# Phylogeny: Definition, Phylogenetic Trees, Examples, and Importance

> Phylogeny explains the evolutionary history and relationships of organisms. Learn how phylogenetic trees are read, inferred, compared, and used in biology.

Canonical URL: https://biologynotesonline.com/phylogeny/
Author: Sourav Pan
Last updated: September 17, 2026

![Phylogeny: Definition, Phylogenetic Trees, Examples, and Importance](https://biologynotesonline.com/wp-content/uploads/2024/03/Phylogeny-tree-of-life.webp)

## What Is Phylogeny?

Phylogeny is the evolutionary history and relationships of organisms or other biological lineages through their descent from common ancestors.

In simple meaning, it is the evolutionary family history of a biological group. The word is pronounced “fy-LOJ-uh-nee”. In biology, phylogeny deals with history of descent, and how different organisms or lineages are related with each other through their ancestry.

The evolutionary history occurred in the past and cannot generally be observed directly. A phylogeny made for a group is therefore an inferred evolutionary history, reconstructed from the available biological evidence. It may not represent every part of the actual evolutionary history exactly.

### Phylogeny and Common Ancestry

Common ancestry is the main relationship represented by a phylogeny. Organisms are related because their lineages have descended from ancestral lineages shared by them. A lineage is a line of descent connecting ancestors with their descendants.

During evolutionary history, an ancestral lineage may split into separate descendant lineages. This is referred to as divergence. Such splitting is represented as branching in a phylogenetic tree. Two lineages having a more recent common ancestor are more closely related than another lineage whose common ancestor occurred farther back in evolutionary history.

### Phylogeny vs Phylogenetics

Phylogeny and phylogenetics are related terms, but they are not the same.

Phylogeny is the evolutionary history or the pattern of relationships among biological lineages. Phylogenetics is the study of these evolutionary relationships and their reconstruction. When the relationships are inferred or estimated from biological evidence, the process is referred to as [phylogenetic analysis](https://biologynotesonline.com/how-to-construct-a-phylogenetic-tree/).

## Anatomy of a Phylogenetic Tree

A [phylogenetic tree](https://biologynotesonline.com/phylogenetic-tree/) consists of different parts such as tips, branches, nodes, root, clades, topology and branch length. These parts are used for reading the evolutionary relationships represented in the tree.

![Rooted phylogenetic tree showing the root, branches, internal nodes, tips, most recent common ancestor, sister taxa, clade, and a branch-length scale.](https://biologynotesonline.com/wp-content/uploads/2024/03/Anatomy-of-a-Phylogenetic-Tree-1024x768.webp)Rooted phylogenetic tree showing the root, branches, internal nodes, tips, most recent common ancestor, sister taxa, clade, and a branch-length scale.

- Tips- Tips are the ends of the branches in a phylogenetic tree. They represent the biological units which are being compared, such as species, populations, genes, or DNA sequences. Tips are also called terminal nodes or leaves.

- Branches- These are the lines present in the tree and represent evolutionary lineages through which descent takes place. Internal branches occur between the ancestral nodes. Terminal branches extend up to the tips.

- Nodes- The points where two or more branches meet or split are referred to as nodes. In a rooted tree, internal nodes generally represent the inferred common ancestors of the descendant lineages. When a node splits into two descendant branches, it is called a bifurcation.

- Root- It is the ancestral point present at the base of a rooted phylogenetic tree. The root represents the inferred common ancestor of all the lineages included in that tree. From the root, branches extend towards the descendants and tips.

- Common ancestors- Different lineages can be traced backward through their branches until they meet at an ancestral node. The nearest shared ancestral node is referred to as the most recent common ancestor (MRCA). Lineages having a more recent common ancestor are more closely related than those whose common ancestor lies farther back.

- Clade- A common ancestor along with all of its descendants forms a clade. It is also referred to as a monophyletic group. A clade can also occur within another larger clade.

- Topology- Topology is the branching pattern of a phylogenetic tree. Simply, it shows how the tips and nodes are connected with each other. Branches around a node can be rotated and the appearance of the tree may change, but its topology and represented relationships remain unchanged.

- Branch length- Branch length does not represent the same thing in every phylogenetic tree. Depending on the tree, it may indicate evolutionary change, genetic distance, or evolutionary time. In some trees such as [cladograms](https://biologynotesonline.com/cladogram-vs-phylogenetic-tree/), the drawn branch length has no biological meaning. Only the branching order is considered.

- Rooted and unrooted trees- A rooted tree contains a root and shows the direction of descent from an ancestral lineage towards its descendants. An unrooted tree has no specified root. It represents the relationships among the included taxa, but does not show the ancestral starting point or direction of evolutionary events.

![Comparison of rooted and unrooted phylogenetic trees, showing that the rooted tree specifies an ancestral root and direction of descent while the unrooted tree does not.](https://biologynotesonline.com/wp-content/uploads/2024/03/Rooted-vs-Unrooted-Phylogenetic-Trees-1024x725.webp)Comparison of rooted and unrooted phylogenetic trees, showing that the rooted tree specifies an ancestral root and direction of descent while the unrooted tree does not.

## How to Read a Phylogeny

A phylogenetic tree is read from its branching pattern. The position of organisms on left or right side, or how close their names appear on the page, is not used for deciding evolutionary relationship.

![How to Read a Phylogenetic Tree Using Common Ancestors](https://biologynotesonline.com/wp-content/uploads/2024/03/How-to-Read-a-Phylogenetic-Tree-Using-Common-Ancestors-1024x576.webp)How to Read a Phylogenetic Tree Using Common Ancestors

The following steps can be followed to read a phylogeny-

### Step 1- Look for the root

First check whether the phylogenetic tree is rooted or unrooted.

In a rooted tree, reading can be started from the root and branches are followed toward the tips. It gives the direction from ancestral lineages to their descendants.

An unrooted tree shows the relationship among taxa, but the ancestral starting point and direction of descent are not given.

### Step 2- Select the organisms and follow their branches

Choose two organisms that are to be compared. Follow their branches backward toward the root.

At some point, the two branches will join at a common node. This node represents their most recent common ancestor (MRCA).

### Step 3- Compare the common ancestors

The common ancestral nodes are then compared. If two organisms meet at a more recent common ancestor, they are more closely related than organisms whose branches meet farther back in the tree.

Do not count branches between two organisms. The number of branches is not used to decide which organisms are more closely related.

### Step 4- Look for sister taxa and clades

Two lineages arising from the same immediate ancestral node are sister taxa.

For finding a clade, select an ancestral node and follow all the branches arising from that node. The ancestor and all of its descendants are included in the clade.

### Step 5- Follow branching order, not the position of tips

Branches around a node can be rotated. For example, two sister taxa can exchange their positions on the page and still have exactly the same common ancestor.

The tree may look different after such rotation. Its represented evolutionary relationships do not change.

### Step 6- Check the branch length

Branch length should be read only according to what it represents in that particular tree. It may show evolutionary change, genetic distance, or evolutionary time.

In some phylogenetic trees, the length of branches has no such meaning. Only the order in which branches split is considered.

### Worked Example

Suppose a rooted phylogenetic tree has four species A, B, C, and D. A and B join together at one node. Their common lineage joins C at another older node. D joins these three farther back toward the root.

- Start with A and B. Their branches join first at the same immediate node. A and B are sister taxa and share the most recent common ancestor with each other.

- Now compare A and C. Follow their branches backward. The branch of A first joins B, and this lineage later joins C at an older node. A is more closely related to B than to C.

- The same occurs when B and C are compared. B shares its more recent ancestral node with A before their lineage joins C.

- D joins the other three at a still older ancestral node. A, B, and C share a more recent common ancestor with one another than any of them shares with D.

- If A and B are rotated around their common node, B may appear above A or on the other side of it. The common node remains the same. Their relationship has not changed.

## How Phylogenies Are Inferred

Phylogenies are inferred by comparing different biological characters among organisms. The characters may be morphology, DNA, RNA, proteins, and other heritable characters. From these characters, a branching pattern which best fits the evidence is obtained. It represents an estimate of evolutionary history.

![Workflow showing biological character collection, sequence alignment or homology assessment, alternative phylogenetic inference methods, rooting, branch support, and the final phylogenetic hypothesis.](https://biologynotesonline.com/wp-content/uploads/2024/03/How-Phylogenetic-Trees-Are-Inferred-1024x725.webp)Workflow showing biological character collection, sequence alignment or homology assessment, alternative phylogenetic inference methods, rooting, branch support, and the final phylogenetic hypothesis.

- Selection of taxa and characters- The organisms or other biological lineages which are to be studied are first selected. Different characters are then taken for their comparison. Morphological characters can be used. In molecular phylogeny, DNA or protein sequences are commonly used, while fossil organisms are often studied mainly from the morphological characters available from them.

- Identification of homologous characters- The characters compared should be the same characters inherited through common ancestry, i.e., homologous characters. Similar-looking features are not necessarily homologous. Some similarities develop independently during evolution. If such characters are directly taken as evidence of common ancestry, they may give a misleading relationship.

- [Sequence comparison and alignment](https://biologynotesonline.com/sequence-alignment-definition-types-tools-applications/)- In molecular phylogeny, homologous DNA, RNA, or protein sequences are compared. First, the sequences are aligned so that corresponding positions of the selected organisms can be examined. Differences and similarities at these positions provide the characters for analysis.

- Tree inference- The character data are then analyzed for finding a tree or a set of trees which fits the evidence. Different methods are used for this process. Distance methods, such as neighbor-joining, convert the sequence differences into distances between taxa. Maximum parsimony searches for the trees requiring fewer character-state changes.

- Maximum likelihood- It is a model-based method. Different possible trees are evaluated using a model of evolutionary change. The tree having the highest likelihood for producing the observed data is selected.

- Bayesian inference- This method also uses models of evolution. Bayesian analysis estimates the posterior probabilities of trees using the observed data, the model, and specified prior information. Maximum likelihood and Bayesian methods are widely used in molecular phylogenetic inference.

- Rooting the tree- The inferred tree may be rooted using an outgroup. It is a taxon outside the group mainly under study (ingroup). By comparison with the outgroup, the root can be placed and the direction of character change is determined.

- Testing support- All the branches obtained from an analysis may not have equal support. Bootstrap analysis is commonly used for testing such support. In this method, characters in the dataset are repeatedly resampled and trees are reconstructed. How frequently a particular group is recovered gives its bootstrap support. Bayesian analysis, on the other hand, commonly gives posterior probabilities for branches or clades. Both are not the same measure.

- Phylogenetic hypothesis- An inferred tree is a hypothesis based on the selected taxa, characters, evolutionary model, and analytical method. With new organisms or sequence data, some relationships may change. Another suitable analysis can also give changes in some parts of the tree.

## Importance of Phylogeny

Phylogeny is important for studying organisms according to their evolutionary history and descent. Some of the important uses of phylogeny are as follows-

- Understanding evolutionary relationships- Phylogeny shows the relationships of different organisms or biological lineages through common ancestry. Patterns of descent and divergence can be traced using a phylogenetic tree. Evolutionary changes occurring over long periods of time are also studied.

- Classification and systematics- Phylogenetic relationships are used in the [classification of organisms](https://biologynotesonline.com/taxonomy/). Organisms having common ancestry can be placed together into groups which better represent their evolutionary relationships, instead of grouping them only from general similarities.

- Study of character evolution- Morphological, physiological, behavioral, and molecular characters can be studied using phylogenies. Changes in a character can be followed across different lineages of the tree. The ancestral character states can also be estimated. Rates and patterns of evolutionary changes are studied in this way.

- Comparing organisms- Closely related species are not completely independent observations because some of their characters have been inherited from their common ancestors. Phylogenetic comparative methods take this shared evolutionary history into account while comparing the traits of different species.

- Biogeography- Phylogeny along with geographical information is used to study the present distribution of organisms. It can be used for examining dispersal, separation of lineages, and their evolutionary history in different geographical regions.

- Conservation biology- Phylogenetic information is used for studying phylogenetic diversity, which considers the evolutionary history represented by a species or group of species. It is also used for identifying evolutionarily distinct lineages. In some approaches, this information is applied for setting conservation priorities.

- Study of infectious diseases- Phylogenies of viruses, bacteria, and other pathogens are used to study their origin, genetic relationships, spread, and changes through time. In molecular epidemiology, closely related pathogen sequences are compared for investigating transmission. Their geographical movement can also be studied.

- Understanding diversification- Branching patterns of a phylogeny provide information for studying speciation, extinction, and diversification of different groups. Different clades can also be compared for changes in evolutionary rates and traits.

![Three phylogenetic trees with the same topology showing arbitrary branch lengths in a cladogram, evolutionary change in a phylogram, and time-scaled branches in a chronogram.](https://biologynotesonline.com/wp-content/uploads/2024/03/Cladogram-vs-Phylogram-vs-Chronogram-1024x341.png)Three phylogenetic trees with the same topology showing arbitrary branch lengths in a cladogram, evolutionary change in a phylogram, and time-scaled branches in a chronogram.

## Quick Facts about Phylogeny

TopicQuick Summary for ExamsPhylogenyPhylogeny is the evolutionary history and relationships among organisms or other biological lineages through common ancestry. It represents an inferred evolutionary history.Common ancestryOrganisms are related because they descended from shared ancestral lineages. More recent common ancestor indicates a closer evolutionary relationship.LineageA lineage is a line of descent connecting ancestors with their descendants.DivergenceSplitting of one ancestral lineage into separate descendant lineages is called divergence.TipsTips are the ends of a phylogenetic tree. They represent species, populations, genes, or other taxa being compared.BranchesBranches represent evolutionary lineages connecting ancestors and descendants.NodesNodes are points where branches meet or split. Internal nodes generally represent inferred common ancestors.RootThe root represents the inferred common ancestor of all taxa present in a rooted tree.CladeA clade contains a common ancestor and all of its descendants. It is also called a monophyletic group.TopologyTopology is the branching pattern of a phylogenetic tree and shows how taxa are related.Branch lengthDepending on the tree, branch length may represent evolutionary change, genetic distance, or time. In some trees, it has no biological meaning.Rooted treeIt has a root and shows the direction of evolutionary descent from ancestor toward descendants.Unrooted treeIt shows relationships among taxa but does not specify the ancestral root or direction of descent.How to read a phylogenyFollow the branching pattern and common ancestral nodes. Do not judge relationships from left-right position or physical distance between names.Sister taxaTwo lineages arising from the same immediate ancestral node are called sister taxa.MRCAMost Recent Common Ancestor (MRCA) is the nearest shared ancestor between two or more lineages.Inference of phylogenyPhylogenies are inferred using morphological characters, DNA, RNA, proteins, fossils, and other heritable characters.Major inference methodsCommon methods include distance methods, maximum parsimony, maximum likelihood, and Bayesian inference.OutgroupAn outgroup is a taxon outside the main study group and can be used to help root a phylogenetic tree.ImportancePhylogeny is used in classification, systematics, study of character evolution, biogeography, conservation, infectious disease studies, and understanding diversification.CladogramShows branching order. Branch length usually has no evolutionary meaning.PhylogramBranch length represents amount of evolutionary change.ChronogramBranch length represents evolutionary time.Bifurcating treeEach ancestral node divides into two descendant branches.Multifurcating treeA node gives rise to more than two descendant branches. This is called a polytomy.Phylogeny vs PhylogeneticsPhylogeny is the evolutionary history or relationship itself. Phylogenetics is the study and inference of those evolutionary relationships.

## References

- Brown, T. A. (2002). Genomes (2nd ed.). Wiley-Liss. [https://www.ncbi.nlm.nih.gov/books/NBK21128/](https://www.ncbi.nlm.nih.gov/books/NBK21128/)

- Cardillo, M. (2023). Phylogenetic diversity in conservation: A brief history, critical overview, and challenges to progress. Cambridge Prisms: Extinction, 1, e11. [https://doi.org/10.1017/ext.2023.8](https://doi.org/10.1017/ext.2023.8)

- Castiglione, S., Serio, C., Mondanaro, A., Di Febbraro, M., Profico, A., Girardi, G., & Raia, P. (2019). Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species. PLOS ONE, 14(1), e0210101. [https://doi.org/10.1371/journal.pone.0210101](https://doi.org/10.1371/journal.pone.0210101)

- Clark, M. A., Douglas, M., & Choi, J. (2018). Biology 2e. OpenStax. [https://openstax.org/books/biology-2e/pages/1-introduction](https://openstax.org/books/biology-2e/pages/1-introduction)

- Dees, J., Momsen, J. L., Niemi, J., & Montplaisir, L. (2014). Student interpretations of phylogenetic trees in an introductory biology course. CBE—Life Sciences Education, 13(4), 666–676. [https://doi.org/10.1187/cbe.14-01-0003](https://doi.org/10.1187/cbe.14-01-0003)

- Domagal-Goldman, S. D., Wright, K. E., Adamala, K., De La Rubia, L. A., Bond, J., Dartnell, L. R., Goldman, A. D., Lynch, K., Naud, M. E., Paulino-Lima, I. G., Singer, K., Walter-Antonio, M., Abrevaya, X. C., Anderson, R., Arney, G., Atri, D., Azuá-Bustos, A., Bowman, J. S., Brazelton, W. J., … Wong, T. (2016). The Astrobiology Primer v2.0. Astrobiology, 16(8), 561–653. [https://doi.org/10.1089/ast.2015.1460](https://doi.org/10.1089/ast.2015.1460)

- Fowler, S., Roush, R., & Wise, J. (2013). Concepts of biology. OpenStax. [https://openstax.org/books/concepts-biology/pages/1-introduction](https://openstax.org/books/concepts-biology/pages/1-introduction)

- Furniss, K., & Hammarlund, S. (n.d.). Introduction to the evolution & biology of sex. University of Minnesota Libraries. [https://open.lib.umn.edu/evosex/](https://open.lib.umn.edu/evosex/)

- Introductory biology: Evolutionary and ecological perspectives. (n.d.). University of Minnesota Libraries. [https://pressbooks.umn.edu/introbio/](https://pressbooks.umn.edu/introbio/)

- Janies, D. (2019). Phylogenetic concepts and tools applied to epidemiologic investigations of infectious diseases. Microbiology Spectrum, 7(4). [https://doi.org/10.1128/microbiolspec.AME-0006-2018](https://doi.org/10.1128/microbiolspec.AME-0006-2018)

- Kinene, T., Wainaina, J., Maina, S., & Boykin, L. M. (2016). Rooting trees, methods for. In R. M. Kliman (Ed.), Encyclopedia of evolutionary biology (Vol. 3, pp. 489–493). Academic Press. [https://doi.org/10.1016/B978-0-12-800049-6.00215-8](https://doi.org/10.1016/B978-0-12-800049-6.00215-8)

- Lin, G. N., Zhang, C., & Xu, D. (2011). Polytomy identification in microbial phylogenetic reconstruction. BMC Systems Biology, 5(Suppl. 3), S2. [https://doi.org/10.1186/1752-0509-5-S3-S2](https://doi.org/10.1186/1752-0509-5-S3-S2)

- Meisel, R. P. (2010). Teaching tree-thinking to undergraduate biology students. Evolution: Education and Outreach, 3(4), 621–628. [https://doi.org/10.1007/s12052-010-0254-9](https://doi.org/10.1007/s12052-010-0254-9)

- Mondal, A., Rangel, L. T., Payette, J. G., Fournier, G. P., & Bansal, M. S. (2023). DaTeR: Error-correcting phylogenetic chronograms using relative time constraints. Bioinformatics, 39(2), btad084. [https://doi.org/10.1093/bioinformatics/btad084](https://doi.org/10.1093/bioinformatics/btad084)

- National Academies of Sciences, Engineering, and Medicine. (2016). Eliminating the public health problem of hepatitis B and C in the United States: Phase one report. The National Academies Press. [https://doi.org/10.17226/23407](https://doi.org/10.17226/23407)

- National Research Council. (1989). Opportunities in biology. The National Academies Press. [https://doi.org/10.17226/742](https://doi.org/10.17226/742)

- National Research Council. (2005). Catalyzing inquiry at the interface of computing and biology. The National Academies Press. [https://doi.org/10.17226/11480](https://doi.org/10.17226/11480)

- Pardi, F., & Gascuel, O. (2012). Combinatorics of distance-based tree inference. Proceedings of the National Academy of Sciences of the United States of America, 109(41), 16443–16448. [https://doi.org/10.1073/pnas.1118368109](https://doi.org/10.1073/pnas.1118368109)

- Pavlopoulos, G. A., Soldatos, T. G., Barbosa-Silva, A., & Schneider, R. (2010). A reference guide for tree analysis and visualization. BioData Mining, 3, 1. [https://doi.org/10.1186/1756-0381-3-1](https://doi.org/10.1186/1756-0381-3-1)

- Tolkoff, M. R., Alfaro, M. E., Baele, G., Lemey, P., & Suchard, M. A. (2018). Phylogenetic factor analysis. Systematic Biology, 67(3), 384–399. [https://doi.org/10.1093/sysbio/syx066](https://doi.org/10.1093/sysbio/syx066)

- Zou, Y., Zhang, Z., Zeng, Y., Hu, H., Hao, Y., Huang, S., & Li, B. (2024). Common methods for phylogenetic tree construction and their implementation in R. Bioengineering, 11(5), 480. [https://doi.org/10.3390/bioengineering11050480](https://doi.org/10.3390/bioengineering11050480)