The task of classification of organisms has remained a daunting task ever since we humans began to group what we consider to be closely related living beings together.
In the mid 1700s, Swedish botanist, zoologist, and physician Carolus Linnaeus wrote the System Naturae, a way of organizing living beings into a hierarchical fashion. Combined with Darwin’s mechanism behind the divergence of species, German biologist Will Hennig established the modern approach to hierarchical classification which we call phylogenetic systematics, or the classification of organisms according to their evolutionary histories.
Phylogenetics, or the branching relationship of populations, is based on the observation of traits displayed by an organism, whether that be an anatomical feature, behaviour, genetic sequence, or developmental process. These traits are important for two reasons: 1. Observations of traits can be used to infer patterns of ancestry and 2. We can study the sequence and timing of majour events in an organism’s evolutionary past.
The main result of the phylogenetic approach to systematics is the creation of a phylogenetic tree which is a branching structure that serves to hypothesize evolutionary relationships between organisms based on fossils, molecular data, and phylogeographic data. Basic trees are known as cladograms, while trees which show evolutionary change are known as phylograms and trees which show actual time are known as chronograms.
Each branch tip is a group or related organisms, known as a taxon. Moving toward the base of the tree, the point which a single branch splits into two or more recent branches is known as a node, and represents the common ancestor for two branches. The base of the tree is known as the root and serves to represent the common lineage from which all species on the tree came from.
Once we pick a branch to focus on, we can compare our focal branch with other branches throughout the tree a number of different ways. An outgroup is a taxon related to our focal group but the branched of earlier in history. A sister taxa is a taxon which came from the same node. Polytomy is a node from which more than two branches arise from it, and a clade is a group of taxa that share a single common ancestor. A monophyletic group is a taxonomic group which consists of a common ancestor and all of it’s descendants, while a paraphyletic group contains the most common ancestor but not all of the descendants.
Comparing between two different trees, we can find rooted and unrooted trees. A rooted tree has a distinct common ancestor while an unrooted tree gives multiple possible common ancestors. As such, an unrooted tree does not give a direction of time and we cannot tell which taxon are more recent than others.
When placing a trait on a branch, we can compare between branches and hypothesize as to the evolutionary origin of that trait as well as identify patterns in evolutionary time. A homologous trait is a trait which is found on two or more taxa because those organisms have inherited that trait from an ancestor. Meanwhile, analogous traits are traits which are shared by two or more taxa but did not come from a shared common ancestor and instead arose separately, such as through a common selection pressure. A trait which has come from another trait is known as derived. We look for shared derived traits when building evolutionary trees and aim to build trees that have the least number of evolutionary steps to get from one trait to another, known as parsimony. However, some traits have no known current function, despite possibly being important in the past. We call these traits vestigial traits and there are two possible explanations as to why we see it today: 1. The trait is not costly and so it stays, and 2. The trait is being actively selected against and one day will be lost.
It is important to note that systematics is inferential – we make inferences on what happened in the past based on data that we can collect right now. This field of research can answer questions such as how we test homologous and analogous characteristics as well as how we find the most likely tree based on our data. This information, when combined with the geological and earth science research, can also tell us about how a group of organisms moved across the planet in the past, known as phylogeography.
Scientists are still at odds when it comes to dividing and deciding upon what constitutes an individual taxa, or species. The two modern species concepts are known as the Biological Species Concept and the Phylogenetic Species Concept. The Biological Species Concept, as proposed by Ernst Mayr in 1942, dictates that two individuals are of the same species if they are able to breed and are reproductively isolated from other groups. The Phylogenetic Species Concept, as defined by George G. Simpson in 1961, states that two organisms are from the same species if they have the same parental pattern of ancestry. A third type, known as the Evolutionary Species Concept, seeks to ratify the problems with both of the first two, but requires much more information than is often available in order to infer relatedness.