Character – any heritable attribute of an organism.
Character state – any observed variant of a given character.
Classification – a logical system for organizing organisms.
Homoplasy – character state arising due to convergence, parallelism, or reversal.
Parsimony - preference of simpler explanations over more complex ones.
Phylogeny – a branching diagram representing the evolutionary relationships or history of genes, species, or other taxa.
Synapomorphy – shared, derived character state.
Symplesiomorphy – shared ancestral character state.
Systematist – scientist who studies systematics.
Taxon (pl. taxa) – any group of similar organisms (e.g., family, genus, species).
Taxonomy – science of classifying, defining, naming, and identifying taxa.
Introduction – Perhaps the best definition of Phylogenetic Systematics is found in the Journal Systematic Biology.
“Systematics is the study of biological diversity and its origins. It focuses on understanding evolutionary relationships among organisms, species, higher taxa, or other biological entities, such as genes, and the evolution of the properties of taxa including intrinsic traits, ecological interactions, and geographic distributions. An important part of systematics is the development of methods for various aspects of phylogenetic inference and biological nomenclature/classification.”
Next week we will explore biological diversity a bit, but today we are going to study some of the methods that systematists use to infer the evolutionary relationships of organisms. A brief history of the field will serve as an introduction.
For many years, no rigorous, repeatable method for classifying organisms and estimating evolutionary relationships existed. In this traditional systematics, researchers relied on their intuition and a lifetime of experience with a particular taxon to generate classifications and phylogenies. In the 1960’s a new school of systematics arose, termed phenetics or numerical taxonomy. Proponents of these methods argued that organisms should be classified and phylogenies inferred based on the overall similarity of the taxa in question. Their methods were rigorous and repeatable. In the late 1960’s and 1970’s a new methodology, largely based on the writings of the German entomologist Willi Hennig (1966), gained standing. Proponents of cladisticsused the principle of parsimony to argue that species should only be grouped using shared, derived traits (synapomorphies) and not shared ancestral traits (symplesiomorphies) or convergent traits (homoplasies – singular forms of all these terms end in -y). For example, body covering is a character whose character states (scales, hair, fur, feathers) can tell us a great deal about the evolutionary relationships within the Vertebrata through patterns of synapomorphies. On the other hand, the presence of a vertebral column tells us nothing about evolutionary relationships within the Vertebrata. It is a symplesiomorphy. Similarly, the presence of wings is a homoplasy in different animal groups (e.g., insects, birds, bats) and could mislead us (or pheneticists). Cladistic methods are still widely used (as are some phenetic methods) but for the analysis of DNA data, mathematically intensive statistical methods like Maximum Likelihood are now very popular. These methods rely on complex models of DNA and protein mutation, and prefer the phylogenetic hypothesis that is the most likely given the data.
Our Project – Working in groups of two, you will find the best phylogenies for two groups: 1) selected vertebrates and 2) eight primate species. In each case, you will employ the principle of parsimony – that is, you will accept the tree of shortest length (i.e., the tree hypothesizing the fewest number of character state changes) as the best estimate of the true phylogeny. Remember, synapomorphies (shared derived character states) are evidence of common ancestry, whereas symplesiomorphies and homoplasies are not.
Steps to create a phylogenetic tree – Vertebrates example
The data files that we are going to work with today are located on the Biology 208 webpage, which can be reached via the Biology Department webpage. Copy the two data files to the desktop of your computer, either by right-clicking on a PC, or by control-clicking on the Macs and selecting “Save Link As” or “Download file” or some variation of this.
Next, working with your partner, open the computer program Mesquite (Maddison and Maddison 2004). Look for the icon with the little green tree branches. Mesquite is a Java application, and so it runs in the same fashion on Macs and PCs. (If Mesquite is not on your computer, go to Mesquiteproject.org to download it.) If any error or other messages appear, click the “OK” button or its equivalent. Once the program is loaded, go to the “File” menu and click “Open File”. Locate the desktop and open the file named “Vertebrates.nex.txt”. The “.nex” suffix means that this file is in Nexus format, which is a commonly used by phylogenetic software. The .txt suffix was added to the file so that it could be transmitted via the WWW.
A navigation window will open. Click on the button labeled “Show Matrix”. A pane will open that shows a morphological data matrix for a select group of vertebrates. The taxa are listed down the left side, and the characters are listed across the top. Maximize the window so that you can see all the character states. Do some vertebrates appear to be related with one another because of shared character states? Based on this cursory examination, make a few hypotheses about evolutionary relationships or clades of taxa. Remember to differentiate between shared, ancestral character states and shared, derived character states.
Next, you will rigorously test your hypotheses using Mesquite. This software provides an interactive environment for exploring phylogenetic hypotheses. It will allow you to quickly manipulate hypothesized phylogenetic trees to search for the most parsimonious tree. As trees are manipulated, the program updates statistics such as tree length and the results are illustrated graphically.
Pull down the “Taxa&Trees” menu and select the first option, “New Tree Window.” For the following window, simply select the top or default option (“With Trees from Source”) by clicking “OK” (do not select the default trees). Now select the “Stored Trees” option. A new pane will open, this time displaying a phylogenetic hypothesis for the vertebrates. This tree was stored in the data file with the character state data.
We need to know how many evolutionary steps are on our tree. So, in the tree window, pull down the “Analysis” menu. Select the “Values for Current Tree” option. In the following two popup windows, select the default or top option. A legend will appear with the name of the tree (Bad Guess) and its length (35 steps).
In order to guide your rearrangement of branches, you can map character state changes onto the tree to identify synapomorphies. Click again on the “Analysis” window. Select “Trace Character History.” Again, choose the default, or top options for the next popup. Now a window appears showing the state changes in character 1 mapped onto the tree. If you click on the blue arrow, you can see the changes for the other characters. Use them to guide your arrangement of branches, trying to group together taxa with the same character states.
Now, as you click on a branch and hold it, you can drag it to a new position within the tree. Once you release the branch, watch the tree length window. Accept only those moves that reduce the overall tree length (that make it more parsimonious). You will move (swap) branches until you find the shortest tree (the tree with the fewest number of steps). You can use the “Edit” menu or control-z (apple-z on Macs) to undo a move. Use the arrow icons to step through each character and alter the groupings until you can no longer reduce the tree length. What’s the most parsimonious tree for these selected vertebrates?
Map character 4 onto your tree. What is going on here? You may want to note answers to question 3 below before you close the vertebrates file.
There is no simple way to save a picture of the tree in Mesquite. In order to do this for your lab write-up, the best way is to use “File: Save Tree as PDF.” You can then copy it from the PDF using the Snapshot Tool and paste it into MSWord for you lab report.
Finding the most parsimonious phylogeny for eight primate species In this exercise, you will examine primate skull replicas and decide how to score the various characters for each species. Some of the characters required for this analysis are post-cranial and ecological. You will find the states of these characters in the following introductory paragraphs. We will introduce you to the skull characters during lab, after you have had a chance to examine the skulls for a few minutes on your own.
The primates include the Suborders Strepsirrhini and Haplorrhini. With a few exceptions (e.g., us), primates all have grasping hands and feet. Hindlimbs dominate locomotion, and eye orbits are rotated forward to allow stereoscopic vision (Patton 2005). All of the primates below have two incisors and one canine tooth on each side of their upper and lower jaws. The teeth beyond these, known as cheek teeth, vary in number. Be careful as you count them! Sometimes the first premolar can look like a canine tooth. With the exception of the great apes, all primates have tails.
Fig. 1. Noses of strepsirrhines.
The strepsirrhines, also known as prosimians, are an Old World group that includes lorises, pottos, bushbabies, and lemurs. We are considering them the outgroup in today’s lab. In addition to several traits visible on their skulls, this group can be recognized by their laterally-directed, slit-like nostrils and the presence of rhinarium, a patch of bare skin adjacent to the nostrils (think of a wet dog nose; Fig. 1; Patton 2005).
Two major groups of haplorrhines are generally recognized. The Platyrrhini, also known as the New World monkeys, include howler, capuchin, spider, squirrel, owl, and other monkeys. The only primates with prehensile tails (tails that the monkey can hang from) are New World Monkeys (e.g., capuchins and howler monkeys). The nostrils of platyrrhines are simple (not slit-like), widely separated, and directed laterally (Fig. 2, top).
The Catarrhini, evolved in Africa and Asia, include Old World monkeys (e.g., macaques, baboons) and great apes (e.g., chimpanzees, apes, humans). Their (our) nostrils are simple, close together, and directed forward (Fig. 2, bottom; Patton 2005). With the exception of the