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Phylogeny

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Biology

How do species evolve? How are two or more species related? What species or groups share the same ancestors? Scientists answer these kinds of questions by reconstructing phylogeny.

What is phylogeny?

Phylogeny refers to the evolutionary history and relationships of organisms. In the following, we will discuss the definition of phylogeny, break down an example of mammal phylogeny, and describe how various lines of evidence are used to reconstruct phylogeny.

What Is the Definition of Phylogeny?

Evolution is a gradual and cumulative change in the heritable traits of a population of organisms. This change has taken place throughout many generations. Scientists observe patterns of evolutionary changes to understand how life forms evolve and branch out into new species.

The evolutionary history and relationship of a species or a group of species are called phylogeny. It is often illustrated using a branching diagram called a phylogenetic tree. Phylogenetic trees show how organisms or groups at any hierarchical level are related to each other through common ancestors.

The hierarchical categories used in taxonomy are (from least to most inclusive):

  • Species

  • Genus

  • Family

  • Order

  • Class

  • Phylum

  • Kingdom

  • Domain

Taxonomists group organisms that share similar traits and features in increasingly broader categories. For example, the leopard (Panthera pardus), the jaguar (P. onca), the African lion (P. leo), and the tiger (P. tigris) are species that belong to Panthera. This genus includes all big cats.

Besides these taxonomic categories, phylogeny can also be shown through cladistics where organisms and groups are classified based on common ancestry. They are grouped into clades which consist of a common ancestor and its descendant species.

Taxonomy: a systematic approach to naming and classifying organisms.

An Example of Animal Phylogeny

Let's use mammal phylogeny as an example of animal phylogeny.

Mammal Phylogeny

The evolutionary history and relationship of mammals are illustrated through a phylogenetic tree, as shown in Figure 1.

For this example, we can see how Mammalia (a class that diverged from other tetrapods through unique anatomical features including specific jawbones and differentiated teeth) diverged into Monotremata (an egg-laying order of mammals) and Theria (a subclass of mammals that give birth to live young).

Therian mammals then diverged into Marsupialia (an infraclass or clade of mammals that use external pouches to raise their newborn offspring) and Placentalia (an infraclass or clade of mammals that have a placenta, a temporary organ that connects the embryo to the mother's uterus).

This example demonstrates how common ancestry can be inferred from similar traits and how divergence can be inferred from the emergence of new traits.

Mammal phylogeny

Figure 1. This phylogenetic tree shows the evolutionary history and relationship of groups under Mammalia. Source: various, Public domain, via Wikimedia Commons.

Phylogenies are not definitive–they are hypotheses that can be revised or updated based on available evidence. They are also presented in different ways. For example, Figure 2 is another phylogenetic tree of Mammalia. This version shows the phylogeny of families under Mammalia. It also shows other information, such as the geographic distribution of these groups of mammals indicated by the points on a map.

Mammal phylogeny

Figure 2. This phylogenetic tree also shows the evolutionary history and relationship of groups under Mammalia, but unlike Figure 1, it traces divergence down to specific families. Source: Graphodatsky et al., CC BY 2.0, via Wikimedia Commons.

What Evidence Is Used to Determine Phylogeny?

Phylogenies are inferred based on different lines of evidence, including fossils, homology, and molecular biology. Let's discuss each of these briefly.

Fossils

Fossils are preserved remnants or traces of organisms from a past geologic age, often found in sedimentary rocks. The fossil record documents the history of life on Earth based primarily on the sequence of fossils in sedimentary rock layers called strata. The arrangement of fossils in strata gives us an idea of what organisms existed in a specific geologic time.

Scientists use fossils to construct the phylogeny of both extinct and extant groups. For example, the fossil record shows that cetaceans (an order of marine mammals that includes whales, dolphins, and porpoises) evolved from terrestrial mammals similar to modern-day hippopotamuses, pigs, and cows. Fossils show that the pelvis and hind limb bones of extinct cetacean ancestors became smaller, eventually disappearing completely and developing into flukes and flippers.

Homology

Homology is useful in determining the evolutionary relationship among different organisms. Organisms that share more traits and features tend to be more closely related. There are three types of homology:

  • Morphological homology is when different species have similar structures with the same basic form due to common ancestry. For example, mammals are classified as monotremes, placentals, and marsupials based on how they produce offspring.

  • Molecular homology is when different species have similar genes or DNA sequences that were inherited from a common ancestor. This will be elaborated on in the next section.

  • Developmental or ontological homology is when different species have similar structures in various stages of development. For example, all vertebrate embryos (even humans!) have gill slits and tails, but these disappear when they are born.

In inferring phylogenies, scientists distinguish between analogous and homologous traits. Analogy means having similar structures, not due to common ancestry but common selection pressures. Only homologous features show the evolutionary relationships among these organisms.

How Are DNA and rRNA Used in Phylogeny?

Although many phylogenies have been constructed using morphological and fossil evidence, molecular evidence has helped scientists build more accurate phylogenetic trees. DNA and rRNA (ribosomal RNA) are useful for studying the evolutionary relationship of organisms because all living organisms–from bacteria to humans–have them.

DNA and rRNA molecules are made up of four chemical bases that pair as follows:

  • Adenine (A) pairs with thymine (T)

  • Cytosine (C) always pairs with guanine (G).

DNA sequencing is the process of determining the order of these chemical bases. Scientists use DNA sequencing to determine the evolutionary relationship of organisms by aligning comparable sequences.

  • If the sequences are different at only one or a few sites, the species are likely very closely related.

  • If there are different bases of various lengths at many sites, the species are likely distantly related.

Figure 3 below demonstrates how two DNA sequences might be aligned.

Figure 3. This diagram shows how two short DNA sequences are aligned. The '-' represents a gap of one base, '- - -' represents a gap of three bases. Source: Tan-R6, CC BY-SA 4.0, via Wikimedia Commons.

Insertions and deletions change the DNA sequence. An insertion adds one or more chemical base pairs, while a deletion removes one or more chemical base pairs. These insertions and deletions accumulate over time, making it challenging to align the sequences.

To address this, scientists have developed computer programs and statistical tools to determine the best way to align DNA sequences and determine if the alignment of DNA sequences is due to homology or coincidence.

Molecular evidence like DNA and rRNA can also be used in dating, much like fossils and rocks.

  • Mitochondrial DNA has high mutation rates, so it can be used to determine the evolutionary history relationships among closely related species.

  • Ribosomal RNA has low mutation rates, so its sequence and structure can be aligned more easily and accurately, even for distantly related species.

What Does “Ontogeny Recapitulates Phylogeny” Mean?

Ontogeny refers to the development or any stage of development of an organism. The phrase “ontogeny recapitulates phylogeny” encapsulates the recapitulation theory by Ernst Haeckel in 1866. The recapitulation theory states that the development of individual organisms (ontogeny) replays (recapitulates) the evolutionary development of the species from its ancestral species (phylogeny).

For example, evolution led fish to diverge into amphibians, then amphibians to reptiles, and then reptiles into birds and mammals. Recapitulation theory implies that, at one point in the development of birds and mammals, they shared similarities with fish.

While the statement "ontogeny recapitulates phylogeny" is not entirely true, we can learn from the recapitulation theory that similarities shared by organisms in various stages of development could mean that they evolved from a common ancestor. This is why all vertebrates, at some point in their development, have gill slits and tails.

Phylogeny - Key takeaways

  • Phylogeny is the evolutionary history and relationship of a species or a group of species. It is often illustrated using a branching diagram called a phylogenetic tree.
  • Phylogenies are inferred based on different lines of evidence, including fossils, homology, and molecular biology.
    • Fossils are useful in constructing the phylogeny of both extinct and extant groups.
    • Homology is useful in determining the evolutionary relationship among different organisms. Organisms that share more traits and features tend to be more closely related.
    • DNA and rRNA (ribosomal RNA) are useful for studying the evolutionary relationship of organisms because all living organisms–from bacteria to humans–have them. Scientists use DNA sequencing to determine the evolutionary relationship of organisms by aligning comparable sequences.
  • Although many phylogenies have been constructed using morphological and fossil evidence, molecular evidence obtained through DNA sequencing has helped scientists build more accurate phylogenetic trees.

Phylogeny

Phylogeny is the evolutionary history and relationship of a species or a group of species.

DNA and rRNA (ribosomal RNA) are useful for studying the evolutionary relationship of organisms because all living organisms–from bacteria to humans–have them. Scientists use DNA sequencing to determine the evolutionary relationship of organisms by aligning comparable sequences.

Phylogenies are determined based on different lines of evidence including fossils, homology, and molecular biology.

Phylogenies are inferred based on different lines of evidence including fossils, homology, and molecular biology.

Ribosomal RNA has low mutation rates, so its sequence and structure can be aligned more easily and accurately, even for distantly related species. 

Final Phylogeny Quiz

Question

Which of the following refers to the evolutionary history and relationship of a species or a group of species?

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Answer

Phylogeny

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Question

How do phylogenetic trees illustrate the evolutionary history and relationship of organisms?

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Answer

Phylogenetic trees show how organisms or groups of organisms are related to each other through common ancestors.

Show question

Question

Which of the following refers to the systematic approach to naming and classifying organisms?

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Answer

Taxonomy

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Question

What is cladistics?

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Answer

Cladistics is a systematic approach to classifying organisms based on common ancestry.

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Question

What are clades?

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Answer

Clades are groups consisting of a common ancestor and its descendant species.

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Question

How are morphological similarities used to construct mammal phylogeny?

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Answer

Mammals are classified as monotremes and therians and then therian mammals are classified as placentals and marsupials based on similarities and differences in traits. In this example, they are classified based on how they produce offspring.

Show question

Question

How is DNA used in inferring phylogeny?

Show answer

Answer

Scientists use DNA sequencing to determine the evolutionary relationship of organisms by aligning comparable sequences. 

  • If the sequences are different at only one or a few sites, the species are likely very closely related.

  • If there are different bases of various lengths at many sites, the species are likely distantly related. 

Show question

Question

What does insertion mean in DNA sequencing?

Show answer

Answer

Insertion is the addition of one or more chemical base pairs in a DNA sequence.

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Question

What does deletion mean in DNA sequencing?

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Answer

Deletion is the removal of one or more chemical base pairs in a DNA sequence. 

Show question

Question

How do insertions and deletions affect DNA sequencing?

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Answer

Insertions and deletions make it challenging to align DNA sequences.

Show question

Question

How do scientists determine the best way to align DNA sequences?

Show answer

Answer

Scientists have developed computer programs and statistical tools to determine the best way to align DNA sequences and to determine if the alignment of DNA sequences is due to homology or coincidence.  

Show question

Question

Why is ribosomal RNA (rRNA) used in inferring phylogeny?

Show answer

Answer

Ribosomal RNA has low mutation rates so its sequence and structure can be aligned more easily and accurately, even for distantly related species. It is also present in all organisms from bacteria to humans.

Show question

Question

Which of the following refers to the development or any stage of development of an organism?

Show answer

Answer

Ontogeny

Show question

Question

What does “ontogeny recapitulates phylogeny” refer to?

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Answer

“Ontogeny recapitulates phylogeny” refers to recapitulation theory.

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Question

What does “ontogeny recapitulates phylogeny” or recapitulation theory mean?

Show answer

Answer

Recapitulation theory states that the development of individual organisms (ontogeny) replays (recapitulates) the evolutionary development of the species from its ancestral species (phylogeny).

Show question

Question

Why is mitochondrial DNA used in inferring phylogeny?

Show answer

Answer

Mitochondrial DNA has high mutation rates, so it can be used to determine the evolutionary history relationships among closely related species.

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