Phylogeny

From The Book of THoTH (Leaves of Wisdom)

In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations). Also known as phylogenetic systematics, phylogenetics treats a species as a group of lineage-connected individuals over time. Phylogenetic taxonomy, which is an offshoot of, but not a logical consequence of, phylogenetic systematics, constitutes a means of classifying groups of organisms according to degree of evolutionary relatedness.

Phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually a set of species. A major task of systematics is to determine the ancestral relationships among known species (both living and extinct). The most commonly used methods to infer phylogenies include cladistics, phenetics, maximum likelihood, and MCMC-based Bayesian inference. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences.

1 Ernst Haeckel's recapitulation theory
2 Gene transfer
3 Taxon sampling
4 See also
5 References
6 External links

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Ernst Haeckel's recapitulation theory

During the late 19th century, Ernst Haeckel's recapitulation theory, or biogenetic law, was widely accepted. This theory was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of an organism exactly mirrors the evolutionary development of the species. The early version of this hypothesis has since been rejected as being oversimplified. However, most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using evolutionary theory, or view them as supporting evidence for that theory.

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Gene transfer

Organisms can generally inherit genes in two ways. 1. By speciation (vertical gene transfer). Meaning from parent to offspring. 2. By Horizontal or lateral gene transfer. Meaning genes might jump between unrelated organisms a common phenomenon in prokaryotes.

Lateral gene transfer has therefore complicated the determination of phylogenies of organisms since inconsistences have been reported dependent on the gene of choice being used.

Karl Woese came up with the three domain theory of life (i.e. Eubacteria, Archaea and Eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no Lateral gene transfer. Therefore rDNA are commonly recommended as molecular clocks for reconstructing phylogenies.

This has been particularly useful for the phylogeny of microorganisms to which the species concept does not apply and that are too morphologically simple to be classified based on phenotypic traits.

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Taxon sampling

Due to the development of advanced sequencing techniques in molecular biology, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to estimate phylogenies. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes. However, it has been proposed that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa, the more robust is the resulting phylogeny. This is partly due to the breaking up of long branches. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible.

Using simulations, Zwickl and Hillis (2002) found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.

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