Please wait while we load your article...

Home > Phylogenetics

Learn more about "Phylogenetics"

Phylogenetics

In biology, phylogenetics is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations), which is discovered through molecular sequencing data. The term '''phylogenetics''' is of Greek origin from the terms '''phyle/phylon''' (φυλή/φῦλον), meaning "tribe, race," and '''genetikos''' (γενετικός), meaning "relative to birth" from ''genesis'' (γένεσις ) "birth"). Alpha taxonomy|Taxonomy, the classification of organisms according to similarity, has been richly informed by phylogenetics but remains methodologically and logically distinct. The fields overlap however in the science of '''phylogenetic systematics''' or '''cladism''', where only phylogenetic trees are used to delimit taxa, each representing a group of lineage-connected individuals. Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, Hybrid (biology)|hybridize together, or terminate by extinction. This may be scientific visualization|visualized as a multidimensional scaling|multidimensional character-space that a population moves through over time. The problem posed by phylogenetics is that genetics|genetic data are only available for the present, and fossil records (osteometric data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree. There are some terms that describe the nature of a grouping in such trees. For instance, all birds and reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow in the diagram) is called Monophyly|monophyletic. "Modern reptile" (cyan in the diagram) is a grouping that contains a common ancestor, but does not contain all descendents of that ancestor (birds are excluded). This is an example of a Paraphyly|paraphyletic group. A grouping such as warm-blooded animals would include only mammals and birds (red/orange in the diagram) and is called Polyphyly|polyphyletic because the members of this grouping do not include the most recent common ancestor. Thus, a phylogenetic tree is based on a hypothesis of the order in which evolutionary events are assumed to have occured. Y-DNA HAPLOGROUP TREE. 2002. http://www.familytreedna.com/haplotree.html
Cladistics is today the method of choice to infer phylogenetic trees. The Computational phylogenetics|most commonly used methods to infer phylogenies include parsimony, maximum likelihood, and Markov chain Monte Carlo|MCMC-based Bayesian inference. '''Phenetics''', popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. 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.

Molecular phylogenetics

The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time which can not be observed directly, biologists must continually reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms. Fossils can aid with the reconstruction of phylogenies, however, fossil records are often too poor to be of good help. Therefore, biologists tend to be restricted with analysing present-day organisms to identify their evolutionary relationships. Phylogenetic relationships in the past were reconstructed by looking at phenotypes, often anatomical characteristics. Today, molecular data, which includes protein and DNA sequences, are used to construct phylogenetic trees.

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. Haeckel's early version of this hypothesis the embryo mirrors ''adult'' evolutionary ancestors has since been rejected, and the hypothesis amended as the embryo's development mirroring ''embryos'' of its evolutionary ancestors. Most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using Evolutionary developmental biology|evolutionary theory, or view them as supporting evidence for that theory. Donald Williamson suggested that larvae and embryos represented adults in other taxa that have been transferred by hybridization (the larval transfer theory).

Gene transfer

Organisms can generally inherit genes in two ways: vertial gene transfer and horizontal gene transfer. Vertitcal gene transfer is the passaged of genes from parent to offspring, and horizontal gene transfer or lateral gene transfer occurs when genes jump between unrelated organisms, a common phenomenon in prokaryotes. Lateral gene transfer has complicated the determination of phylogenies of organisms since inconsistencies have been reported depending on the gene chosen. Carl Woese came up with the three-domain theory of life (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 rRNA 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 which are too morphologically simple to be classified based on phenotypic traits.

Taxon sampling and phylogenetic signal

Owing 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 branch attraction|long branches. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible. Using simulations, Derrick Zwickl and Hillis found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses. Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contains a useful phylogenetic signal, a term that is used generally to denote whether related organisms tend to resemble each other with respect to their genetic material or phenotypic traits.

References

Related Images

Sources: StartLearningNow, Wikipedia | Usage license: GNU FDL

Welcome to Start Learning Now. Explore to your heart's content, and we hope you enjoy reading the material we have assembled for you here!

Related News

Further Resources


	home lucky pick

Related Resources