Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome.
Entrez PubMed: "The use of likelihood as a framework for statistical modeling in phylogenetics has played a fundamental role in studying molecular evolution, enabling rigorous and robust conclusions to be drawn from sequence data. The first half of this article is a general introduction to the likelihood method for inferring phylogenies, the properties of the models used, and how it can be used for statistical testing. The latter half of the article focuses on the emerging new generation of phylogenetic models that describe heterogeneity in the evolutionary process along sequences, including the recoding of protein coding sequence data to amino acids and codons, and various approaches for describing dependencies between sites in a sequence. We conclude with a detailed case study examining how modern modeling approaches have been successfully employed to identify adaptive evolution in proteins."
Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome. Kosiol C, Bofkin L, Whelan S. J Biomed Inform. 2005 Sep 15; [Epub ahead of print]
Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome. Kosiol C, Bofkin L, Whelan S. J Biomed Inform. 2005 Sep 15; [Epub ahead of print]
1 Glossary:
Taxonomies aim to group organisms according to shared characteristics against the background of biological diversity.
Phenetic system: groupings of organisms based on mutual similarity of phenotypic (physical and chemical) characteristics. Phenetic groupings may or may not correlate with evolutionary relationships.
Numerical Taxonomy: a common approach to phenetic taxonomy, which employs a number of phenotypic characteristics to generate similarity coefficients that may be mapped in dendrograms. Groupings based on numerical taxonomy may or may not correlate with evolutionary relationships.
Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.
Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.
Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.
Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy.—characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.
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