Phylogenomics

Phylogenomics uses genome-scale data to infer evolutionary relationships among organisms. It combines phylogenetic methods with evidence from many genes or entire genomes.

Multiple sequence alignment: A computational arrangement of DNA, RNA, or protein sequences that identifies corresponding positions. Alignments establish which genomic positions can be compared across organisms.
Genome: The complete set of genetic material in an organism or cell. Genome-scale evidence expands analysis beyond a small selection of genes.
Metagenomics: The study of genetic material recovered directly from environmental samples. Environmental genomes extend phylogenomic analysis to organisms difficult to culture.
Molecular systematics: The study of evolutionary relationships using molecular characters, often from selected genes or markers. Phylogenomics extends molecular systematics through genome-scale evidence.
Orthology: A relationship between genes in different species that descended from one gene in their last common ancestor. Orthologous genes are often compared to reconstruct species relationships.
Molecular evolution: Changes in genetic material across generations and evolutionary lineages. Phylogenomics interprets genome differences as products of molecular evolution.
Phylogenomics of eukaryotes: The use of genome-scale data to infer evolutionary relationships among eukaryotic lineages. Eukaryote-wide datasets have tested competing hypotheses about deep lineage relationships.
Morphological phylogenetics: The inference of evolutionary relationships from observable anatomical or structural characters. It uses organismal traits rather than genome-wide sequence data.
Maximum likelihood estimation: A statistical method that selects model parameters making observed data most probable. Likelihood methods estimate trees from sequence data under explicit models of evolution.
Gene duplication: The production of an additional copy of a gene within a genome. Duplicated genes can be mistaken for equivalent copies across species.

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