Millions of years ago, a single cell started an evolution that gave rise to the tree of life and its three main domains: Archaea, Bacteria and Eukaryota.

Each branch is an example of a clade. A clade represents a group that includes a common ancestor and all descendants. Cladistics is a modern form of taxonomy that places organisms on a branched diagram called a cladogram (like a family tree) based on traits such as DNA similarities and phylogeny.

In the field of biology, cladistics is a system of taxonomy that involves classifying and arranging of organisms on a phylogenetic tree of life. Prior to DNA analysis, classification relied heavily on observations of similar and different traits and behavior.

Western societies have used classification since the days of Aristotle in ancient Greece when living organisms were simply divided into categories of plants and animals for purposes of study.

In the 1700s, Carolus (Carl) Linnaeus developed a taxonomy of systematic biology based on classification of organisms by outward appearances and shared traits. He developed a schema for placing organism in a hierarchal taxon (a group; singular) that included several taxa (groups; plural). Linnaeus also developed binomial nomenclature – a system of assigning scientific names like Homo sapiens (human) to organisms.

Charles Darwin and Alfred Russel Wallace proposed the idea of natural selection, and Darwin formalized the the theory of evolution in the mid-1800s. Darwin’s On the Origin of Species jolted the scientific community by suggesting that all organisms descended from a common ancestor and could be classified according to their evolutionary relationships.

Ornithologist Ernst Mayr was a preeminent evolutionary biologist of the 20th century who extensively studied bird taxonomy while traveling and working as curator at the American Museum of Natural History in New York. His groundbreaking book Systematics and the Origin of Species was published in 1942 by the Columbia University Press.

Mayr is known for his work on genes, heredity, variation and speciation of populations in isolated areas, which can be used for classification purposes.

Cladistics is a biological classification system based on analysis of traits, genetic makeup or physiology that were shared with a common ancestor until some type of divergence occurred, producing new species. German taxonomist Willi Hennig jumpstarted cladistic classification in 1950 when he wrote his book on phylogenetic systematics.

The book was later translated into English and widely read in America after being published by the University of Illinois Press in 1966.

Hennig’s theory of phylogenetic systematics challenged contemporary approaches to taxonomy introduced by Darwin and Wallace.

He argued that species should be identified and classified based on genetics and clade relationships, particularly monophyletic groups. Hennig honed in on recent ancestry and the identification of evolved, modified traits of organisms that shared a direct lineage – even if derived characteristics were nothing like those of the common ancestor.

Phylogenetics is the study of known or hypothesized evolutionary relationships based on the phylogeny (lineage) of grouped organisms. The phylogenetic tree of life illustrates how taxa (groups of organisms) evolved in a specific order as life diversified and branched out from a common ancestor.

The process of evolutionary speciation looks like branches on a family tree. Because there is no sure way of knowing what happened so long ago, sciences must draw inferences about how life evolved based on fossil records, comparative anatomy, physiology, behavior, embryology and molecular data. Evolutionary biology is a dynamic field where new discoveries are continually being made.

Evolutionary biologists infer hypothetical evolutionary relationships between taxa based on a detailed comparison of similar and different characteristics.

Studying evolutionary descent helps pinpoint when certain traits arose and were passed down to subsequent generations. Cladistic analysis, like phylogenetic systematics, examines evolutionary patterns of descent that help piece together the evolutionary history of species while also explaining the diversity of life and species extinctions.

Cladistics works on the central premise that life on Earth originated only once, meaning that all life can be traced back to that first ancestral organism. The next assumption is that existing species split into two groups demarcated by a node on a tree branch. Lastly, organisms presumably change, adapt and evolve.

The point of divergence represents the beginning of two new lineages branching out and forming two new species.

Cladograms are used to make meaningful comparisons between groups.

In biology, a cladogram is a visual representation of related characteristics in various organisms. Usually, grouping is done according to certain specified traits of interest. However, different data points can be combined to create a more accurate evolutionary tree that explains complex relationships.

A distinction can be made between a cladogram and a phylogenetic tree, but the terms are also used interchangeably at times. Cladograms focus on characteristics at the macro and molecular level that indicate relatedness. A cladogram suggests likely evolutionary relationships between groups of organism or taxa that can be small or large in number:

• Monophyletic taxon. A clade of organisms that includes their most recent common ancestor and all the living and extinct descendants. For instance, there are three clades of mammals: monotremes, marsupials and eutherians. Mammals share many characteristics but differ in the way they reproduce.
  

• Paraphyletic taxon. A group of organisms that includes the most common ancestor of all members but leaves out some of the descendants that trace back to that same common ancestor. Bryophyta are paraphyletic because the group includes hornworts, liverworts and mosses but excludes vascular plants.

• Polyphyletic taxon. A group of organisms that don’t have much in common other than some similar traits. At one time, pachyderms like elephants and hippopotamuses were lumped together because of their skin type even though they actually belong to different mammalian families.
  

Multicellular eukaryotes gave rise to an abundance of increasingly complex organisms.

For instance, fish and humans trace back to a common ancestor millions of years ago. That complicated relationship can be depicted on a simple cladogram illustrating the cladistic relationships. Start by picturing an ancestral eukaryote at the base of the tree.

As the common ancestor evolved, one node on the tree branched off into aquatic vertebrates like jawless fish. At the next node, the branch diverged into four-legged tetrapods.

The next node shows a divergence when animals developed amniotic eggs, followed by a split when animals developed fur or hair. Much later, humans and primates diverged and evolved down separate paths.

Cladistic classification looks at certain characteristics of organisms that directly bear on ancestral states in evolutionary biology. Hennig developed many scientific terms to describe his approach to categorization, which were instrumental to his ideas and theories. The terms describe groups of organisms in relation to a specific node on a phylogenetic tree or cladogram:

• Plesiomorphy. This is an ancestral trait passed down and retained from ancestor species to descendent species during evolution between a single or multiple taxa.

• Apomorphy. This is a derived trait describing a specific clade.

• Autapomorphy. This is a derived trait only found in one of the groups being compared.

• Synapomorphy. This is a derived trait shared by two or more groups of organisms descended from a common ancestor.
  

Character states are traits derived through the process of natural selection, adaptation and inherited variance that lead to biodiversity in life. As such, only synapomorphies are relevant when discerning evolutionary relationships. Multiple synapomorphies in organisms with a shared ancestor are monophyletic:

• Autapomorphies are traits found in only one species or group that stems from a common ancestor, such as the snake taxa that has no functional legs, while the next closest taxa have two or more legs.

• Synapomorphies refer to a trait seen in an entire clade such as opposable thumbs in humans and primates.
  

• Homoplasy is a trait shared by multiple groups, species and taxa that is not derived from a shared common ancestor. Birds and mammals are warm-blooded but do not have a directly shared ancestor that had that trait, which is an example of convergent evolution. 
  

Scientists called cladists arrange taxa in a phylogenetic tree that may reveal new evolutionary relationships. Groupings are made based on physical, molecular, genetic and behavioral characteristics.

A diagram called a cladogram displays relatedness, whenever species branched off from a common ancestor at various point in evolutionary history.

Cladograms are branching diagrams of cladistic data that arrange certain characteristics using comparative physical data sets or molecular data, for instance. Researchers today often use computer programs to combine data sets to create more accurate cladograms that show cohesive and comprehensive relationships between organisms.

Basic methodology is not difficult, but each step must done meticulously:

1. Choose taxa to study, such as several species of birds.
   
2. Choose and chart the characteristics you wish to study.
   
3. Ascertain whether similarities are homologous or the product of convergent evolution.
   
4. Analyze whether the shared characteristics are derived from a common ancestor or derived later.
   
5. Group the synapomorphies (shared derived homologous traits).
   
6. Build a cladogram by arranging groups of organisms on a treelike diagram.
   
7. Use nodes on branches to represent points where two species diverged.
   
8. Place taxa on the endpoints of branches, not at nodes.
   

The origins of traditional evolutionary methods of classification date back to antiquity. All living organisms were assumed to be plants or animals. Classic methods made no distinction between whether observed traits were inherited from a distant ancestor or a more recent one.

The goal was to devise a map of how life on Earth may have evolved from the sea.

Characteristics used for classification are determined by experts who look at obvious differences such as fur, scales or feathers. The approach worked better for classifying vertebrates than invertebrates. Evolutionary classification places organisms in groups of decreasing size under three domains that are further divided into kingdom, phylum/division, class, order, family, genus and species.

Cladistic methods are not tied to the Linnean classification system, and they probe deeper for connectivity.

Traditional systematics arrange organisms on an evolutionary tree according to when and how a species changed as an adaptation to a new lifestyle or habitat, for instance. The tree shows direction of evolution in time. Subjective assessments of traits and characteristics in traditional methods can potentially bias results and make a study difficult or impossible to replicate.

Cladistic and phylogenetic methods of classification are preferred nowadays over traditional methods in of classification in the natural sciences. The newer approach is more scientific, evidence-based and irrefutable. For instance, DNA and RNA sequencing is being used to study organisms at the molecular level for nuanced placement on a cladogram.

Organisms are arranged according to their shared derived characteristics.

Cladistics in the field of biology allows scientists to identify patterns, form a hypothesis, test hypotheses and make predictions.

“Cladistics, then, is about discovery,” as described by contemporary cladists, David M. Williams and Malte C. Ebach, in 2018. Williams and Ebach envision cladistics as a process of natural classification that does not require grounding in evolutionary theory.

Technology adds a level of precision and sophistication to cladistics methods. In particular, DNA sequencing of genes indicates degree of relatedness and shared ancestry with a high degree of confidence. Differences in DNA can provide insight into how long ago species shared a common ancestor.

New findings can either corroborate or correct previous assumptions about how organisms evolved and help classify new species as they are discovered.