2.1.3: Determining Evolutionary Relationships

Learning Objectives

• Compare homologous and analogous traits.
• Discuss the purpose of cladistics.
• Describe the concept of maximum parsimony.

Scientists must collect accurate information that allows them to make evolutionary connections among organisms. Similar to detective work, scientists must use evidence to uncover the facts. In the case of phylogenies, evolutionary investigations focus on two types of evidence: morphologic (form and function) and genetic.

Two Options for Similarities

In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures and stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures (Figure \(\PageIndex{1}\)), as do the leaves of monocots and eudicots (Figure \(\PageIndex{2}\)).

Figure \(\PageIndex{1}\): Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past. Both the bird wing and the bat wing share common bones, analogous to the bones in the arms and fingers of humans. However, in the bat wing, the finger bones are long and separate and form a scaffolding on which the wing’s membrane is stretched. In the bird wing, the finger bones are short and fused together at the front of the wing. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM)

Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more likely any kind of overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms.

In plants, we see similar trends. An example of a homologous structure in plants is the leaf. Groups of vascular plants have evolved from a shared common ancestor that formed leaves. In particular, we could look at leaves formed by flowering plants (Angiosperms), the most recent major clade within kingdom Plantae. The developmental pathway and internal anatomy of these leaves have similarities due to shared ancestry, though they may appear outwardly different.

Figure \(\PageIndex{2}\): Monocots and eudicots are two major divisions within flowering plants. The leaves of these plants have differences in anatomy and morphology that allow us to distinguish between the two groups. However, the overall structure is very similar. This is because their leaves are homologous, derived from a shared common ancestor but diverging in appearance over evolutionary time. Figure created by Maria Morrow with modification of work by Simon A. Eugster (eudicot leaf), CC BY-SA 4.0, via Wikimedia Commons.

Misleading Appearances

Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very much alike. This usually happens because both organisms were in common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures (Figure \(\PageIndex{3}\) and Figure \(\PageIndex{4}\)).

Similar traits can be either homologous or analogous. Homologous traits are shared due to common ancestry; analogous traits have a similar function but are not similar due to common ancestory. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm, though one is specialized for swimming and the other climbing. These structures are not analogous. The wings of a bee and the wings of a bird are analogous but not homologous, both specialized for flying but of completely different biological arrangement. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous, both used for flight and both with a similar biological arrangement. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.

Figure \(\PageIndex{3}\): The (c) wing of a honeybee is similar in shape to a (b) bird wing and (a) bat wing, and it serves the same function. However, unlike the bat and bird wings, the honeybee wing is not composed of bones and has a distinctly different structure and embryonic origin. These wing types (insect versus bat and bird) illustrate an analogy—similar structures that do not share an evolutionary history. (credit a: modification of work by Steve Hillebrand, USFWS; credit b: modification of work by U.S. DOI BLM; credit c: modification of work by Jon Sullivan)

Link to Learning: This website has several examples to show how appearances can be misleading in understanding the phylogenetic relationships of organisms.

Analogous structures are often caused by convergent evolution of structures used for similar functions. For example, there are many different groups of unrelated organisms that photosynthesize. Plants are one lineage of photosynthetic organisms, whose ancestors are shared with the green and red algae. The brown algae have a completely different evolutionary history and do not share a common ancestor with plants (they are more closely related to water molds). However, many brown algae form flat, leaf-like structures similar to plants, as both groups use these structures for photosynthesis. Many brown algae, such as the kelps, also form stem- and root-like structures (see Figure \(\PageIndex{4}\)).

Figure \(\PageIndex{4}\): Analogous structures. Brown algae, such as this sea palm (Postelsia palmaeformis) are not closely related to plants. However, because they have a similar nutritional strategy (photosynthesis), they have evolved similar looking features. Sea palms have an anchorage system called a holdfast that looks like roots emerging from the base. A stem-like stipe holds the leaf-like blades aloft. Photo by Peter Pearsall/U.S. Fish and Wildlife Service, USFWS - Pacific Region, Public domain, via Wikimedia Commons.

Molecular Comparisons

With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated.

Sometimes two segments of DNA code in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships, and, ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.

Figure \(\PageIndex{5}\): This image shows amino acid sequences for the same protein (VEGF) in humans and mice. Each line represents the sequence of a different individual. Each letter represents an amino acid. The sequences have been aligned to find similarities and differences. The bars across the sequences show amino acids that are unchanged across the organisms tested. These positions are considered shared ancestral characteristics. At all other locations, there may be differences in the amino acids between organisms. We can use these as synapomorphies to build a tree, assuming that organisms who share more similar sequences are more closely related. This information has revolutionized the way phylogenies are built. "Alignment of the VEGF Homology Domain of representative VEGFs (all mammalian VEGFs from human and mouse plus one VEGF-E (viral) and one VEGF-F (snake venom)" Mjeltsch, CC BY-SA 4.0, via Wikimedia Commons.

Why does phylogeny matter? Evolutionary biologists could list many reasons why understanding phylogeny is important to everyday life in human society. For botanists, phylogeny acts as a guide to discovering new plants that can be used to benefit people. Think of all the ways humans use plants—food, medicine, and clothing are a few examples. If a plant contains a compound that is effective in treating cancer, scientists might want to examine all of the relatives of that plant for other useful drugs.

A research team in China identified a segment of DNA thought to be common to some medicinal plants in the family Fabaceae (the legume family) and worked to identify which species had this segment (Figure \(\PageIndex{6}\)). After testing plant species in this family, the team found a DNA marker (a known location on a chromosome that enabled them to identify the species) present. Then, using the DNA to uncover phylogenetic relationships, the team could identify whether a newly discovered plant was in this family and assess its potential medicinal properties.

Figure \(\PageIndex{6}\): Dalbergia sissoo (D. sissoo) is in the Fabaceae, or legume family. Scientists found that D. sissoo shares a DNA marker with species within the Fabaceae family that have antifungal properties. Subsequently, D. sissoo was shown to have fungicidal activity, supporting the idea that DNA markers can be used to screen for plants with potential medicinal properties.

Building Phylogenetic Trees

How do scientists construct phylogenetic trees? After the homologous and analogous traits are sorted, scientists often organize the homologous traits using a system called cladistics. This system sorts organisms into clades: groups of organisms that descended from a single ancestor. For example, in Figure \(\PageIndex{7}\), all of the organisms in the orange region evolved from a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Clades must include all of the descendants from a branch point.

Figure \(\PageIndex{7}\): A phylogeny of vertebrates. Lizards, rabbits, and humans all descend from a common ancestor that had an amniotic egg. Thus, lizards, rabbits, and humans all belong to the clade Amniota. Vertebrata is a larger clade that also includes fish and lamprey. Descriptive text: Lancelets are at the left tip of the V, and humans are at the right tip. Four more lines are drawn parallel to the lancelet line; each of these lines starts further up the right arm of the V than the next. At the end of each line, from left to right, are lampreys, fish, lizards, and rabbits. Lizards, rabbits, and humans are in the clade Amniota, which form a small V nested in the upper right-hand corner of the V-shaped Vertebrata clade.

Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in the clade or monophyletic group stem from a single point on the tree. This can be remembered because monophyletic breaks down into “mono,” meaning one, and “phyletic,” meaning evolutionary relationship. Figure \(\PageIndex{8}\) shows various examples of clades. Notice how each clade comes from a single point, whereas the non-clade groups show branches that do not share a single point.

Figure \(\PageIndex{8}\): All the organisms within a clade stem from a single point on the tree. A clade may contain multiple groups, as in the case of animals, fungi and plants, or a single group, as in the case of flagellates. Groups that diverge at a different branch point, or that do not include all groups in a single branch point, are not considered clades. Descriptive text: In order from the bottom, these are diplomonads, microsporidia, trichomonads, flagellates, entamoebae, slime molds, and ciliates. At the top of the tree, animals, fungi and plants all branch from the same point and are shaded to show that they belong in the same clade. Flagellates are on a branch by themselves, and they also form their own clade and are shaded to show this. In another image, Flagellates and ciliates are shaded to show that they branch from different points on the tree and are not considered clades. Likewise, a grouping of animals and plants but not fungi would not be considered a clade cannot exclude a branch originating at the same point as the others.

Phylogenetic trees can be constructed by scoring similarities and differences between the taxa of interest (check out this supplementary video to see how it is done). These traits can be morphological or developmental features (Figure \(\PageIndex{7}\)) or genetic traits called single nucleotide polymorphisms (SNPs, or snips, for short). Taxa with the most similarities are placed into the same clade.

Shared Characteristics

Organisms evolve from common ancestors and then diversify. Scientists use the phrase “descent with modification” because even though related organisms have many of the same characteristics and genetic codes, changes occur. This pattern repeats over and over as one goes through the phylogenetic tree of life:

1. A change in the genetic makeup of an organism leads to a new trait which becomes prevalent in the group.
2. Many organisms descend from this point and have this trait.
3. New variations continue to arise: some are adaptive and persist, leading to new traits.
4. With new traits, a new branch point is determined (go back to step 1 and repeat).

If a characteristic is found in the ancestor of a group, it is considered a shared ancestral character because all of the organisms in the taxon or clade have that trait. The vertebrate in Figure \(\PageIndex{7}\) is a shared ancestral character. Now consider the amniotic egg characteristic in the same figure. Only some of the organisms in Figure \(\PageIndex{7}\) have this trait, and to those that do, it is called a shared derived character because this trait derived at some point but does not include all of the ancestors in the tree.

The tricky aspect to shared ancestral and shared derived characters is the fact that these terms are relative. The same trait can be considered one or the other depending on the particular diagram being used. Returning to Figure \(\PageIndex{8}\), note that the amniotic egg is a shared ancestral character for the Amniota clade, while having hair is a shared derived character for some organisms in this group. These terms help scientists distinguish between clades in the building of phylogenetic trees.

Choosing the Right Relationships

Imagine being the person responsible for organizing all of the items in a department store properly—an overwhelming task. Organizing the evolutionary relationships of all life on Earth proves much more difficult: scientists must span enormous blocks of time and work with information from long-extinct organisms. Trying to decipher the proper connections, especially given the presence of homologies and analogies, makes the task of building an accurate tree of life extraordinarily difficult. Add to that the advancement of DNA technology, which now provides large quantities of genetic sequences to be used and analyzed. Taxonomy is a subjective discipline: many organisms have more than one connection to each other, so each taxonomist will decide the order of connections.

To aid in the tremendous task of describing phylogenies accurately, scientists often use a concept called maximum parsimony. Maximum parsimony is a principles that assumes the fewest evolutionary events occurred in a given phylogeny. This is also called Ockham's razer - that we should also select the simplest hypothesis that explains the data. Maximum likelihood, another principle used when constructing phylogenies, suggests that the most likely sequence of evolutionary events most likely occured.

For example, if you saw a friend who was wearing a blue shirt, then saw them again in the evening and they were still wearing that blue shirt, you'd probably assume that they had been wearing that same blue shirt all day. However, it is possible that they went home, changed, and changed back or changed into a shirt that looks very similar. It is just less likely, and so we often assume the former.

For scientists deciphering evolutionary pathways, the same idea is used: the pathway of evolution probably includes the fewest major events that coincide with the evidence at hand. Starting with all of the homologous traits in a group of organisms, scientists look for the most obvious and simple order of evolutionary events that led to the occurrence of those traits.

These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the evolutionary history of life on Earth. Recently, newer technologies have uncovered surprising discoveries with unexpected relationships, such as the fact that people seem to be more closely related to fungi than fungi are to plants. Sound unbelievable? As the information about DNA sequences grows, scientists will become closer to mapping the evolutionary history of all life on Earth.

Summary

To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes. Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths (analogies). Newer technologies can be used to help distinguish homologies from analogies. After homologous information is identified, scientists use cladistics to organize these events as a means to determine an evolutionary timeline. Scientists apply the principles of maximum parsimony and maximum likelihood, which state that the order of events probably occurred in the most obvious and simple way with the least amount of steps and that the the most likely sequence of evolutionary events probably occured. For evolutionary events, this would be the path with the least number of major divergences that correlate with the evidence.

Contributors and Attributions

Curated and authored by Maria Morrow using the following sources:

• 20.2 Determining Evolutionary Relationships from Biology by OpenStax (licensed CC-BY). Access for free at openstax.org.