Cladistics

Cladistic Methodology

Method to determine natural relationships of organisms based on the history or evolution of groups
Computer programs (algorithms) calculate the evolutionary relationships of groups based on the coded features for each taxa in the study
- Coded means that the feature is either "present" (1), "absent" (0), or even "unknown" (?) for this taxa
  - For example, plants could be coded for vascular tissue, in which mosses would be "absent" for this trait, but ferns, conifers, and flowering plants would be "present" for this trait.
- The result is a cladogram or phylogenetic tree, which, based on the data, is a hypothesis for the evolution of these plant groups in the study

Ancestral vs. Derived Features

Researchers also need to determine which characters or features are “ancestral” (appeared long ago), and which are “derived” (recently appeared in evolutionary history)
- Apomorphy: A derived feature, called an apomorphy, is a uniquely evolved feature of a group and is passed on to its descendants, and thus defines a group or a clade (e.g., the angiosperm carpel evolved once in the Mesozoic)
  - When comparing groups, researchers may refer to a synapomorphy or shared derived trait. This is a feature that is shared among plant groups, arising from a common ancestor (e.g., all living groups of flowering plants share the feature of possessing a carpel).
- Pleisomorphy: An ancestral feature, called a pleisomorphy, is one that is shared by many taxa, and does not help define the origin of a group
  - When comparing groups, researchers may refer to a synpleisomorphy, or shared ancestral trait. This feature is shared among many groups, deep in evolutionary history but won't help resolve more derived clades (e.g., all eukaryotes share the feature of possessing a nucleus).
  - The nucleus is not informative for resolving the relationships between angiosperm families, although a nucleus would be a useful trait for defining eukaryotes versus prokaryotes.
  - The nucleus would be pleisomorphic for resolving angiosperm phylogenetics, but it would be apomorphic for resolving domain-level phylogenetics (e.g., bacteria, archaea, eukaryotes)
Note: taxa that exhibit pleisomorphic features are not called "primitive"; taxa with apomorphic features are not called "advanced".
- The terms "primitive" and "advanced" denote inferiority and superiority, respectively, but species are adapted to their niche in the environment.
- Therefore, comparing groups, such as mosses to pines, is meaningless. One is not more advanced or primitive than the other. There are tradeoffs and adaptations that each has to their niche in the environment.
We use "ancestral" or "derived" to refer to features, and "sisters" to refer to taxa or groups
- e.g., mosses are sister to other land plants and exhibit some ancestral features (pleisomorphies) such as spore-bearing, but also derived features (apomorphies) such as leaves in the gametophyte phase.

Clades & Grades

The goal of cladistics is to find true evolutionary groups
- True groupings come from a single/common ancestor, which passed along 1 or more features to their descendants during evolution.
- This feature(s) is an apomorphy that defines the group.
- We call this grouping a clade or a monophyletic group

Monophyletic groupings

These clades include a common ancestor and all its descendants
e.g., "Angiosperms" come from a single common ancestor and include all flowering plant descendants
Monophyletic groupings are referred to as clades; these are preferred in cladistics

Paraphyletic groupings

These groups include an ancestor and some descendants, but not all; one evolutionary branch is not included in the grouping
e.g., "Gymnosperms" are seed plants that come from a common ancestor, but they also include the angiosperms. We would need to remove the angiosperm branch to make them a clade or monophyletic group.
Paraphyletic groupings are referred to as grades and are not preferred.

Polyphyletic groupings

These include an ancestor and a few descendants scattered on the tree, but more than one evolutionary branch is not included in the group.
Another way to interpret this is that these groupings include organisms that have many different origins, and not a common ancestor
e.g., "Algae" are aquatic plant-like organisms, but this term can refer to many unrelated groups like green algae, brown algae, and blue-green algae. They do not come from a single common algal ancestor that gave rise to just these algae.
Polyphyletic groupings should be avoided in evolutionary groupings.

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