What is Phylogeny or Cladistics?

Cladistics is a method of biological classification where organisms are classified based on their ancestors and their relationship with them. It is defined as the concepts and methods for determining the branching patterns of evolution and evolutionary history. Some scientists, however, have preferred the term phylogenetic systematics or phylogenetic taxonomy to emphasize the reliance on a phylogeny for classification. It is the most common and accepted method for classifying organisms.

Important terms


A homoplasy or homoplasious character is a character that species share through convergent evolution. It is a similarity in appearance but not in origin. Example- wings of birds, insects, and bats. These characters do not help to determine the phylogenetic relationship.


It is a shared character between species that were also present in their common ancestor. Example- arms of a human and wings of a bird.


It refers to a primitive or ancestral character, i.e., a character or trait that is unchanged from those of the ancestors. For example- all reptiles are ectotherms that do not maintain constant body temperature.

Phylogeny of animals

Flow chart showing animal phylogeny of metazoans

Animals or metazoans are derived from a common ancestor, i.e., a monophyletic group. Animals are divided into two groups depending on tissue differentiation. Those who have true tissue differentiation belong to the eumetazoan group, those who do not have true tissue differentiation belong to Placozoa and Porifera. There is a similarity between the feeding cells of choanocytes and the choanoflagellate protist. So, it is recommended that metazoans come from a common ancestral organism that bears a resemblance to modern colonial choanoflagellate.

Eumetazoans are divided into two groups, one radially symmetrical animals and the other bilaterally symmetrical animals. Further, the bilaterally symmetrical animals are divided into two groups; bilateria and radiata.


Animal phylum, which lacks bilateral symmetry are refrred to as non-bilateria. Example- sponges (Porifera); comb jellies (Ctenophora); corals (Cnidaria); placozoans. Sponge cells are not organized into distinct tissues. Ctenophora and Cnidaria are diploblastic. They have a single opening in the digestive chamber. The tiny placozoans are similar, but they have no permanent digestive chambers.


All the remaining animals (including more than a million species from 29 phyla) have formed a clad called bilateria. Zoologists have come to understand the relationship between bilateria through phylogenomic studies. They found that some bilaterian animals have a combination of circular muscles and some bilaterian phyla have primary larvae which swim with cilia and have a sensory cell.

There is also an evolutionary relationship between two sister-group, Hemichordate and Echinodermata, together forming Ambulacraria.

Up-to-dated data of the genome sequence agrees with Urochordata as Craniata's sister group, not Cephalochordata.

Xenacoelomorpha are the basalmost bilaterian.

Bilaterally symmetrical animals are divided into deuterostomes and protostomes. The protostomes are further divided into two clades.

Protostomes and deuterostomes

In the first stage of development, during cell division, deuterostome embryos have radial cleavage, but protostomes embryos have spiral cleavage. The deuterostome phyla are Echinodermata, Chordata and Hemichordata or acorn worms.


It belongs to the protostome. They are called ecdysis for growth through molting. Their exoskeletal molting is followed by the stripping of the outer cuticular layer. This is called ecdysis. These include the most common animal phylum Arthropoda (insects, spiders, crabs, and their relatives), probably the second-largest animal phylum Nematoda or roundworms, Nematomorpha or horse hairworms, and the Kinorhyncha, Priapulida, and Loricifera.


The spiralia is a large group of animal trees. During cell division, its initial embryo develops by spiral cleavage. Spiral phylogeny is widely debated, but it also includes large groups such as Lophotrocozoa as well as small groups such as Rouphozoa. Lophotrochozoa and Rouphozoa are grouped to form Platytrochozoa, the sister group of Gnathifera, which includes Rotifera. Lophotrochozoa includes mollusks (the second largest in terms of species diversity), Brachiopods, Annelids, Nemerteans, Entoprocts and Bryozoa. Myzostomida, Echiura, and Sipuncula, as well as many other groups, belong to Annelida.

The study of animal phylogeny (the branching sequence of evolution) aims to determine the evolutionary relationships between phyla.

Molecular analysis

The modern phylogenetic understanding that we are studying has been discovered from molecular analysis.
Protein and nucleic acid analysis were performed by collecting data from various molecular sources, such as mitochondrial genomes, nuclear DNA or deoxyribonucleic acid, ribosomal ribonucleic acid or rRNA, protein-coding genes, and some cellular proteins. Using this analysis, many new evolutionary relationships have now been established with the help of molecular evidence. For example, Lophophorata, which included Brachiozoa and Bryozoa, have long been considered deuterostomes. Using rRNA data, it has been discovered that animals are more closely related to annelids and mollusks, i.e., protostomes.

New animal phylogeny has developed a completely new phylum of worms called Acoelomorpha. Because the morphology of these acoel flatworms is similar to that of flatworms, they have belonged to the Platyhelminthes. However, phylogenomic studies reveal this to be a false relation and these acoel flatworms are thought to belong to the bilaterians. Recent studies on acoelomorphs have also refuted this theory and reported that acoelomorphs are more closely related to deuterostomes.

Ctenophora has been identified as the basal clad of the animal kingdom through phylogenetic reorganization. For the presence of nerve and muscle cells in both Ctenophora and Cnidaria, Ctenophora or comb jelly was thought to be the sister group of Cnidaria. And Porifera was considered a basal group of animals due to the absence of nerve and muscle cells. Recent molecular analysis has shown that muscle cells originate from mesoglea cells, and many genes for nerve development in other genes are missing from the Ctenophore genome. The mitochondrial genome of ctenophores is small, and many genes found in the mitochondrial genome of other animals are deficient. In addition, the hox gene is missing from Ctenophores. These arguments suggest that Ctenophores should be considered as basal or sister groups of Porifera.

In phylogenetic tree development, molecular analysis and re-analysis are not complete evidence. Data and analytical methods also play an important role. So we cannot dismiss an ex-phylogenetic tree as wrong based on molecular analysis only. A good example of this is the ongoing debate over the location of sponges and comb jelly in the "family tree." An international group of evolutionary biologists recently analyzed molecular evidence and discovered that sponges were the first phylum to be separated from the ancestors of metazoans. As a result, the oldest metazoan group in phylogenetics is comb jellies- this theory has been rejected.

There are mainly three sources of information for creating images of phylogenetic evolutionary trees that explain such relationships; morphological data, fossil record data, and molecular data. The phylogenetic tree also changes frequently as new information is received. At present, molecular data analysis has played a great role in research on phylogenetic relations.

Context and Applications

This topic is significant in courses like:

  • Masters in Science in Zoology
  • Bachelors in Science in Zoology

Practice Problems

Q 1. Which is the closely related sister group of animal or metazoan?

  1. Ambularia
  2. Choanoflagellates
  3. Fungi
  4. Nephrozoa

Answer: (b).

Explanation- Molecular genomics analysis has shown that metazoa or animal and Choanoflagellata originate from the same group, holozoa. So, the correct answer is Choanoflagellata.

Q 2. Which of the following is included in Chordata?

  1. Craniata
  2. Porifera
  3. Deuterostomia
  4. Spiralia

Answer: (a)

Explanation-The Chordata is grouped into Cephalochordata, Craniata, and Urochordata. So, Craniata is included in Chordata.

Q.3 Which of the following does not belong to bilateria?

  1. Bryozoa
  2. Ctenophora
  3. Echinodermata
  4. Hemichordata

Answer: (b)

Explanation- Of all the above, Ctenophora is diploblastic. They lack bilateral symmetry. So the correct answer is Ctenophora

Q.4 Which is the closely related sister group of Arthropoda?

  1. Loricifera
  2. Onychophora
  3. Placozoa
  4. Rotifera

Answer: (b)

Explanation- Molecular genomics analysis has shown that Arthropoda and Onychophora originate from the same clade, Panarthropoda. So, the correct answer is Onychophora.

Q.5 Which group is formed by combining protostomes and deuterostomes?

  1. Bilateria
  2. Bryozoa
  3. Nephrozoa
  4. Mollusca

Answer: (a)

Explanation- Protostomes and deuterostomes combine to form the nephrozoa clade, the major group of bilaterians. So, bilateria is the correct answer.

  • Animal Evolution
  • Classification of Animals
  • Animal Physiology

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