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- Title
An overview of phylogenetics.
- Authors
Cronin, M.
- Abstract
Phylogeny generally refers to the genealogy of a group of organisms. For example, the phylogeny of the ruminants would include all of the ancestors, including the common ancestor, of the extant species of cattle, sheep, goats, deer, etc. In this paper, I present basic concepts of phylogenetics, and give examples of phylogenies of domestic and wild species above and below the species level. Taxonomic classifications are based on phylogenetic relationships, which can be inferred from paleontology, morphology, or genetics. Phylogeny can also be inferred for genes, as the genealogy of genes derived from a common ancestral gene. Gene phylogenies and species phylogenies are not always concordant for a variety of reasons. It is also important to recognize that phylogenetics is an historical science, and phylogenetic relationships can only be inferred. Nevertheless, phylogenetic inference has become a rigorous science, with important empirical and theoretical advances in the last few decades. The phylogeny of the horse, including ancestors with progressively decreasing numbers of toes over time, is an example of classical phylogenetic inference from fossils and morphology. The advances of molecular genetics have greatly enhanced and expanded phylogenetic inference from DNA sequences. In general, DNA sequences are assumed to evolve as a function of time, and similarity of sequences indicates recent common ancestry. However, is important to understand the factors affecting molecular sequences that may invalidate this assumption, including linkage, selection, modes of inheritance, lineage sorting of ancestral alleles, and gene duplication. The importance of distinguishing molecular sequence data from gene frequency data is also discussed. Examples are given of mitochondrial DNA (mtDNA) and nuclear DNA sequences that have been used to infer relationships of taxa at the levels of family, genus, species, and intra-species. At the level of higher taxa, the phylogeny of artiodactyls (even toed ungulates) has been inferred from molecular sequences for several genes. This includes the relationships among artiodactyls including non-ruminants (e.g. pig), ruminants (e.g., cattle sheep, deer), and more distantly related groups (e.g. whales). At the level of species, subspecies, and breeds, examples of cattle, bison, and several deer species are described. This includes groups in which molecular phylogenies are discordant with classical understanding of relationships from morphology, distribution, and natural history. The phylogenies of some domestic and wild ruminants are compared, and the concepts of wild subspecies and domestic breeds are discussed.
- Subjects
MOLECULAR genetics; RUMINANTS; NATURAL history; NUCLEAR DNA; NUCLEOTIDE sequence; MITOCHONDRIAL DNA; GOAT diseases; MOLECULAR phylogeny
- Publication
Journal of Animal Science, 2006, Vol 84, p421
- ISSN
0021-8812
- Publication type
Article