7.4 Applications of phylogenetics in computational biology

Phylogenetics is a powerful tool in computational biology, helping us understand how organisms and genes are related. It's used in many areas, from tracking disease outbreaks to studying biodiversity and developing new drugs.

By looking at the similarities in DNA or physical traits, scientists can build family trees for species or genes. This helps them figure out how things evolved and how different biological systems work together.

Phylogenetics in Computational Biology

Applications of Phylogenetics

Top images from around the web for Applications of Phylogenetics

• 

  Compact graphical representation of phylogenetic data and metadata with GraPhlAn [PeerJ] View original

  Is this image relevant?

• 

  Tree of life (biology) - Wikipedia View original

  Is this image relevant?

• 

  Iroki: automatic customization and visualization of phylogenetic trees [PeerJ] View original

  Is this image relevant?

• 

  Compact graphical representation of phylogenetic data and metadata with GraPhlAn [PeerJ] View original

  Is this image relevant?

• 

  Tree of life (biology) - Wikipedia View original

  Is this image relevant?

1 of 3

Top images from around the web for Applications of Phylogenetics

• 

  Compact graphical representation of phylogenetic data and metadata with GraPhlAn [PeerJ] View original

  Is this image relevant?

• 

  Tree of life (biology) - Wikipedia View original

  Is this image relevant?

• 

  Iroki: automatic customization and visualization of phylogenetic trees [PeerJ] View original

  Is this image relevant?

• 

  Compact graphical representation of phylogenetic data and metadata with GraPhlAn [PeerJ] View original

  Is this image relevant?

• 

  Tree of life (biology) - Wikipedia View original

  Is this image relevant?

1 of 3

• Phylogenetics studies the evolutionary relationships among organisms, genes, or other biological entities based on their molecular or morphological similarities
• Phylogenetic methods infer the evolutionary history and construct phylogenetic trees depicting the branching patterns and divergence times of the studied entities
• Comparative genomics uses phylogenetics to identify conserved regions, detect selection pressures, and reconstruct ancestral sequences (ancient gene variants)
• Molecular epidemiology employs phylogenetic approaches to trace the origin and spread of pathogens (SARS-CoV-2), investigate disease outbreaks, and develop targeted interventions
• Biodiversity studies apply phylogenetics to assess species richness, understand evolutionary processes shaping communities (adaptive radiations), and prioritize conservation efforts
• Drug discovery and development utilize phylogenetic methods to identify potential drug targets, predict drug resistance, and guide the selection of model organisms for testing (zebrafish)

Phylogenetic Diversity and Community Analysis

• Phylogenetic diversity measures, such as Faith's phylogenetic diversity and UniFrac distances, quantify the evolutionary distinctiveness and relatedness of microbial communities
• These measures help compare the diversity and structure of microbial communities across different environments (human gut, soil, marine ecosystems)
• Phylogenetic approaches uncover the functional potential and evolutionary adaptations of microbial communities in various ecological niches
• Integrating phylogenetic information with environmental factors and community dynamics provides insights into the assembly and functioning of microbial ecosystems

Phylogenetic Methods for Gene Evolution

Gene Family Evolution

• Gene families are groups of genes that have evolved from a common ancestral gene through duplication, speciation, and divergence events
• Phylogenetic analysis of gene families distinguishes between orthologous and paralogous relationships, providing insights into the evolutionary history and functional divergence of genes
• Orthologous genes are homologous genes that have diverged due to a speciation event (human and mouse insulin genes)
• Paralogous genes have diverged due to a duplication event within a species (human alpha and beta hemoglobin genes)
• Studying gene family evolution using phylogenetics enables the identification of lineage-specific gene expansions, contractions, and adaptations (olfactory receptor genes in mammals)

Orthology and Comparative Genomics

• Reconciliation methods compare gene trees with species trees to infer gene duplication, loss, and horizontal transfer events
• Orthology relationships inferred from phylogenetic analysis are crucial for functional annotation, comparative genomics, and evolutionary studies across species
• Comparative genomics relies on accurate orthology assignments to identify conserved functional elements (transcription factor binding sites) and study the evolution of gene regulation
• Phylogenetic profiling, which compares the presence or absence of orthologous genes across species, can reveal co-evolving gene sets and predict functional associations (enzymes in a metabolic pathway)

Phylogenetic Analysis of Microbial Communities

Metagenomics and Microbial Diversity

• Metagenomics involves the sequencing and analysis of DNA from environmental samples, enabling the study of microbial communities without the need for cultivation
• Phylogenetic methods are applied to metagenomics data to assess the taxonomic composition and diversity of microbial communities
• Marker gene-based approaches, such as 16S rRNA gene sequencing, construct phylogenetic trees and compare microbial community structures across samples (healthy vs. diseased gut microbiomes)
• Whole-genome shotgun metagenomics allows for the reconstruction of draft genomes and the identification of novel microbial lineages using phylogenetic placement methods

Microbial Community Structure and Function

• Phylogenetic approaches reveal the taxonomic composition and evolutionary relationships within microbial communities
• Comparing the phylogenetic structure of microbial communities across different environments (soil, water, host-associated) provides insights into the factors shaping community assembly and function
• Phylogenetic diversity metrics quantify the evolutionary distinctiveness and relatedness of microbes within a community, serving as indicators of community stability and resilience
• Integrating phylogenetic information with functional annotations and metabolic capabilities helps elucidate the functional roles and interactions of microbes in complex ecosystems (nutrient cycling, host-microbe symbiosis)

Phylogenetic Integration with Omics Data

Multi-Omics Integration

• Phylogenetic information can be combined with other omics data, such as transcriptomics, proteomics, and metabolomics, to gain a systems-level understanding of biological processes
• Phylogenetic trees serve as a framework for integrating and visualizing multi-omics data, allowing for the identification of evolutionary patterns and co-evolution of molecular components
• Phylogenetic comparative methods study the evolution of gene expression, protein abundance, and metabolic pathways across species (brain gene expression in primates)
• Ancestral state reconstruction techniques infer the evolutionary history of molecular traits and identify key evolutionary events associated with functional changes (evolution of photosynthetic pathways)

Evolutionary Systems Biology

• Integrating phylogenetics with other omics data enables the identification of evolutionarily conserved or divergent molecular mechanisms, providing insights into the functional diversification and adaptation of biological systems
• Phylogenetic information guides the selection of representative species or strains for multi-omics experiments, ensuring a broad evolutionary coverage and maximizing the information gained
• Evolutionary systems biology approaches combine phylogenetics, omics data, and computational modeling to unravel the evolutionary dynamics of complex biological networks (gene regulatory networks, signaling pathways)
• Comparative analyses of omics data across species reveal the evolutionary conservation and divergence of molecular processes, helping to identify functionally important elements and evolutionary innovations (mammalian brain evolution)