divergence and fossil calibration to estimate evolutionary timescales. The article highlights significant computational challenges in the genomic era, particularly handling massive datasets and site heterogeneity. Advanced algorithms and workflows, such as the Phylogenetic and Molecular Evolutionary (PhaME) pipeline and the Chronological Supertree Algorithm (Chrono-STA), are introduced as solutions for processing large-scale genomic data and integrating thousands of published phylogenies with limited taxonomic overlap. Furthermore, the text addresses the critical issues of model misspecification and confirmation bias, advocating for rigorous goodness-of-fit tests, such as Pearson's X2 test with binning, and explicit alternative hypothesis testing to ensure robust phylogenetic estimates. Beyond fundamental evolutionary biology, the guide emphasizes the practical applications of phylogenetics in public health and drug development. Phylodynamics is explored as a framework for tracking pathogen transmission and evolution, crucial for managing infectious disease outbreaks like SARS-CoV-2. Additionally, comparative genomics within a phylogenetic context is presented as a powerful strategy for identifying novel, bacteria-specific drug targets to combat the escalating antimicrobial resistance crisis. By integrating molecular data with morphological and fossil evidence through models like the fossilized birth-death process, researchers can achieve unprecedented accuracy in evolutionary reconstruction. Ultimately, this integration of advanced computational methods, rigorous statistical validation, and comprehensive data synthesis empowers scientists to address complex biological questions and develop targeted biomedical interventions. Source: https://www.molevosci.com/posts/molecular-phylogenetics-and-the-tree-of-life-from-genomic-data-to-biomedical-applications |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_20022042 |
| institution | Zenodo |
| language | eng |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Molecular Phylogenetics and the Tree of Life: From Genomic Data to Biomedical Applications molecular evolution science Molecular Phylogenetics Tree of Life Phylogenomics Molecular Clock Supertree Construction Drug Discovery Antimicrobial Resistance Phylodynamics Comparative Genomics Molecular phylogenetics has evolved from analyzing single conserved genes to leveraging genome-scale data, a transition defining the modern era of phylogenomics. This comprehensive guide explores the methodological frameworks and computational tools essential for reconstructing the Tree of Life. It begins by establishing fundamental terminology and tree interpretation, detailing the construction of rooted and unrooted trees using distance-based, maximum parsimony, maximum likelihood, and Bayesian inference methods. A critical component is the molecular clock hypothesis, which utilizes genetic divergence and fossil calibration to estimate evolutionary timescales. The article highlights significant computational challenges in the genomic era, particularly handling massive datasets and site heterogeneity. Advanced algorithms and workflows, such as the Phylogenetic and Molecular Evolutionary (PhaME) pipeline and the Chronological Supertree Algorithm (Chrono-STA), are introduced as solutions for processing large-scale genomic data and integrating thousands of published phylogenies with limited taxonomic overlap. Furthermore, the text addresses the critical issues of model misspecification and confirmation bias, advocating for rigorous goodness-of-fit tests, such as Pearson's X2 test with binning, and explicit alternative hypothesis testing to ensure robust phylogenetic estimates. Beyond fundamental evolutionary biology, the guide emphasizes the practical applications of phylogenetics in public health and drug development. Phylodynamics is explored as a framework for tracking pathogen transmission and evolution, crucial for managing infectious disease outbreaks like SARS-CoV-2. Additionally, comparative genomics within a phylogenetic context is presented as a powerful strategy for identifying novel, bacteria-specific drug targets to combat the escalating antimicrobial resistance crisis. By integrating molecular data with morphological and fossil evidence through models like the fossilized birth-death process, researchers can achieve unprecedented accuracy in evolutionary reconstruction. Ultimately, this integration of advanced computational methods, rigorous statistical validation, and comprehensive data synthesis empowers scientists to address complex biological questions and develop targeted biomedical interventions. Source: https://www.molevosci.com/posts/molecular-phylogenetics-and-the-tree-of-life-from-genomic-data-to-biomedical-applications |
| title | Molecular Phylogenetics and the Tree of Life: From Genomic Data to Biomedical Applications |
| topic | Molecular Phylogenetics Tree of Life Phylogenomics Molecular Clock Supertree Construction Drug Discovery Antimicrobial Resistance Phylodynamics Comparative Genomics |
| url | https://doi.org/10.5281/zenodo.20022042 |