Phylogenomik

Phylogenomik is a field of biology that uses genome-scale data to infer evolutionary relationships, histories, and the genetic basis of phenotypic traits. The term, a variant of phylogenomics, emphasizes the integration of phylogenetic methods with large-scale sequencing data from whole genomes, transcriptomes, and targeted gene sets to improve resolution and robustness of evolutionary inference.

Core approaches in phylogenomik include assembly and annotation of sequence data, identification of orthologous genes, and construction of gene trees and species trees. Analyses may use concatenation of multiple loci into a single alignment, coalescent-based methods that account for gene tree discordance, and models that incorporate sequence evolution, gene duplication and loss, and horizontal gene transfer. Computational pipelines and high-performance computing are often required to process and analyze the volume of data.

Applications span systematics, comparative genomics, molecular dating, detection of adaptive evolution, and reconstruction of ancestral genomes and traits. Phylogenomik has been especially transformative for resolving deep branches in the tree of life, studying microbial diversity, and tracing the spread of pathogens.

Limitations include incomplete lineage sorting, paralogy and gene tree conflict, horizontal gene transfer, model misspecification, and sampling biases. Ongoing developments—improved models of genome evolution, long-read and single-cell sequencing, and integration with functional and ecological data—aim to address these challenges and expand the field’s ability to reconstruct evolutionary processes.