Phylogenetics - A Beginner's Reference

• What is phylogenetics (and how does it fit into the grand scheme of taxonomy)?
• Glossary of Terminology
• Online Tutorials
• Tree Building Methods
• Short Summaries
• Getting Started
• Examples to Work Through

Taxonomy Background

Well, one of the oldest and most frustrating problems in biology has been devising a system to keep track of all the organisms on earth. From the simplest bacteria to the tallest tree, we need a comprehensive system to classify organisms. This is the field of taxonomy.

Taxonomy-(from Greek taxis meaning arrangement or division and nomos meaning law) is the science of classification according to a pre-determined system, with the resulting catalog used to provide a conceptual framework for discussion, analysis, or information retrieval. In theory, the development of a good taxonomy takes into account the importance of separating elements of a group (taxon) into subgroups (taxa) that are mutually exclusive, unambiguous, and taken together, include all possibilities. In practice, a good taxonomy should be simple, easy to remember, and easy to use.
(See reference)

The Linnaeus Classification System
One of the best known taxonomies is the one devised by the Swedish scientist, Carl Linnaeus, whose classification for biology is still widely used (with modifications). The Linnaeus Classification System is probably the one you remember from high school biology. It goes from general to specific:

• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

(See a general diagram, example with dog, example with human)

Numerical Taxonomy
The major problem with the Linnaeus system is that it becomes a very subjective system. There is room for different people to interpret different groups because each level is arbitrarily defined. So, beginning in the 1950's, scientists started looking for alternative methods of classifying organisms. This gave rise to numerical taxonomy.

Numerical taxonomy- The classification of organisms by purely mathematical means. It is based on quantifying observable characteristics of organisms and may be operated at various taxonomic levels to deal with species or higher taxa. It involves the grouping and computation of the similarity of characters; the results are usually displayed graphically, as a phenogram or dendrogram.
(See reference)

The goal of numerical taxonomy was to be objective. This was to be achieved by converting all observations into numbers and then using a predefined calculation to divide organisms into taxa. However, it was quickly realized that there was a lot of subjectivity in which observations were used and how these observations were converted into numbers. So, the problem of subjectivity still existed. This is when phylogenetics emerged.

Phylogenetics
The basic idea of phylogenetics is to classify organisms the way they evolved. This first means that you have to accept Darwin's Theory of Evolution (which is not without question). The basic idea is that life began as a single cell and that everything on earth has developed from the one cell through mutation and natural selection. So, naturally, all organisms can be related through an evolutionary "family tree". A project called The Tree of Life has begun to organize the information we have now.

Today, phylogenetics is most commonly done at a molecular level. A gene (DNA) or protein sequence is chosen based on a number of criteria. This same sequence is then determined for a number of different organisms and all the sequences are aligned to each other using a multiple sequence alignment program. From this alignment, a phylogenetic tree is created from tree building algorithms to graphically show the sequences (and hopefully) how they are related. There are many ways of determining evolutionary relatedness from the multiple sequence alignment including maximum likelihood, maximum parsimony, pairwise distance and more (see Tree-building section).

Phylogenetics has emerged as a leading taxonomic method. However, there is still controversy as to its validity and reliability. Since evolution is a historical event, each step in the phylogenetics process requires certain assumptions to be made. For a great reference on the assumptions, see Baxevanis and Ouellette's "Bioinformatics: A Practical to the Analysis of Genes and Proteins", Chapter 14 - Phylogenetic Analysis. (Sorry, it's not online, but it is a great reference.) As well, different tree building methods do different types of analysis and mean different things. To make an analysis as valid as possible, the appropriate method must be used with the appropriate data.

As the popularity of phylogenetics has increased, so has the need to manage the data generated from these analyses. The database TreeBASE has been created for this purpose. "TreeBASE is a relational database of phylogenetic information hosted by the University at Buffalo. TreeBASE stores phylogenetic trees and the data matrices used to generate them from published research papers." Biologists may submit their data to this database as a way to make it available to the general community, especially if their publication didn't or couldn't give complete details as to what was done.

Phylogenetics can be a powerful method of taxonomy when properly understood. And, hopefully, this page will help you on your way to that understanding.

Online Phylogenetics Class Page

• This is a great webpage that was put together by a group of students that were taking a course on phylogenetics. The glossary of terms can be found under their Misc. section called Phylogenetic and Evolutionary terms.

Comprehensive Glossary

• A list of phylogenetic terms with paragraph descriptions / comparisons. (Great for the terms that really can't be explained in one or two sentences.)

Online Phylogenetics Class Page

• This is the same page listed above in the glossary section, but it also has a great introduction page that gives an overview of phylogenetics, a methods page that describes the substitution models well and other great tidbits under their Misc. section.

Berkeley's Phylogenetics

• A step-by-step walk through of phylogenetics/cladistics. The nice thing is, its written in simple language.

Phylogenetics Lab from the Virtual Paleobotany Lab

• This is an online lab for a plant biology class. It is a step-by-step walk through of phylogenetics.

Introduction to Tree Building

• This is a 5 page pfd file that describes the main tree building methods and compares them.

Tree-Building Methods

• Although this page is very plain and can be tedious to read, it has a good summary of the major tree-building methods.

Distance Based Phylogenies

• By choosing the Slides Bullet (third one on the list), you can view a PowerPoint presentation that focuses on distance-methods of creating phylogenetic trees. (As an extra, on this page they have a cool picture of Homer Simpson in a phylogenetic tree.

How to Make a Phylogenetic Tree

• From the HIV Sequence database, this link has another way of explaining some tree-building methods, as well as common mistakes in trees and checking reliability (bootstrapping).

Introduction to Phylogenetic Systematics

• Summary of some relevant topics from a logic perspective.

Molecular Phylogenetics

• Very short summary of why we use evolution and some basic terminology.

Principles of Phylogeny

• Everything-you-really-needed-to-know-about-phylogenetics-but-was-too-lazy-to-read-more-than-one-page kind of website.

Determining the Evolutionary Relationships of Species

• If your having a hard time wrapping your head around the idea of natural groups and "trees", this page gives a nice overview of how this works.

Actually Doing Phylogenetics

• This page lists the practical steps you have to do if you were to do a phylogenetic analysis on a set of sequences.

• ClustalW from EBI
• T-Coffee from SwissEMB
• WebPhylip - the popular Phylip package online
• Ribosomal Database Project II - online tools to work with ribosomal sequences (a favorite for phylogenetists)
• PhyloBLAST - takes an inputted protein sequence, does a BLAST search of the SwissProt database, then allows you to perform a phylogenetic analysis

To download software for your own use (all of it is free):

• Phylip - multi-functional phylogenetic package
• PAUP: Phylogenetic Analysis Using Parsimony - multi-functional phylogenetic package
• ClustalX - multiple sequence alignment program
• ClustalW and ClustalX - multiple sequence alignment programs (choose /dos or /mac folder [depending on your computer] and scroll down to clustalW or clustalX)
• T-Coffee - multiple sequence alignment program
• Genedoc - multiple sequence alignment manipulator
• Treeview - displays and prints publication quality phylogenetic trees

Introduction to Bioinformatics

• This takes you to the Institute for Computational Biomedicine's education site. Here they have a well laid out tutorial/example series. The example is broken down into 4 sections: Sequence retrieval, Homology searching, Sequence alignment and Phylogenetic analysis. All you have to do is start at the beginning and work your way through the "workedexamples" to retrieve, align and perform a phylogenetic analysis on a series of cannabinoid receptors. (Note: the "help" link with each worked example is great for extra information.)

• This uses HIV/SIV as an example of how to create a neighbour-joining phylogenetics tree. Although it is not interactive, you can follow through the example to see what values and formulas were used to create their concluding tree.