Cladistics

Cladistics is a way scientists group living things based on how they are related through their most recent common ancestors. It helps us understand how different species, like animals and plants, are connected over time. In cladistics, scientists look at special traits that certain groups share, which helps them decide how these groups are related.

When scientists use cladistics, they create groups called "clades." These clades include all the descendants of a common ancestor. This means that if we talk about a group like "worms" in a strict cladistic way, it would actually include humans too, because we all share ancient ancestors. Usually, people use these group names in a looser way, which can make things confusing, especially when we think about extinct species.

Cladistics has become the most common method scientists use to classify living things today. It has also been used in other areas besides biology. However, it sometimes causes problems for traditional taxonomy, because the way groups are named can change based on new discoveries.

History

Willi Hennig 1972

The study of grouping living things based on shared traits began with a German scientist named Willi Hennig. He called this method phylogenetic systematics in his 1966 book. Other researchers later introduced the words "cladistics" and "clade" to describe these grouping methods.

Early ideas about this way of grouping living things appeared as far back as 1901. Over time, it became very popular, especially after scientists could use computer programs to study large amounts of data from DNA and other molecules. Today, most scientists use cladistics to understand how different species are related.

Methodology

Main articles: Phylogenetics and Cladogram

Terminology for character states

Here are some important words scientists use to describe traits in living things:

A plesiomorphy or "close form" is a trait that a group of animals has kept from their ancestors. For example, being cold-blooded is a trait shared by many reptiles but not birds, who are warm-blooded. This shared trait doesn’t mean reptiles are more closely related to each other than to birds.
An apomorphy or "separate form" is a new trait that appears in a group. These traits help scientists identify groups of related animals. For example, having digits similar to humans is a trait that helps identify a group of animals called tetrapods. Even animals without digits, like snakes, are still tetrapods because they come from ancestors that had these digits.

Scientists also use the word homoplasy for when different animals share a trait that their common ancestor did not have. For example, both mammals and birds can keep a constant warm body temperature, but this trait evolved separately in each group.

Terminology for taxa

Different groups of living things can be described in special ways depending on how they are connected through their family tree. These groups are called mono-, para-, and polyphyletic taxa, and we can learn about them by looking at the shape of the tree and the traits they share.


Term	Node-based definition	Character-based definition
Holophyly, Monophyly	A clade, a monophyletic taxon, is a taxon that consists of the last common ancestor and all its descendants.	A clade is characterized by one or more apomorphies: derived character states present in the first member of the taxon, inherited by its descendants (unless secondarily lost), and not inherited by any other taxa.
Paraphyly	A paraphyletic assemblage is one that is constructed by taking a clade and removing one or more smaller clades. (Removing one clade produces a singly paraphyletic assemblage, removing two produces a doubly paraphyletic assemblage, and so on.)	A paraphyletic assemblage is characterized by one or more plesiomorphies: character states inherited from ancestors but not present in all of their descendants. As a consequence, a paraphyletic assemblage is truncated, in that it excludes one or more clades from an otherwise monophyletic taxon. An alternative name is evolutionary grade, referring to an ancestral character state within the group. While paraphyletic assemblages are popular among paleontologists and evolutionary taxonomists, cladists do not recognize paraphyletic assemblages as having any formal information content – they are merely parts of clades.
Polyphyly	A polyphyletic assemblage is one which is neither monophyletic nor paraphyletic.	A polyphyletic assemblage is characterized by one or more homoplasies: character states which have converged or reverted so as to be the same but which have not been inherited from a common ancestor. No systematist recognizes polyphyletic assemblages as taxonomically meaningful entities, although ecologists sometimes consider them meaningful labels for functional participants in ecological communities (e. g., primary producers, detritivores, etc.).

Criticism

Cladistics has faced questions since it began. Some people argue that deciding which traits are related can involve guessing and personal opinions.

In the late 1970s, a new idea called transformed cladistics tried to fix some of these issues by not assuming things about family trees before studying. But this method did not become very popular.

Issues

The cladistic method does not identify fossil species as actual ancestors of a group. Instead, fossils are seen as part of separate extinct branches. While a fossil might be an ancestor, we cannot know for sure. So, scientists assume fossils are related to other fossils and living species based on shared features.

Hybridization can make it hard to clearly define the ancestors of a species. Many species can interbreed for millions of years, creating complex branching patterns. This complexity can make it difficult to create simple family trees.

Horizontal gene transfer is when genetic information moves between different organisms. This can happen through several natural processes and does not usually affect the ancestry of the organisms. However, it can make it harder to determine ancestry. Cladistics can help map these gene transfers by studying the family trees of individual genes.

Naming groups can be challenging in cladistics. If relationships are unclear, there may be many possible family trees. Assigning names to each possible group might not be wise. Established names may no longer fit as new groups are discovered. Naming changes happen when our understanding of relationships changes, especially for extinct species. Keeping old names might not accurately show true relationships. For example, groups like Archaea, protists, and worms include humans in a broader sense. Scientists sometimes use a more limited meaning for these names to better match actual relationships.

In disciplines other than biology

Cladograms can be used in many areas besides biology to show how different things might be related. Any group of items that might share a common origin can be compared if we can identify and measure their features.

Cladistic methods help us understand how cultures, stories, and even languages change over time. For example, they have been used to study old myths, folktales, and manuscripts like the Canterbury Tales. In language studies, these methods help us see how languages are related by looking at their features. They also help us understand the history of galaxies in space.