Phylogenetics

Phylogenetics
n.,[ˌfaɪləd͡ʒəˈnɛtɪks]
Definition: the scientific study of taxonomic relatedness of organisms based on evolutionary features and history

Phylogenetics Definition

Phylogenetics is the scientific study of phylogeny. It studies evolutionary relationships among various groups of organisms based on evolutionary history, similarities, and differences. It makes use of molecular sequencing data (such as homologous sequences, protein sequences, nucleotide sequences, etc.) and morphological data matrices to understand and analyze the protein and gene evolutions of genetically-related groups of organisms.

Etymology: Greek from the terms phyle/phylon, meaning “tribe”, “race,” and genetikos, meaning “relative to birth” from genesis (“birth”).

Key Concepts

Common concepts that are highly relevant and important in understanding phylogenetics:

• Phylogenetic tree

A phylogenetic tree is a “tree” diagram that shows the hypothetical evolutionary relatedness and history of groups of organisms based on the phylogenies of different biological species. The phylogenetic tree has been used to understand biodiversity, genetics, evolutions, and the ecology of organisms.

Evolutionary trees are essential phylogenetic tools for learning about common ancestors based on evolutionary closeness and branch lengths. Below is an example of a phylogenetic tree depicting the evolution of biological entities both the extinct and the living. The “root” (bottom) depicts the last universal common ancestor of life on Earth. The “branches” representing the genealogy of a group of organisms and the “node” is where the lineages come together at (or bifurcate from, depending on the point of view)  this common point. Each node represents the origin (ancestor) of a group. The “tips” of the branches represent the living organisms at present and the most recent lineage.

Watch this vid about phylogenetics and interpreting phylogenetic trees:

• Monophyly, polyphyly, and paraphyly

Monophyly is defined as the condition of being a clade. A monophyletic group is a group of organisms that descended from a common ancestor. Hence, members of this group are more closely related to each other than any other group of organisms. The unique or exclusive characteristic(s) present in the most recent common ancestor is called synapomorphy. Synapomorphies, when identified, are what define the monophyly of a group.

For example, chordates (of phylum Chordata) are a monophyletic group that consists of descendants of a single common ancestor, which is a chordate. They share a single evolutionary history and if represented by a phylogenetic tree, they would come form the same single node.

Polyphyly is when the members of a group are an assemblage of organisms that descended from more than one common ancestor. Thus, a polyphyletic group refers to a group of organisms descending from multiple ancestral lineages. They have a mixed evolutionary origin.

Paraphyly refers to a group of organisms that descended from a single common ancestor but excludes other descendants. A paraphyletic group, therefore, is one in which it includes only some of the descendants of the common ancestor as opposed to monophyly, which includes all.

• Clade and taxon

A clade refers to a monophyletic group of organisms. A taxon refers to any group or rank in biological classification. Taxa (plural form) are essentially used in classifying organisms based on the characteristics depicting relatedness (e.g., morphological, behavioral, and/or genetic features common among members of the taxon). Examples of taxonomic ranks or groups are phylum, family, genus, etc.

A taxon is a wider concept than a clade. A taxon may be monophyletic, polyphyletic, or paraphyletic. Remember our definition of a clade? A monophyletic taxon is a clade. All members of a monophyletic taxon descended from the most recent common ancestor. Apart from chordates, other examples of monophyletic taxa are mammals, insects, and angiosperms. Take, for instance, the mammals. All of them have mammary glands, which is a trait believed to have originated from a common ancestry. This trait that is passed down to its descendants is described as homologous (contrary to the analogous trait that is not).

A polyphyletic taxon is a taxon where members of a taxon descended from two or more recent common ancestors. An example of a polyphyletic group is trees. Trees share typical morphology, such as having a sturdy upright single stem that supports the branches, but they have different most recent common ancestors — the most recent ancestor of angiosperm and the most recent ancestor of gymnosperm, for instance.

A paraphyletic taxon is a taxon consisting of members that descended from a single most recent ancestor however not all of its descendants are members of the taxon. Gymnosperms, for example, exclude some of the descendants of their most recent ancestor.

To better understand this, take, for instance, cellular organisms. All cellular organisms belong to a monophyletic taxon for sharing a common characteristic — being made up of cell(s) — and descended from a single common ancestor. However, not all cells have a nucleus. Cellular organisms that do not have a nucleus in their cell belong to the paraphyletic taxon, Prokaryota (the prokaryotes), which excludes the clade of cellular organisms that have a nucleus, Eukaryota (the eukaryotes).

Frequently Asked Questions on Phylogenetics

• What is the purpose of phylogenetics?

Phylogenetics is important in understanding the evolutionary processes and for the phylogenetic classification of organisms. It also helps formulate an evolutionary theory through constructions of molecular evolutionary trees. Phylogenetics, thus, helps us understand phylogenetic diversity and phylogenetic history of various groups of organisms.

• How is phylogenetics done?

One way of studying phylogeny is by framing theories through phylogenetic trees. These diagrams proved useful in phylogenetic tree construction of the evolution and the distribution of a character trait, which can be used for phylogenetic inferences as basis for cladistic analysis. Trait hierarchy via phylogenetic trees can be used to identify which characteristics appeared in order.

In essence, phylogeneticists aim to answer the general questions, such as, “how do sequences evolve”, “how the organisms of interest (at individual or genetic level)  are evolutionary or phylogenetically related with other organisms”, or “how to come up with a sound evolutionary model”…

Initially, these diagrams are heavily based on morphological analyses and identification of phylogenetic branching patterns. Phylogenetics revolutionized when molecular biology techniques and methods came about. Such approach eventually found their way to phylogenetics.

Some of these molecular revolutionary approaches are the generation and analyses of biomolecular sequences by way of DNA sequences, nucleotide sequences, homologous sequences, and protein sequences.

Molecular sequencing (e.g., DNA sequencing) became an indispensable tool for phylogenetic methods/phylogenetic analyses of observable heritable traits. It helps verify whether a trait is homologous or analogous (thus, avoiding ‘false positives’ of common ancestry).

Alignment-based or alighment-free methods are used for sequence comparisons. Sequence alignment helps identify homologous sequences. It can be done pair-wise (where two sequences are compared) or by multiple sequence alignment (where multiple sequences are simultaneously compared).

These molecular methods provide a rather mathematical and molecular data to back up phylogenetic inferences.

Statistical data analyses, e.g., by the use of maximum likelihood methods, became essential to phylogeneticists, too, as they can now estimate the parameters of a probability distribution, such as in evolutionary models. This approach is used in phylogenetic inference, evaluating competing hypotheses about evolutionary histories by seeking the ‘best‘ hypothetical tree.

Bayesian phylogenetic inference (or simply, Bayesian inference) is one of the most popular methods use in molecular phylogenetics. It has been the standard statistical approach. Bayesian methods have been used by phylogeneticists to infer phylogenies and phenotypic trait evolution, evaluate phylogenetic uncertainty, analyze molecular dating and dynamics of species diversification and extinction, among others. Some of the common phylogenetic softwares used for Bayesian analysis are MrBayes, Bayesian Evolutionary Analysis Sampling Trees (BEAST), PhyloBayes / PhyloBayes MPI (Bayesian Monte Carlo Markov Chain (or Markov Chain Monte Carlo) method/ sampler for phylogenetic reconstruction).

These phylogenetic techniques and approaches helped phylogeneticists in developing better evolutionary models by the availability of rapid computer programs that help manage a large set of statistical and sequence data. And as such, they are able to infer more reliably phylogenetic relationships and sequence evolution in a phylogenetic tree.

• Is phylogeny the same as phylogenetics?

Not quite but they are related. Phylogeny is defined as the evolutionary history of a group of organisms. Phylogenetics is the science that studies phylogeny. The phylogenetic approach of studying evolutionary relatedness and histories of organisms makes use of a phylogenetic tree. Data sequencing is also used in inferring phylogenies. As already discussed above, the phylogenetic tree depicts how a group of organisms can be related to another group and molecular sequencing is applied to provide a genetic basis for their relatedness.

Related Sciences

Here, you will find some of the scientific disciplines that are closely related to phylogenetics. Thus, topics could overlap between or among them.

• Systematics and Evolutionary biology

Phylogeny looks into the evolutionary history of a taxonomic group of organisms. Thus, phylogenetics is mainly concerned with the phylogenetic relationships and molecular evolution of organisms according to evolutionary similarities and differences. Phylogenetics, therefore, is a part of biological systematics, which has a wider scope as it involves not only the phylogenetics of organisms but also the identification and classification of organisms. For that matter, systematics encompasses two fields of study: taxonomy and phylogenetics. In particular, phylogenetic systematics is a subfield of systematics where a phylogenetic approach is applied in studying the divesities and relationships of organisms through time.

The subfields of systematics include molecular systematics, which explores via molecular approach, numerical systematics or numerical taxonomy, which is based on bio-statistical analysis and data, and experimental systematics or evolutionary systematics, which attempts to understand systematics through the factors affecting the process of evolution.

• Taxonomy

Phylogenetics is also related to taxonomy, which is a branch of science concerned also in finding, describing, classifying, and naming organisms, including the studying of the relationships between taxa and the principles underlying such a classification. Phylogenetics provides information to taxonomy when it comes to the classification and identification of organisms.

• Genetics

The study of phylogenies is heavily based on the core principles and practice of genetics. It helps us understand how species evolve at the level of genes and genomes, particularly genetic changes through time.

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Further Reading

• systematics
• phylogeny
• evolutionary biology
• evolution
• genetics
• phylogenetic tree

References

• Systematics: Meaning, Branches and Its Application. (2016, May 27). Biology Discussion. https://www.biologydiscussion.com/animals-2/systematics-meaning-branches-and-its-application/32374
• Graphical explanation of phylogenetic terms. (2022). Berkeley.edu. https://ucmp.berkeley.edu/glossary/gloss1/phyly.html‌‌
• Haber, M., & Velasco, J. (2021). Phylogenetic Inference (Stanford Encyclopedia of Philosophy). Stanford.edu. https://plato.stanford.edu/entries/phylogenetic-inference/#:~:text=At%20its%20core%2C%20phylogenetic%20inference,underdetermination%20of%20theory%20by%20evidence%20.‌

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