Introduction to Phylogenetics

Phylogenetics is the science of Phylogeny, and as such I will be focusing on it instead of the more generic Phylogeny for this post. I have found this article as a starting point.

The goal of Phylogeny is to construction a phylogenetic tree that maps the genetic relationships of all species (past and present) on earth.

Phylogeny uses evolutionary distance/evolutionary relationships to determine the taxonomy of species.

Taxonomy is the science of naming, classifying and describing species.

Taxonomy groups organisms into taxa (groups)

Taxa are then further grouped by biological similarity.

Systematics adds to taxonomy and allows for taxa to be grouped into species, based on evolutionary similarities and mechanisms for evolution.

William Hennig (1950s) said systematics should follow known evolutionary lineage, thereby creating the field of phylogenetic semantics.

Phylogenetic systematics deals with the classification of organisms based on evolutionary relationships.

Phylogenetic relationships used to be determined by morphological data, this was found to be insufficient.

Cladistics was the field that developed to determine phylogentic relationships based on shared, derived characteristics.

There are two types of characteristics: primitive traits and derived traits.

Primitive traits are those inherited from the ancestor of the group. Such as all monkeys have tails so having a tail is a primitive trait for a monkey.

Derived traits are those that have evolved in the group under study. Size, colouring, behaviour and diet are derived traits (as I understand it). Birds are an excellent example of derived traits like the differences between a hummingbird and an eagle.

The simple explanation of the source of a derived trait is that it is from a evolutionarily more recent ancestor than the earlier ancestor being examined.

There are two main types of analysis to determine phylogenetic relationships: Phenetic and Cladistic.

Phenetic methodology (numerical taxonomy) uses over all similarities to classify relationships, once similarities are determined the organisms are grouped into clusters called phenograms.

Cladistic methodology uses the idea that members of a group share a common ancestry and are more closely related to each other than any other organism, so my children are in the same group (siblings) since they are one step removed from me as an ancestor. The shared derived characteristics in the group are called synapomorphies.

There are two recent tools that have helped phylogenetics: computer algorithms that can automatically place groups into a phylogenetic tree and the ability of using molecular sequence data (DNA?) for phylogenetic studies.

Phylogenetics can use both molecular and morphological data to classify organisms.

Molecular studies use genes as the basis of comparison. The assumption is that organisms that share genes will be more closely related than those that don't.

Morphological studies use an organism's phenotype to determine relationships.

phenotype ( ) n. The observable physical or biochemical characteristics of an organism, as determined by both genetic makeup (sic) and environmental. according to Answers.com

Both methods are related as the genome is used in both methodologies and the genome has a strong influence in the phenotype. The molecular methodology has an advantage in that it can be studied with out morphological expressions.

Closely related species have a more recent ancestor than a distantly related species (two different types of hummingbird versus an eagle) and those relationships can be expressed by a phylogenetic tree.

A phylogenetic tree is a graphical representation of how species are interrelated and have nodes and branches. A node is a taxonomical species and the branch is how it is related to another taxonomical species with the length of the branch reprisenting the amount of evolutionary distance between taxonomical species.

There are two main types of tree construction methods: Cladastic (maximum parsimony and maximum likelyhood) and Phenetic (distance matrix method).

picture of a simple phylogenetic tree

Maximum parsimony asserts that Occam's razor should be applied and that simple hypotheses are preferable to complex ones, the minimum number of genetic changes should be used to show phylogenetic relationships, the procedure compares a number of parsimony trees and chooses the simplest one.

Maximum likelihood examines a number of possible trees and chooses the best one based on some criteria. This approach takes into concideration the evolutionary process that can change one gene into another.

Distance matrix examines the mean changes in the genetics of a pair of taxa to determine the distance relationship between the two taxa. Gene sequences must be simplified in order for them to be compared and the difference in the two genomes can be interrupted as the distance between the two taxonomical species.

Molecular phylogeny was first proposed by Pauling and Zuckerkandl (1962) when they noted the rates at which amino acids were substituted in animal hemoglobin at a predictable rate over time. This is advantageous as genotypes can be studied directly and organisms can be compared directly even if they are morphologically very different, as such this method does not rely on phenotype.

Biologist calculate that there are between 5 and 10 million species alive today and genetic information indicates that all of them may have a common ancestor, hence the reason to study the Tree of Life to determine the root of all life on the planet.