Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits?

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My question is contextualised for basic phylogeny knowledge. Here is my understanding: similar or identical traits between any two species, at the basic level, can be either homologous, meaning the trait is developed from a common ancestor, or homoplastic, meaning that the trait was independently developed.

Homologous traits can be either ancestral or derived, and derived traits are a subset of ancestral traits as derived traits need to be from the most recent common ancestor.

Homoplastic traits can be analogous, meaning they developed independently without any common ancestor or commmon initial trait, or can be traits that arose due to convergence, where species with the same (distance/close) ancestor independently developed the traits.

Please evaluate whether my understanding is correct.

As a complement to the other answer: homoplasy and analogy are not synonyms, but not for the reason described in your question.

According to Ridley (2011):

Analogy: A term mainly not used in this edition of the text, but close in meaning to homoplasy. That is, a character shared by a set of species but not present in their common ancestor - a convergently evolved character. Some biologists distinguish between homoplasies and analogies. (emphases mine)

Most of books on phylogenetic systematics treat analogy as a special case of homoplasy. A good explanation can be found, surprisingly (because he was not a systematicist), in Stephen J. Gould's last book (2002):

We now encounter the logical dilemma that underlies nearly all our exten-sive and lamentable confusion on this issue. Homoplasy and analogy might strike us, at first, as fully synonymous, for both invoke natural selection as the source of separate evolution for similar structures in two lineages. This synonymy certainly applies for convergence. But homoplasy comes in two flavors: parallelism and convergence - with parallelism as the historical root (in Lankester's original definition of homoplasy), but only convergence carry-ing the full flavor of synonymy [… ] Unfortunately, a common error of human thinking leads us to define broad and variable categories by their clearest extreme cases. Thus, many scientists have assumed that all homoplasy, whether by parallelism or by convergence, must originate entirely for functional reasons, and not at all by constraint.

Therefore, all analogies are homoplasies, but not all homoplasies are analogies. As suggested by @Remi.b in the comments:

In short, an analogy is a homoplasy caused by convergent evolution. However, a homoplasy not caused by convergent evolution is not an analogy.


  • Gould, S. (2002). The structure of evolutionary theory. Cambridge (Mass.): Harvard University Press.
  • Ridley, M. (2011). Evolution. Malden, Mass. [u.a.]: Blackwell.

This vocabulary is common in textbook but not in the peer-reviewed literature

First please note that while those terms are often used in intro class to evolutionary biology, they are actually rarely used in the peer-reviewed literature.

No trait value is fundamentally derived / ancestral

Note also that any given set of shared trait could be called ancestral or derived depending on the size of the tree that you consider. A trait is therefore not fundamentally ancestral / derived, it depends upon what other trait value you compare it to. Per consequence, it would easier to have a tree under our eyes to discuss these terms.

Note that there is one exception to that. Traits that are shared with LUCA are fundamentally ancestral!

Two states in different lineages can be fundamentally homologous / homoplastic

In general, when we are interest in a given trait, we display a tree so that all homologous trait states appear ancestral. While it is true that homoplastic trait state are necessarily derived when shown, homologous trait state can be shown as derived from a yet more ancestral trait state.

Analogy vs homoplasy

Many think of an analogy as a synonym of homoplasy. However, have a look at @GerardoFurtado's answer for the subtle difference between the two.

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits? - Biology

Since a phylogenetic tree is a hypothesis about evolutionary relationships, we want to use characters that are reliable indicators of common ancestry to build that tree. We use homologous characters — characters in different organisms that are similar because they were inherited from a common ancestor that also had that character. An example of homologous characters is the four limbs of tetrapods. Birds, bats, mice, and crocodiles all have four limbs. Sharks and bony fish do not. The ancestor of tetrapods evolved four limbs, and its descendents have inherited that feature — so the presence of four limbs is a homology.

Not all characters are homologies. For example, birds and bats both have wings, while mice and crocodiles do not. Does that mean that birds and bats are more closely related to one another than to mice and crocodiles? No. When we examine bird wings and bat wings closely, we see that there are some major differences.

Bat wings consist of flaps of skin stretched between the bones of the fingers and arm. Bird wings consist of feathers extending all along the arm. These structural dissimilarities suggest that bird wings and bat wings were not inherited from a common ancestor with wings. This idea is illustrated by the phylogeny below, which is based on a large number of other characters.

Bird and bat wings are analogous — that is, they have separate evolutionary origins, but are superficially similar because they have both experienced natural selection that shaped them to play a key role in flight. Analogies are the result of convergent evolution.

Interestingly, though bird and bat wings are analogous as wings, as forelimbs they are homologous. Birds and bats did not inherit wings from a common ancestor with wings, but they did inherit forelimbs from a common ancestor with forelimbs.

Difference Between Homologous and Analogous

Analogous characters and homologous characters are characters used in phylogenetic analysis.

Homologous Characters

When a group of organisms has a homologous structure, which is specialized to perform a variety of different functions, it shows a principle known as adaptive radiation. For an example, all the insects share the same basic plant for the structure of the mouth parts. A labrum, a pair of mandibles, a hypopharynx, a pair of maxillae and a labium together form the basic plan of the mouth parts structure. In certain insects, certain mouth parts are enlarged and modified, and others are reduced and lost. Due to this they can utilize a maximum range of food material. This gives rise to a variety of feeding structures. Insects show a relatively high degree of adaptive radiation. This shows the adaptability of the basic features of the group. This can also be called the evolutionary plasticity. This has enabled them to occupy a wide range of ecological niches. A structure present in an ancestral organism becomes greatly modified and specialized. This can be called a process of descent by modification. The significance of adaptive radiation is that it indicated the existence of divergent evolution, which is based on the modification of homologous structures over time.

Analogous Characters

Structures and physiological processes can be similar in organisms that are not closely phylogenetically related and they may show similar adaptations to perform the same function. These are referred to as analogous. Some examples for analogous structures are eyes of vertebrates and cephalopods, wings of insects and birds, jointed legs of vertebrates and insects, thorns on plants and spines on animals etc. Similarities found in analogous structures are only superficial. For example, insect wings and wings of bats and birds are analogous structures, but the wings of the insects are supports by veins composed of cuticle and the wings of birds and bats are supported by bones. Also, vertebrate eyes and cephalopod eyes are analogous structures, but the embryological development of the two is different. Cephalopods have erect retina and photoreceptors facing the incoming light. In contrast, in vertebrates the retina is inverted and the photoreceptors are separated from the incoming light by the connecting neurons. Therefore, the vertebrates have a blind spot and the cephalopods do not have a blind spot. Convergent evolution is supported by the presence of analogous structures.

What is the difference between Homologous and Analogous Characters?

• Characters that are similar in function but have different evolutionary origins are known as analogous characters, whereas characters that have the same evolutionary origin are known as homologous characters.

• Analogous characters cannot be used to infer evolutionary relationships between taxa whereas homologous characters are used to construct evolutionary relationships and phylogeny of taxa.

What is the difference between homology and Homoplasy?

Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The opposite of convergence is divergent evolution, where related species evolve different traits.

Similarly, what are the causes of Homoplasy? Patterns of homoplasy Homoplasy can occur by convergence or by parallelism. Convergence describes similarities between two species that evolved independently from different features in their common ancestor.

Similarly, it is asked, what is a Homoplasy?

A homoplasy is a character shared by a set of species but not present in their common ancestor. A good example is the evolution of the eye which has originated independently in many different species. When this happens it is sometimes called a convergence.

Which is an example of a structural homology?

A great example of homologous structures are the wings of a bat and the arms of a human. Bats and humans are both mammals, so they share a common ancestry. Both a bat's wing and a human's arm share a similar internal bone structure, even though they look very different externally.

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits? - Biology

To begin, we supply some definitions:

We see in retrospect characters shared between two species. How do we decide if a character is homologous or analogous?

First we hypothesize them to be so. Then we look at the preponderance of other characters to test our hypothesis. Cladistics gives us a framework in which to do this. Cladistics was basically invented by Willi Hennig who was a specialist in flies. Here is a link to a site that describes in detail and in a different way how we do cladistics:

In cladistics we assume that we wish to focus on genealogical relationships and that our classifications of taxa should depend on our analysis of these genealogical relationships. Of prime importance is the historical sequence in which the taxa descended from a common ancestor. Hence, our cladistic hypotheses are based on our estimate of the historical sequence of the acquisition of novel characters.

Next, some more definitions:

Let´s look at a specific example of a cladogram



10th EDITION BIOLOGY Chapter 23

All organisms share many biological characteristics. They are composed of one or more cells, carry out metabolism and transfer energy with ATP, and encode hereditary information in DNA. Yet, there is also a tremendous diversity of life, ranging from bacteria and amoebas to blue whales and sequoia trees. For generations, biologists have tried to group organisms based on shared characteristics. The most meaningful groupings are based on the study of evolutionary relationships among organisms. New methods for constructing evolutionary trees and a sea of molecular sequence data are leading to improved evolutionary hypotheses to explain life’s diversification.

Learning Outcomes
1. Understand what a phylogeny represents.
2. Explain why phenotypic similarity does not necessarily indicate close evolutionary relationship.

One of the great challenges of modern science is to understand the history of ancestor-descendant relationships that unites all forms of life on Earth, from the earliest single-celled organisms to the complex organisms we see around us today. If the fossil record were perfect, we could trace the evolutionary history of species and examine how each arose and proliferated however, as discussed in chapter 21, the fossil record is far from complete. Although it answers many questions about life’s diversification, it leaves many others unsettled.
Consequently, scientists must rely on other types of evidence to establish the best hypothesis of evolutionary relationships. Bear in mind that the outcomes of such studies are hypotheses, and as such, they require further testing. All hypotheses may be disproved by new data, leading to the formation of better, more accurate scientific ideas.
The reconstruction and study of evolutionary relationships is called systematics. By looking at the similarities and differences between species, systematists can construct and evolutionary tree, or phylogeny, which represents a hypothesis about patterns of relationship among species.

Branching diagrams depict evolutionary relationships

Darwin envisioned that all species were descended from a single common ancestor, and that the history of life could be depicted as a branching tree. In Darwin’s view, the twigs of the tree represent existing species. As one works down the tree, the joining of twigs and branches reflects the pattern of common ancestry back in time to the single common ancestor of all life. The process of descent with modification from common ancestry results in all species being related in this branching, hierarchical fashion, and their evolutionary history can be depicted using branching diagrams or phylogenetic trees. Evolutionary relationships are depicted with a branching diagram. Humans and chimpanzees are descended from a common ancestor and are each other’s closest living relative. Humans, chimps, and gorillas share an older common ancestor, and all great apes share a more distant common ancestor. One key to interpreting a phylogeny is to look at how recently species share a common ancestor, rather than looking at the arrangement of species across the top of the tree. If you compare the different versions of a phylogeny, you can see that the relationships are the same: Regardless of where they are positioned, chimpanzees and humans are still more closely related to each other than to any other species.
Moreover, even though humans can be placed next to gibbons, the pattern of relationships still indicates that humans are more closely related (that is, share a more recent common ancestor) with gorillas and orangutans than with gibbons. Phylogenies are also sometimes displayed on their side, rather than upright, but this arrangement also does not affect its interpretation.

Similarity may not accurately predict evolutionary relationships

We might expect that the greater the time since two species diverged from a common ancestor, the more different they would be. Early systematists relied on this reasoning and constructed phylogenies based on overall similarity. If, in fact, species evolved at a constant rate, then the amount of divergence between two species would be a function of how long they had been diverging, and thus phylogenies based on degree of similarity would be accurate. As a result, we might think that chimps and gorillas are more closely related to each other than either is to humans.
But as chapter 22 revealed, evolution can occur very rapidly at some times and very slowly at others. In addition, evolution is not unidirectional–sometimes species’ traits evolve in one direction, and then back the other way (a result of oscillating selection see chapter 20). Species invading new habitats are likely to experience new selective pressures and may change greatly those staying in the same habitats as their ancestors may change only a little. For this reason, similarity is not necessarily a good predictor of how long it has been since two species shared a common ancestor.
A second fundamental problem exists as well: Evolution is not always divergent. In chapter 21, we discussed convergent evolution, in which two species independently evolve the same features. Often, species evolve convergently because they use similar habitats, in which similar adaptations are favored. As a result, two species that are not closely related may end up more similar to each other than they are to their close relatives. Evolutionary reversal, the process in which species re-evolves the characteristics of an ancestral species, also has this effect.

Learning Outcomes Review 23.1
Systematics is the study of evolutionary relationships. Phylogenies, or phylogenetic trees, are graphic representations of relationships among species. Similarity of organisms alone does not necessarily correlate with their relatedness because evolutionary change is not constant in rate and direction.

Why might a species be most phenotypically similar to a species that is not its closes evolutionary relative?

Learning Outcomes
1. Describe the difference between ancestral and derived similarities.
2. Explain why only shared, derived characters indicate close evolutionary relationship.
3. Demonstrate how a cladogram is constructed.

Because phenotypic similarity may be misleading, most systematists no longer construct their phylogenetic hypotheses solely on this basis. Rather, they distinguish similarity among species that is inherited from the most recent common ancestor of an entire group, which is called derived, from similarity that arose prior to the common ancestor of the group, which is termed ancestral. In this approach, termed cladistics, only shared derived characters are considered informative in determining evolutionary relationships.

The cladistic method requires that character variation be identified as ancestral or derived

To employ the method of cladistics, systematists first gather data on a number of characters for all species in the analysis. Characters can be any aspect of the phenotype, including morphology, physiology, behavior, and DNA. As chapter 18 and 24 show, the revolution in genomics should soon provide a vast body of data that may revolutionize our ability to identify and study character variation.
To be useful, the characters should exist in recognizable character states. For example, consider the character “teeth” in amniote vertebrates (namely birds, reptiles, and mammals see chapter 35). This character has two states: presence in most mammals and reptiles and absence in birds and a few other groups such as turtles.
A cladistic analysis begins by determining the states for a number of characters for each taxon (taxa are species or higher level groups, such as genera or families) in the analysis.

Examples of ancestral versus derived characters

The presence of hair is a shared derived feature of mammals in contrast, the presence of lungs in mammals is an ancestral feature because it is also present in amphibians and reptiles (represented by a salamander and a lizard) and therefore presumably evolved prior to the common ancestor of mammals. The presence of lungs, therefore, does not tell us that mammal species are all more closely related to one another than to reptiles or amphibians, but the shared, derived feature of hair suggests that all mammal species share a common ancestor of mammals, amphibians, and reptiles.
To return to the question concerning the relationships of humans, chimps, and gorillas, a number of morphological and DNA characters exist that are derived and shared by chimps and humans, but not by gorillas or other apes. These characters suggest that chimps and humans diverged from a common ancestor that existed more recently than the common ancestor of gorillas, chimps, and humans.

Determination of ancestral versus derived

Once the data are assembled, the first step in a manual cladistic analysis is to polarize the characters–that is, to determine whether particular character states are ancestral or derived. To polarize the character “teeth,” for example, systematists must determine which state–presence or absence–was exhibited by the most recent common ancestor of this group.
Usually, the fossils available do not represent the most recent common ancestor–or we cannot be confident that they do. As a result, the method of outgroup comparison is used to assign character polarity. To use this method, a species or group of species that is closely related to, but not a member of, the group under study is designated as the outgroup. When the group under study exhibits multiple character states, and one of those states is exhibited by the outgroup, then that state is considered to be ancestral and other states are considered to be derived. However, outgroup species also evolve from their ancestors, so the outgroup species will not always exhibit the ancestral condition.
Polarity assignments are most reliable when the same character state is exhibited by several different outgroups. In the preceding example, teeth are generally present in the nearest outgroups of amniotes–amphibians and fish–as well as in many species of amniotes themselves. Consequently, the presence of teeth in mammals and reptiles is considered ancestral, and their absence in birds and turtles is considered derived.

Construction of a cladogram

Once all characters have been polarized, systematists use this information to construct a cladogram, which depicts a hypothesis of evolutionary relationships. Species that share a common ancestor, as indicated by the possession of shared derived characters, are said to belong to a clade. Clades are thus evolutionary units and refer to a common ancestor and all of its descendants. A derived character shared by clade members is called a synapomorphy of that clade. A simple cladogram is a nested set of clades, each characterized by its own synapomorphies. For example, amniotes are a clade for which the evolution of an amniotic membrane is a synapomorphy. Within that clade, mammals are a clade, with hair as a synapomorphy, and so on.
Ancestral states are also called plesiomorphies, and shared ancestral states are called symplesiomorphies. In contrast to synapomorphies, symplesiomorphies are not informative about phylogenetic relationships.
Consider, for example, the character state “presence of a tail,” which is exhibited by lampreys, sharks, salamanders, lizards, and tigers. Does this mean that tigers are more closely related to–and shared a more recent common ancestor with–lizards and sharks than to apes and humans, their fellow mammals? The answer, of course, is no: Because symplesiomorphies reflect character states inherited from a distant ancestor, they do not imply that species exhibiting that state are closely related.

Homoplasy complicates cladistic analysis

In real-world cases, phylogenetic studies are rarely as simple as the examples we have shown so far. The reason is that in some cases, the same character has evolved independently in several cases, the same character has evolved independently in several species. These characters would be categorized as shared derived characters, but they would be false signals of a close evolutionary relationship. In addition, derived characters may sometimes be lost as species within a clade re-evolve to the ancestral state.
Homoplasy refers to a shared character state that has not been inherited from a common ancestor exhibiting that character state. Homoplasy can result from convergent evolution or from evolutionary reversal. For example, adult frogs do not have a tail. Thus, absence of a tail is a synapomorphy that unites not only gorillas and humans, but also frogs. However, frogs are not closely related to gorillas and humans they have neither an amniotic membrane nor hair, both of which are synapomorphies for clades that contain gorillas and humans.
In cases such as this, when there are conflicts among the characters, systematists rely on the principle of parsimony, which favors the hypothesis that requires the fewest assumptions. As a result, the phylogeny that requires the fewest evolutionary events is considered the best hypothesis of phylogenetic relationships. In the example just stated, therefore, grouping frogs with salamanders is favored because it requires only one instance of homoplasy (the multiple origins of taillessness), whereas a phylogeny in which frogs were most closely related to humans and gorillas would require two homoplastic evolutionary events (the loss of both amniotic membranes and hair in frogs.)
The examples presented so fare have all involved morphological characters, but systematists increasingly use DNA sequence data to construct phylogenies because of the large number of characters that can be obtained through sequencing. Cladistics analyzes sequence data in the same manner as any other type of data: Character states are polarized by reference to the sequence of an outgroup, and a cladogram is constructed that minimizes the amount of character evolution required.

Other phylogenetic methods work better than cladistics in some situations

If characters evolve from one state to another at a slow rate compared with the frequency of speciation events, then the principle of parsimony works well in reconstructing evolutionary relationships. In this situation, the principle’s underlying assumption–that shared derived similarity is indicative of recent common ancestry–is usually correct. In recent years, however, systematists have realized that some characters evolve so rapidly that the principle of parsimony maybe misleading.

Rapid rates of evolutionary change and homoplasy

Of particular interest is the rate at which some parts of the genome evolve. As discussed in chapter 18, some stretches of DNA do not appear to have any function. As a result, mutations the occur in these parts of the DNA are not eliminated by natural selection, and thus the rate of evolution of new character states can be quite high in these regions as a result of genetic drift.
Moreover, because only four character states are possible for any nucleotide base (A,C, G, or T), there is a high probability that two species will independently evolve the same derived character state at any particular base position. If such homoplasy dominates the character data set, then the assumptions of the principle of parsimony are violated, and as a result, phylogenies inferred using this method are likely to be inaccurate.

Inquiry question Why do high rates of evolutionary change and a limited number of character states cause problems for parsimony analyses?

Statistical approaches
Because evolution can sometimes proceed rapidly, systematists in recent years have been exploring other methods based on statistical approaches, such as maximum likelihood, to infer phylogenies. These methods start with an assumption about the rate of at which characters evolve and then fit the data to these models to derive the phylogeny that best accords (i.e., “maximally likely”) with these assumptions.
One advantage of these methods is that different assumptions of rate of evolution can be used for different characters. If some DNA characters evolve more slowly than others–for example, because they are constrained by natural selection–then the methods can employ different models of evolution for the different characters. This approach is more effective than parsimony in dealing with homoplasy when rates of evolutionary changes are high.

In general, cladograms only indicate the order of evolutionary branching events they do not contain information about the timing of these events. In some cases, however, branching events can be timed, either by reference to fossils, or by making assumptions about the rate at which characters change. One widely used but controversial method is the molecular clock, which states that the rate of evolution of a molecule is constant through time. In this model, divergence in DNA can be used to calculate the times at which branching events have occurred. To make such estimates, the timing of one or more divergence events must be confidently estimated. For example, the fossil record may indicate that two clades diverged from a common ancestor at a particular time. Alternatively, the timing of separation of two clades may be estimated from geological events that likely led to their divergence, such as the rise of a mountain that now separates the two clades. With this information, the amount of DNA divergence separating the two clades, which produces an estimate of the rate of DNA divergence per unit of time (usually, per million years). Assuming a molecular clock, this rate can then be used to date other divergence events in a cladogram.
Although the molecular clock appears to hold true in some cases, in many others the data indicate that rates of evolution have not been constant through time across all branches in an evolutionary tree. For this reason, evolutionary dates derived from molecular data must be treated cautiously. Recently, methods have been developed to date evolutionary events without assuming that molecular evolution has been clocklike. These methods hold great promise for providing more reliable estimates of evolutionary timing.

Learning Outcomes Review 23.2

In cladistics, derived character states are distinguished from ancestral character states, and species are grouped based on shared derived character states. Derived characters are determined from comparison to a group known to be closely related, termed an outgroup. A clade contains all descendants of a common ancestor. A cladogram is a hypothetical representation of evolutionary relationships based on derived character states. Homoplasies may give a false picture of relationships.

Why is cladistics more successful at inferring phylogenetic relationships in some cases than in others?
Why are only shared derived, instead of all derived, characters useful in cladistics for reconstructing phylogenies?

23.3 Systematics and Classification

Learning Outcomes
1. Differentiate among monophyletic, paraphyletic, and polyphyletic groups.
2. Explain the meaning of the phylogenetic species concept and why it is controversial.

Whereas systematics is the reconstruction and study of evolutionary relationships, classification refers to how we place species and higher groups–genus, family, class, and so forth–into the taxonomic hierarchy (a topic we discuss in greater detail in chapter 26).

Current classification sometimes does not reflect evolutionary relationships

Systematics and traditional classification are not always congruent to understand why, we need to consider how species may be grouped based on their phylogenetic relationships. A monophyletic group includes the most recent common ancestor of the group and all of its descendants. By definition, a clade is a monophyletic group. A paraphyletic group includes the most recent common ancestor of the group, but not all of its descendants, and a polyphyletic group does not include the most recent common ancestor of all members of the group.
Taxonomic hierarchies are based on shared traits, and ideally they should reflect evolutionary relationships. Traditional taxonomic groups, however, do not always fit well with new understanding of phylogenetic relationships. For example, birds have historically been placed in the class Aves, and dinosaurs have been considered part of the class Reptilia. But recent phylogenetic advances make clear that birds evolved from dinosaurs. The last common ancestor of all birds and a dinosaur was a meat-eating dinosaur.
Therefore, having two separate monophyletic groups, one for birds and one for reptiles (including dinosaurs and crocodiles, as well as lizards, snakes, and turtles), is not possible based on phylogeny. And yet the terms Aves and Reptilia are so familiar and well established that suddenly referring to birds as a type of of dinosaur, and thus a type of reptile, is difficult for some. Nonetheless, biologists increasingly refer to birds as a type of dinosaur and hence a type of reptile.
Situations like this are not uncommon. Another example concerns the classification of plants. Traditionally, three major groups were recognized: green algae, bryophytes, and vascular plants. However, recent research reveals that neither the green algae nor the bryophytes constitute monophyletic groups. Rather, some bryophyte groups are more closely related to vascular plants than they are to other bryophytes, and some green algae are more closely related to bryophytes and vascular plants than they are to other green algae. As a result, systematists no longer recognize green algae or bryophytes as evolutionary groups, and the classification system has been changed to reflect evolutionary relationships.

The phylogenetic species concept focuses on shared derived characters

In the preceding chapter, you read about a number of different ideas concerning what determines whether two populations belong to the same species. The biological species concept (BSC) defines species as groups of interbreeding populations that are reproductively isolated from other groups. In recent years, a phylogenetic perspective has emerged and has been applied to the question of species concepts. Advocates of the phylogenetic species concept (PSC) propose that the term species should be applied to groups of populations that have been evolving independently of other groups of populations. Moreover, they suggest that phylogenetic analysis is the way to identify such species. In this view, a species is a population or set of populations characterized by one or more shared derived characters.
This approach solves two of the problems with the BSC that were discussed in chapter 22. First, the BSC cannot be applied to allopatric populations because scientists cannot determine whether individuals of the populations would interbreed and produce offspring if they ever came together. The PSC solves this problem: Instead of trying to predict what will happen in the future if allopatric populations ever come into contact, the PSC looks to the past to determine whether a population (or group of populations) has evolved independently for a long enough time to develop its own derived characters.
Second, the PSC can be applied equally well to both sexual and asexual species, in contrast to the BSC, which deals only with sexual forms.

The phylogenetic species concept also has drawbacks

The PSC is controversial, however, for several reasons. First, some critics contend that it will lead to the recognition of every slightly differentiated population as a distinct species. In Missouri, for example, open, desert-like habitat patches called glades are distributed throughout much of the state. These glades contain a variety of warmth-loving species of plants and animals that do not occur in the forests that separate the glades. Glades have been isolated from one another for a few thousand years, allowing enough time for populations on each glade to evolve differences in some rapidly evolving parts of the genome. Does that mean that each of the hundreds, if not thousands, of Missouri glades contains its own species of lizards, grasshopper, and scorpions? Some scientists argue that if one takes the PSC to its logical extreme, that is exactly what would result.
A second problem is that species may not always be monophyletic, contrary to the definition of some versions of the phylogenetic species concept. Consider, for example, a species composed of five populations. Suppose that population C becomes isolated and evolves differences that make it qualify as a species by any concept (for example, reproductively isolated, ecologically differentiated). But this distinction would mean that the remaining populations, which might still be perfectly capable of exchanging genes, would be paraphyletic, rather than monophyletic. Such situations probably occur often in the natural world. Phylogenetic species concepts, of which there are many different permutations, are increasingly used, but are also contentious for the reasons just discussed. Evolutionary biologists are trying to find ways to reconcile the historical perspective of the PSC with the process-oriented perspective of the BSC and other species concepts.

Learning Outcomes Review 23.3

By definition, a clade is monophyletic. A paraphyletic group contains the most recent common ancestor, but not all its descendants a polyphyletic group does not contain the most recent common ancestor of all members. The phylogenetic species concept focuses on the possession of shared derived characters, in contrast to the biological species concept, which emphasizes reproductive isolation. The PSC solves some problems of the BSC but has difficulties of its own.

Under the biological species concept, is it possible for a species to be polyphyletic?

23.4 Phylogenetics and Comparative Biology

Learning Outcomes
1. Explain the importance of homoplasy for interpreting patterns of evolutionary change.
2. Describe how phylogenetic trees can reveal the existence of homoplasy.
3. Discuss how a phylogenetic tree can indicate the timing of species diversification.

Phylogenies not only provide information about evolutionary relationships among species, but they are also indispensable for understanding how evolution has occurred. By examining the distribution of traits among species in the context of their phylogenetic relationships much can be learned about how and why evolution may have proceeded. In this way, phylogenetic is the basis of all comparative biology.

Homologous feature are derived from the same ancestral source homoplastic features are not

In chapter 21, we pointed out that homologous structures are those that are derived from the same body part in a common ancestor. Thus, the forelegs of a dolphin (flipper) and of a horse (leg) are homologous because they are derived from the same bones in an ancestral vertebrate. By contrast, the wings of birds and those of dragonflies are homoplastic structures because they are derived from different ancestral structures. Phylogenetic analysis can help determine whether structures are homologous or homoplastic.

Homologous parental care in dinosaurs, crocodiles, and birds

Recent fossil discoveries have revealed that many species of dinosaurs exhibited parental care. They incubated eggs laid in nests and took care of growing baby dinosaurs, many of which could not have fended for themselves. Some recent fossils show dinosaurs sitting on a nest in exactly the same posture used by birds today! Initially, these discoveries were treated as remarkable and unexpected–dinosaurs apparently had independently evolved behaviors similar to those of modern-day organisms. But examination of the phylogenetic position of dinosaurs indicates that they are most closely related to two living groups of animals–crocodiles and birds–both of which exhibit parental care.
It appears likely, therefore, that the parental care exhibited by crocodiles, dinosaurs, and birds did not evolve convergently from different ancestors that did not exhibit parental care rather, the behaviors are homologous, inherited by each of these groups from their common ancestor that cared for its young.

Homoplastic convergence: Saber teeth and plant conducting tubes

In other cases, by contrast, phylogenetic analysis can indicate that similar traits have evolved independently in different clades. This convergent evolution from different ancestral sources indicates that such traits represent homoplasies. As one example, the fossil record reveals that extremely elongated canine teeth (saber teeth) occurred in a number of different groups of extinct carnivorous mammals. Although how these teeth were actually used is still debated, all saber-toothed carnivores had body proportions similar to those of cats, which suggests that these different types of carnivores all evolved into a similar predatory lifestyle. Examination of the saber-toothed character state in a phylogenetic context reveals that it most likely evolved independently at least three times.
Conducting tubes in plants provide a similar example. The tracheophytes, a large group of land plants discussed in chapter 30, transport photosynthetic products, hormones, and other molecules over long distances through elongated , tubular cells that have perforated walls at the end. These structures are stacked upon each other to create a conduit called a sieve tube. Sieve tubes facilitate long-distance transport that is essential for the survival of tall plants on land.
Most members of the brown algae, which includes kelp, also have sieve elements that aid in the rapid transport of materials. The land plants and brown algae are distantly related, and their last common ancestor was a single-celled organism that could not have had a multicellular transport system. This indicates that the strong structural and functional similarity of sieve elements in these plant groups is an example of convergent evolution.

Complex characters evolve through a sequence of evolutionary changes

Most complex character do not evolve, fully formed, in one step. Rather, they are often built up, step-by-step, in a series of evolutionary transitions. Phylogenetic analysis can help discover these evolutionary sequences.
Modern-day birds–with their wings, feathers, light bones, and breastbone–are exquisitely adapted flying machines. Fossil discoveries in recent years now allow us to reconstruct the evolution of these features. When the fossils are arranged phylogenetically, it becomes clear that the features characterizing living birds did not evolve simultaneously. The features important to flight evolved sequentially, probably over a long period of time, in the ancestors of modern birds.
One important finding often revealed by studies of the evolution of complex characters is that the initial stages of a character evolved as an adaptation to some environmental selective pressure different from that for which the character is currently adapted. The first feathery structures evolved deep in the theropod phylogeny, in animals with forearms clearly not modified for flight. Therefore, the initial feather-like structures must have evolved for some other reason, perhaps serving as insulation or decoration. Through time, these structures have become modified to the extent that modern feathers produce excellent aerodynamic performance.

Phylogenetic methods can be used to distinguish between competing hypotheses

Understanding the causes of patterns of biological diversity observed today can be difficult because a single pattern of ten could have resulted from several different processes. In many cases, scientists can use phylogenies to distinguish between competing hypotheses.

Larval dispersal in marine snails

An example of this use of phylogenetic analysis concerns the evolution of larval forms in marine snails. Most species of snails produce microscopic larvae that drift in the ocean currents, sometimes traveling hundreds or thousands of miles before becoming established and transforming into adults. Some species, however, have evolved larvae that settle to the ocean bottom very quickly and thus don’t disperse far from their place of origin. Studies of fossil snails indicate that the proportion of species that produce nondispersing larvae has increased through geological time.
Two processes could produce an increase in nondispersing larvae through time. First, if evolutionary change from dispersing to non dispersing occurs more often than change in the opposite direction, then the proportion of species that are non-dispersing would increase through time.
Alternatively, if species that are non dispersing speciate more frequently, or become extinct less frequently, than dispersing species, then through time the proportion of nondispersers would also increase (assuming that the descendants of non dispersing species also were nondispersing). This latter case is a reasonable hypothesis because nondispersing species probably have lower amounts of gene flow than dispersing species, and thus might more easily become geographically isolated, increasing the likelihood of allopatric speciation.
These two process would result in different phylogenetic patterns. If evolution from a dispersing ancestor to a non-dispersing descendant occurred more often than the reverse, then an excess of such changes should be evident in the phylogeny, as shown by more dispersing –> nondispersing branchpoints. In contrast, if nondispersing species underwent greater speciation, then clades of nondispersing species would contain more species than clades of dispersing species.
Evidence for both processes was revealed in an examination of the phylogeny of marine snails in the genus Conus, in which 30% of species are nondispersing. The phylogeny indicates that possession of dispersing larvae was the ancestral state nondispersing larvae are inferred to have evolved eight times, with no evidence for evolutionary reversal from nondispersing to dispersing larvae.
At the same time, clades of nondispersing larvae tend to have on average 3.5 times as many species as dispersing larvae, which suggests that in nondispersing species, rates of speciation are higher, rates of extinction are lower, or both.
This analysis therefore indicates that the evolutionary increase in nondisperisng larvae through time may be a result both of a bias in the direction in which evolution proceeds plus an increase in rate of diversification (that is, speciation rate minus extinction rate) in nondispersing clades.
The lack of evolutionary reversals is not surprising because when larvae evolve to become nondispersing, they often lose a variety of structures used for feeding while drifting in the ocean current. In most cases, once a structure is lost, it rarely re-evolves, and thus the standard view is that the evolution of nondispersing larvae is a one-way street, with few examples of re-evolution of dispersing larvae.

Loss of the larval stage in marine invertebrates

A related phenomenon in many marine invertebrates is the loss of the larval stage entirely. Most marine invertebrates–in groups as diverse as snails, sea stars, and anemones–pass through a larval stage as they develop. But in a number of different types of organisms, the larval stage is omitted, and the eggs develop directly into adults.
The evolutionary loss of the larval stage has been suggested as another example of a nonreversible evolutionary change because once the larval stages are lost, it is difficult for them to re-evolve–or so the argument goes. A recent study on one group of marine limpets, shelled marine organisms related to snails, shows that this is not necessarily the case. Among these limpets, direct development has evolved many times however, in three cases, the phylogeny strongly suggests that evolution reversed and a larval stage re-evolved.
It is important to remember that patterns of evolution suggested by phylogenetic analysis are not alway correct–evolution does not necessarily occur parsimoniously. In the limpet study, for example, it is possible that within a clade, presence of a larva was retained as the ancestral state, and direct development evolved independently six times. Phylogenetic analysis cannot rule out this possibility, even if it is less phylogenetically parsimonious.
If the re-evolution of lost traits seems unlikely, then the alternative hypothesis that direct development evolved six times–rather than only once at the base of the clade, with two instances of evolutionary reversal–should be considered. For example, studies of the morphology or embryology of direct-developing species might shed light on whether such structures are homologous or convergent. In some cases, artificial selection experiments in the laboratory or genetic manipulations can test the hypothesis that it is difficult for lost structures to re-evolve. Conclusions from phylogenetic analyses are always stronger when supported by results of other types of studies.

Phylogenetics helps explain species diversification

One of the central goals of evolutionary biology is to explain patterns of species diversity: Why do some types of plants and animals exhibit more species richness–a greater number of species per clade–than others? Phylogenetic analysis can be used both to suggest and to test hypotheses about such differences.

Species richness in beetles

Beetles (order Coleoptera) are the most diverse group of animals. Approximately 60% of all animal species are insects, and approximately 80% of all insect species are beetles. Among beetles, families that are herbivorous are particularly species-rich.
Examination of the phylogeny provides insight into beetle evolutionary diversification. Among the Phytophaga, the clade which contains most herbivorous beetle species, the deepest branches belong to beetle families that specialize on conifers. This finding agrees with the fossil record because conifers were among the earliest seed plant groups to evolve. By contrast, the flowering plants (angiosperms) evolved more recently, in the Cretaceous, and beetle families specializing on them have shorter evolutionary branches, indicating their more recent evolutionary appearance.
This correspondence between phylogenetic position and timing of plant origins suggests that beetles have been remarkably conservative in their diet. The family Nemonychidae, for example, appears to have remained specialized on conifers since the beginning of the Jurassic, approximately 210 MYA.

Phylogenetic explanations for beetle diversification

The phylogenetic perspective suggests factors that may be responsible for the incredible diversity of beetles. The phylogeny for the Phytophaga indicates that it is not the evolution of herbivory itself that is linked to great species richness. Rather, specialization on angiosperms seems to have been a prerequisite for great species diversification. Specialization on angiosperms appears to have arisen five times independently within herbivorous beetles in each case, the angiosperm-specializing clade is substantially more species-rich than the clade to which it is most closely related (termed a sister clade) and which specializes on some other type of plant.
Why specialization on angiosperms has led to great species diversity is not yet clear and is the focus of much current research. One possibility is that this diversity is linked to the great species-richness of angiosperms themselves. With more than 250,000 species of angiosperms, beetle clades specializing on them may have had a multitude of opportunities to adapt to feed on different species, thus promoting divergence and speciation.

Learning Outcomes Review 23.4

Homologous traits are derived from the same ancestral character states, whereas homoplastic traits are not, even though they may have similar function. Phylogenetic analysis can help determine whether homology or homoplasy has occurred. By correlating phylogenetic branching with known evolutionary events, the timing and cause of diversification can be inferred.

Does the possession of the same character state by all members of a clade mean that the ancestor of that clade necessarily possessed that character state?

23.5 Phylogenetics and Disease Evolution

Learning Outcome
1. Discuss how phylogenetic analysis can help identify patterns of disease transmission.

The examples so far have illustrated the use of phylogenetic analysis to examine relationships among species. Such analyses can also be conducted on virtually any group of biological entities, as long as evolutionary divergence in these groups occurs by a branching process, with little or no genetic exchange between different groups. No example illustrates this better than recent attempts to understand the evolution of the virus that causes autoimmune deficiency syndrome (AIDS).

HIV has evolved from a simian viral counterpart

AIDS was first recognized in the early 1980s, and it rapidly became epidemic in the human population. Current estimates are that ore than 33 million people are infected with the human immunodeficiency virus (HIV), of whom more than 2 million die each year.
At first, scientists were perplexed about where HIV had originated and how it had infected humans. In the mid-1980s, however, scientists discovered a related virus in laboratory monkeys, termed simian immunodeficiency virus (SIV). In biochemical terms, the viruses are very similar, although genetic differences exist. At last count, SIV has been detected in 36 species of primates, but only in species found in sub-Saharan Africa. Interestingly, SIV–which appears to be transmitted sexually–does not appear to cause illness in some of these species.
Based on the degree of genetic differentiation among strains of of SIV, scientists estimate that SIV may have been around for more than a million years in these primates, perhaps providing enough time for these species to adapt to the virus and thus prevent it from having adverse effects.

Phylogenetic analysis identifies the path of transmission

Phylogenetic analysis of strains of HIV and SIV reveals three clear findings. First, HIV obviously descended from SIV. All strains of HIV are phylogenetically nested within the clades of SIV strains, indicating that HIV is derived from SIV.
Second, a number of different strains of HIV exist, and they appear to represent independent transfers from different primate species. Each of the human strains is more closely related to a strain of SIV than it is to other HIV strains, indicating separate origins of the HIV strains.
Finally, humans have acquired HIV from different host species. HIV-1, which is the virus responsible for the global epidemic, has four subtypes. Two of these subtypes are most closely related to strains in chimpanzees, whereas a third is most closely related to a strain in gorillas, indicating transmission from both ape species. The origin of the fourth subtype is not clear further sampling will likely reveal it to be the sister taxon to a currently undiscovered chimp or a gorilla strain.
By contrast, subtypes of HIV-2, which is much less widespread (in some cases known from only one individual), are related to SIV found in West African monkeys, primarily the sooty mangabey (Cercocebus atys). Moreover, the subtypes of HIV-2 also appear to represent multiple cross-species transmission to humans.

Transmission from other primates to humans

Several hypotheses have been proposed to explain how SIV jumped from chimps and monkeys to humans. The most likely idea is that transmission occurred as the result of blood-to-blood contact that may occur when humans kill and butcher monkeys and apes. Recent years have seen a huge increase in the rate at which primates are hunters for the “bush-meat” market, particularly in central and western Africa. This increase has resulted from a combination of increased human populations desiring ever greater amounts of protein, combined with increased access to the habitats in which these primates live as a result of road building and economic development. The unfortunate result is that population sizes of many primate species, including our closest relatives, are plummeting toward extinction. A second consequence of this hunting is that humans are increasingly brought into contact with bodily fluids of these animals, and it is easy to imagine how during the butchering process, blood from a recently killed animal might enter the human bloodstream through cuts in the skin, perhaps obtained through the hunting process.

Establishing the crossover time line and location

Where and when did this cross-species transmission occur? HIV strains are most diverse in Africa, and the incidence of HIV is higher there than elsewhere in the world. Combined with the evidence that HIV is related to SIV in African primates, it seems certain that AIDS appeared first in Africa.
As for when the jump from other primates to humans occurred, the fact that AIDS was not recognized until the 1980s suggests that HIV probably arose recently. Descendants of slaves brought to North America from West Africa in the 19th century lacked the disease, indicating that it probably did not occur at the time of the slave trade.
Once the disease was recognized in the 1980s, scientists scoured repositories of blood samples from the past. The earliest HIV-positive result was found in a sample from 1959, pushing the date of origin back at least two decades. Based on the amount of genetic difference between strains of HIV-1 including the 1959 sample, and assuming the operation of a molecular clock, scientists estimate that the deadly strain of AIDS probably crossed into humans some time before 1940.

Phylogenies can be used to track the evolution of AIDS among individuals

The AIDS virus evolves extremely rapidly, so much so that different strains can exist within a single individual in a single population. As a result, phylogenetic analysis can be applied to answer very specific questions just as phylogeny proved useful in determining the source of HIV, it can also pinpoint the source of infection for particular individuals.
This ability became apparent in a court case in Louisiana in 1998, in which a dentist was accused of injecting his former girlfriend with blood drawn from an HIV-infected patient. The dentist’s records revealed that he had drawn blood from the patient and had done so in a suspicious manner. Scientists sequenced the viral strains from the victim, the patient, and from a large number of HIV-infected people in the local community. The phylogenetic analysis clearly demonstrated that the victim’s viral strain was most closely related to the patient’s. This analysis, which for the first time established phylogenetics as a legally admissible form of evidence in courts in the United States, helped convict the dentist, who is now serving a 50-year sentence for attempted murder.

Learning Outcome Review 23.5

Modern phylogenetic techniques and analysis can track the evolution of disease strains, uncovering sources and progression. The HIV virus provides a prime example: Analysis of viral strains has shown that the progression from simian immunodeficiency virus (SIV) into human hosts has occurred several times. Phylogenetic analysis is also used to track the transmission of human disease.

Could HIV have arisen in humans and then have been transmitted to other primate species?

23.1 Systematics
Branching diagrams depict evolutionary relationships.
Systematics is the study of evolutionary relationships, which are depicted on branching evolutionary trees, called phylogenies.
Similarity may not accurately predict evolutionary relationships.
The rate of evolution can vary among species and can even reverse direction. Closely related species can therefore be dissimilar in phenotypic characteristics.
Conversely, convergent evolution results in distantly related species being phenotypically similar.

23.2 Cladistics
The cladistic method requires that character variation be identified as ancestral or derived.
Derived character states are those that differ from the ancestral condition. Only shared derived characters are useful for inferring phylogenies.
Character polarity is established using an outgroup comparison in which the outgroup consists of one or a group of species, relative to the group under study.
Character states exhibited by the outgrip are assumed to be ancestral, and other character states are considered derived.
A cladogram is a graphically represented hypothesis of evolutionary relationships.
Homoplasy complicates cladistic analysis.
Homoplasy refers to a shared character state, such as wings of birds and wings of insects, that has not been inherited from a common ancestor.
Cladograms are constructed based on the principle of parsimony, which indicates that the phylogeny requiring the fewest evolutionary changes is accepted as the best working hypothesis.
Other phylogenetic methods work better than cladistics in some situations.
When evolutionary change is rapid, other methods, such as statistical approaches and the use of the molecular clock, are sometimes more useful.

23.3 Systematics and Classification
Current classification sometimes does not reflect evolutionary relationships.
A monophyletic group consists of the most recent common ancestor and all of its descendants.
A paraphyletic group consists of the most recent common ancestor and some of its descendants.
A polyphyletic group does not contain the most recent ancestor of the group.
Some currently recognized taxa are not monophyletic, such as reptiles, which are paraphyletic with respect to birds.
The phylogenetic species concept focuses on shared derived characters.
The phylogenetic species concept (PSC) emphasizes the possession of shared derived characters, whereas the biological species concept focuses on reproductive isolation. Many versions of this concept recognize species that are monophyletic.
The phylogenetic species concept also has drawbacks.
Among criticisms of the PSC are that it subdivides groups too far via impractical distinctions, and that the PSC definition of a group may not always apply as selection proceeds.

23.4 Phylogenetics and Comparative Biology
Homologous features are derived from the same ancestral source homoplastic features are not.
Homologous structures can be identified by phylogenetic analysis, establishing whether or not different structures have been built from the same ancestral structure.
Complex characters evolve through a sequence of evolutionary changes.
Most complex features do not evolve in a single step but include stages of transition. They may have begun as an adaptation to a selective pressure different from the one for which the feature is currently adapted.
Phylogenetic methods can be used to distinguish between competing hypotheses.
Different evolutionary scenarios can be distinguished by phylogenetic analysis. The minimum number of times a trait may have evolved can be established, and the direction of trait evolution, the timing, and the cause of diversification can be inferred.
Phylogenetics helps explain species diversification.
Questions regarding the causes of species richness may be addressed with phylogenetic analysis.

23.5 Phylogenetics and Disease Evolution
HIV has evolved from a simian viral counterpart.
Phylogenetic methods have indicated that HIV is related to SIV.
Phylogenetic analysis identifies the path of transmission.
It is clear that HIV has descended from SIV, and that independent transfers from simians to humans have occurred several times.
Phylogenies can be used to track the evolution of AIDS among individuals.
Even though HIV evolves rapidly, phylogenetic analysis can trace the origin of a current strain to a specific source of infection.

What are Homoplastic features Homoplasy?

A homoplasy is a character shared by a set of species but not present in their common ancestor. A good example is the evolution of the eye which has originated independently in many different species. When this happens it is sometimes called a convergence.

Subsequently, question is, what is the difference between homology and Homoplasy? Homology is a product of divergent evolution. This means that a single ancestor species split, or diverges, into two or more species at some time in its history. Homoplasy, on the other hand, is due to convergent evolution. Here, different species develop, rather than inherit, similar traits.

Hereof, what are the causes of Homoplasy?

Patterns of homoplasy Homoplasy can occur by convergence or by parallelism. Convergence describes similarities between two species that evolved independently from different features in their common ancestor.

How do you identify Homoplasy?

If they fall out as symplesiomorphies or synapomorphies in a phylogenetic analysis, their status as homologies remains unfalsified. If they fall out as homoplasies, having evolved independently in more than one clade, their status as homologous is falsified, and a homoplasy is identified.

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits? - Biology

Today, taxonomists construct phylogenetic trees to depict relationships among groups of organisms. It has always been a way to organize the millions of species found on the planet, in some sensible way, by grouping them according to similarities.

We group objects in all sorts of storage areas for the same reason.

You want to buy some cheese for lunch. Do you wander up and down the aisles of a large supermarket without direction until you find the type of cheese you want? No! you go to the dairy or deli section.

These organizations can be used for more than simply increasing our ability to find "like items."

We may expand our knowledge about cheeses by trying samples or watching some demo on how to use a particular type of cheese.

There are two types of classification systems currently in use to construct phylogenetic trees. Each has own "philosophy" regarding the traits or "characters" as they are known used to group organisms.

One is known as evolutionary systematics or simply the classic or traditional method because it is the oldest of the two used.

It attempts to show relationships that depict the lineage or history of descent of a particular group.

It uses as its basic unit or taxa the species. Each species has a name consisting of two words. Note the first word in the examples below are capitalized and the entire name is italicized or underlined.

Canis lupus

Panthera pardus

Eublepharis macularius

Groups form a collective hierarchy (nested grouping) from species to domain. Each higher or larger unit contains one or more groups from lower level.

Kingdom: Animalia

Phylum: Chordata

Class: Mammalia

Order: Carnivora

Family: Canidae

Subfamily: Caninae

Tribe: Canini

Genus: Canis

Species: C. lupus

Taxa distinctions are made following the basic tenet "Taxonomy should reflect phylogeny (evolutionary history=relatedness)." Two species in one taxa at any level must be more closely related (share more in common from descent) to each other than to species in other taxa at the same level.

So, recognizing and using characters that are homologous is important.

Homologous: Structurally similar due to common ancestry. Having the same evolutionary origin but not necessarily the same function.

as opposed to analogous because of convergent evolution. Analogous structures have separate evolutionary origins.

Be able to explain for the diagram below why bat wings and bird wings are examples of convergent evolution or analogous and not homologous.


But remember scientists can construct taxa following homology even if some are older, or some are larger and contain more species than equivalent taxa.

There are more differences between some taxa of equal standing in traditional or evolutionary systematics than accepted by the next school of classification we will discuss. .

Example: The Vertebrate classes recognized in evolutionary systematics, such as Amphibia, Reptilia, Aves and Mammalia.

1. Aves (birds) and Mammalia are younger classes than Amphibia and Reptilia. Both birds and mammals descended from closely related ancestors yet there are more differences between mammals and some modern reptiles than birds and some modern reptiles

2. The platypus could be classified as a mammal or reptile. It has hair and mammary glands that are simple slits. It lays eggs and the skeleton, if only known from fossil limbs and vertebrae, would appear reptilian.

3. Should Chordata be a phylum, given the small number of species in it? Arthropoda contains about 1.25 million described species, Chordata contains only 43,000 species.

So one does not know by simply looking at a tree in evolutionary or traditional systematics whether branching arrangements are based mainly on certain characters or the ancestor shared.

It is this lack of limits, and so in some sense predictive and hypothesis testing value of the trees constructed, via evolutionary systematics, that has led to the greater acceptance today of the second method or cladistics/phylogenetics.

The second school attempts to be more "scientific" and uses more rules in constructing groups, which it terms clades. It is formally known as the phylogenetics approach or more commonly as cladistics.

Phylogenetics or cladistics

This is now the accepted way to classify organisms. It is slowly replacing the evolutionary approach in textbooks. Cladistics is a type of systematics developed by Willi Hennig, who attempted to develop a more scientific method of classifying organisms. This scheme only uses one type of homology (derived) for construction of "clades". Molecular phylogenetic analysis was being at the same time practiced by biologists who were using DNA and/or RNA sequences to group animals but with the same objectives postulated by Hennig. The two approaches have merged for the most part in what is now know formally as phylogenetics or informally as cladistics. Most cladists in fact use molecular data to construct cladograms.

It uses strict monophyly as the only criterion for grouping related species. In cladistic taxonomy, evolution is seen as a process of progressive bifurcations of lineages. Every species, therefore, has a sister species whether recognizable or not, and this pair is derived from an ancestral species.


Cladistics depends on identifying shared derived characters. or synapomorphies. Cladists then distinguish between different types of homologies.

A derived homology or synapomorphy is unique to a particular group of species (and their ancestor), while a shared ancestral homology is found in the ancestor of a group of species but only in some of its descendants.

One way of looking at synapomorphies is that they define nodes, groups of sister species and their closest relative. The very formal and rigorous way synapomorphies and nodes are used, make the trees drawn, true lineage trees.

In the diagram below the clades or groups are indicated at top, for example, Vertebrates and Tetrapods. The shared derived characters for a clade are indicated below the clade, so the tetrapod "clade" all have four limbs, but no other clade has this characteristic and it is a "new" or derived trait (not an ancestral trait or trait found in an remote ancestor to this clade). Again, each branch point is known as a node.

A more detailed tree

A bit on terms used in the diagram above. You should be aware of vertebrate relationships. Please use the explanations below to learn more about the synapomorphies use to divide vertebrates into clades.

Archosaur--------Synapomorphies of archosaurs include
teeth set in sockets,
antorbital and mandibular fenestrae (openings in front of the eyes and in the jaw, respectively) that make skull lighter,
and a fourth trochanter (a prominent ridge on the femur) which provides more surface for muscle attachment.

Anapsid (none), Synapsid (one) and Diapsid (two)
Synapsids contain one ancestral skull opening or temporal fenestrae

Diapsids contain their two ancestral skull openings (temporal fenestrae) posteriorly above and below the eye. This arrangement allows for the attachment of larger, stronger jaw muscles, and enables the jaw to open more widely

A better view of a diapsid skull, but note the fenestrae or holes in front of the eye of alligators and crocodiles have disappeared.

Note: The classification scheme diagrammed revises what we believed formally about vertebrate evolution. Mammals did not evolve as portrayed in many popular movies and books from reptiles. Mammalia is an line as old as the line leading to reptiles.

An good example of why phylogenetics is considered more representative of "true" evolutionary relationships.

We will take as example the relationships between reptiles, more specifically dinosaurs, and birds. In traditional taxonomy, Aves, or birds, are considered a class equivalent to the class Reptilia. In Cladistics they are simple considered a type of extant reptile, because no synapomorphy divides them from the dinosaur line. In other words there were dinosaurs that had feathers, and the modifications to the limbs and skeleton that typify modern birds.

Visit these websites to learn more about the relationships between birds and dinosaurs.

In the top right corner of one of the websites you visited,is a teaching resource on the evolution of flight.

Visit from there or the links below the following explorations in the teaching resource.

If you are not familiar with bird anatomy visit the first two modules

To answer questions on homework:

Please review modules 3-6.

The last three to four modules of this exercise on flight should convince you that what we consider dinosaurs had many of the adaptations we associate today with birds, and so in some sense, birds are just small feathered dinosaurs. There is no separation of birds into a separate clade in cladistics for this reason.

What if the group you are studying does not have a good fossil record?

In lieu of fossils, outgroups can be used. Outgroups are a group that branched from the ancestral group before the groups being classified branched from each other. Outgroups are used by many biologists who use molecular data to build trees because often they cannot determine which came first from an array of nucleotide sequences. Outgroups here can indicate the most primitive sequence and so can be used to "root" a tree.

Cautions on using textbooks in general during the transition between evolutionary systematics and cladistics.

Many textbooks superimpose the names of the evolutionary systematics (also known as the classic or traditional school) for taxa, although these do not formally exist in phylogenetics/cladistics. This right now just adds to the confusion, although in time it may help define what are know as crown clades or the larger groupings in the evolutionary school such as kingdoms, and phyla. That is if the cladistics school can get all involved to agree on which crown clades should be phyla, etc.

In all systems one needs some method to choose among competing trees, although this should be less of a problem with cladistics.

We can use parsimony or essentially pick the tree that minimizes the amount of evolutionary change that has taken place.

We can also see which tree best fits different types of evidence or determine which tree also fits evidence from other areas of biology or science, such as biogeography.

We will explore the usefulness of phylogenetic trees in our next two lessons. As a preview to this, examine the following trees for the genotypes of Hepatitis C in a doctor, his patients and others in the community.

Did the surgeon give his patient Hepatitis C? The letters indicate samples from different parts of the surgeons and patients genome.

20.2 Determining Evolutionary Relationships

To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections among organisms. Using morphological and molecular data, scientists identify both homologous and analogous characteristics and genes. (In a prior chapter we explored the differences between homologous and analogous traits and how they relate to convergent and divergent evolution.) Similarities among organisms stem either from shared ancestral history (homologies) or from separate evolutionary paths (analogies). Cladograms are constructed by using shared derived traits to distinguish different groups of species from one another. For example, lizards, rabbits and humans all descended from a common ancestor that had an amniotic egg thus, lizards, rabbits, and humans all belong to the same clade. Vertebrata is a larger clade that also includes fish, lamprey, and lancelets. The closer two species or groups are located to each on a phylogenetic tree or cladogram, they more recently they shared a common ancestor. With the influx of new information, scientists can revise phylogenetic trees for example, computer programs, such as one called BLAST, which helps determine relatedness using DNA sequencing. Typically, a phylogenetic tree is constructed with the simplest explanation of evolutionary history (maximum parsimony) and the fewest number of evolutionary steps.

Understanding phylogeny extends far beyond understanding the evolutionary history of species on Earth. For botanists, phylogeny acts as a guide to discovering new plants that can be used to make food, medicine, and clothing. For doctors, phylogenies provide information about the origin of diseases and how to treat them, for example, HIV/AIDS.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 1 of the AP ® Biology Curriculum Framework. The AP ® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 1 The process of evolution drives the diversity and unity of life.
Enduring Understanding 1.A Change in the genetic makeup of a population over time is evolution.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question.
Learning Objective 1.9 The student is able to evaluate evidence provided by data from many scientific disciplines that support biological evolution.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 5.2 The student can refine observations and measurements based on data analysis.
Learning Objective 1.10 The student is able to refine evidence based on data from many scientific disciplines that support biological evolution.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 4.2 The student can design a plan for collecting data to answer a particular scientific question.
Learning Objective 1.11 The student is able to design a plan to answer scientific questions regarding how organisms have changed over time using information from morphology, biochemistry, and geology.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales.
Learning Objective 1.12 The student is able to connect scientific evidence from many scientific disciplines to support the modern concept of evolution.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain.
Science Practice 2.1 The student can justify the selection of a mathematical routine to solve problems.
Learning Objective 1.13 The student is able to construct and/or justify mathematical models, diagrams or simulations that represent processes of biological evolution.
Big Idea 1 The process of evolution drives the diversity and unity of life.
Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry.
Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Science Practice 3.1 The student can pose scientific questions.
Learning Objective 1.14 The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insight into the history of life on Earth.
Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas.
Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms.
Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Science Practice 6.1 The student can justify claims with evidence.
Learning Objective 1.16 The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.
Science Practice 3.1 The student can pose scientific questions.
Learning Objective 1.17 The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram.
Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.
Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question.
Learning Objective 1.18 The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or simple cladogram to determine evolutionary history and speciation.
Essential Knowledge 1.B.2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.
Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain.
Science Practice 2.1 The student can justify the selection of a mathematical routine to solve problems.
Learning Objective 1.19 The student is able to create a phylogenetic tree or simple cladogram that correctly represents evolutionary history and speciation from a provided data set.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 1.15][APLO 1.16][APLO 1.18][APLO 1.17][APLO 1.19][APLO 1.26]

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 they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures. This is an example of morphological homology (Figure 20.7).

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.

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 20.8).

Similar traits can be either homologous or analogous. Homologous structures share a similar embryonic origin analogous organs have a similar function. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. These structures are not analogous. The wings of a butterfly and the wings of a bird are analogous but not homologous. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.

Link to Learning

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

  1. The mitochondrial DNA of the two other domains resembles that of other eukaryotes.
  2. The chloroplasts of eukaryotes contain a double cell layer.
  3. All eukaryotic genes are identical to either Archaea or Bacteria.
  4. Some eukaryotic genes resemble those of Archaea, some resemble those of Bacteria, and some are unlike the genes of either domain.

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.

Evolution Connection

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 diseases, 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 20.9). 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.

Examine how the parts of the displayed figure relate to each other. Part b of the figure shows a hypothetical model of the evolution of the cell membrane of gram-negative bacteria, which has a double membrane. If this hypothesis is true, which explanation supports what it suggests about the evolution of mitochondria and chloroplasts in eukaryotic cells and explains why that is the case?

  1. Chloroplasts and mitochondria did not come about through endosymbiosis with gram-negative bacteria because these organelles have a single membrane.
  2. Chloroplasts and mitochondria likely evolved later in eukaryotic cells, as these organelles show no similarities to prokaryotes.
  3. Chloroplasts and mitochondria came about through endosymbiosis with Archaea and gram-positive bacteria because these organelles have prokaryote-like DNA.
  4. Chloroplasts and mitochondria came about through endosymbiosis with gram-negative bacteria because these organelles have a double membrane.

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 20.10, 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.

Visual Connection

  1. Yes, because it shows the prokaryotes and eukaryotes use similar organelles, namely, mitochondria.
  2. Yes, because it suggests the eukaryotes possess traits that were likely conserved from prokaryotic ancestors.
  3. No, because mitochondrial DNA is very different from the DNA within a eukaryote’s nucleus.
  4. No, because mitochondrial DNA is not used by the eukaryotic cells.

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 20.11 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.

Visual Connection

  1. Glycolysis has been conserved despite the independent evolution of the three domains of life.
  2. Prokaryotes would likely not benefit from the Krebs cycle or the ETC.
  3. Prokaryotes likely evolved after eukaryotes.
  4. Glycolysis is the only way in which living things can break down glucose.

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 20.10 is a shared ancestral character. Now consider the amniotic egg characteristic in the same figure. Only some of the organisms in Figure 20.10 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 20.10, 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, which means that events occurred in the simplest, most obvious way. For example, if a group of people entered a forest preserve to go hiking, based on the principle of maximum parsimony, one could predict that most of the people would hike on established trails rather than forge new ones.

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.

Link to Learning

Head to this website to learn how maximum parsimony is used to create phylogenetic trees.

  1. the similarities among organisms
  2. the differences among organisms
  3. the evolution of the shape, size and number of body parts
  4. the relative times in the past that species shared common ancestors

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.

Science Practice Connection for AP® Courses


Using a data set provided by your teacher or other sources, construct a phylogenetic tree or cladogram to reflect the evolutionary history among a group of organisms based on shared characteristics. Then share the phylogenetic tree or cladogram with peers for review and revision.

AP ® Biology Investigative Labs: Inquiry-Based Approach, Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST. Students will learn to use a common tool, BLAST, to compare several genes from different organisms and then use this information to construct a cladogram to determine evolutionary relatedness among species. Then students will use BLAST to track a gene(s) of choice through several species. Bioinformatics has many applications, including understanding genetic disease.

Think About It

Why must scientists distinguish between homologous and analogous characteristics before building phylogenetic trees? Do more closely related organisms share homologous or analogous traits? Which type of trait is used to support convergent or divergent evolution?

Caio Maximino

The first approach to evolutionary neuroscience, sometimes, is made by individuals who have a good grasp of neuroscience themes, but little comprehension of some questions of evolutionary biology &ndash at least, that was my case! What follows is a short explanation of the concept of &ldquosameness&rdquo in evolutionary biology. I will attempt to relate the manifold concept of sameness to different theoretical frameworks, and will use evolutionary neuroscience as long as it is possible.

Homology and homoplasy

The concept of homology is central to biology. It originated in comparative biology, systematics and evolutionary biology, but is also used in developmental and molecular biology. It is a &ldquonatural kind term&rdquo, in the sense that homologues are characters of organisms that are grouped together because they have a unity of form, which is assumed to be due to some non-trivial underlying mechanism &ndash as opposed to being a &ldquonormative kind term&rdquo, in the sense that homologues would be characters of organisms that are grouped together arbitrarily (Wagner, 1996) &ldquoHomology&rdquo refers to similarity by conservation &ndash that is, a given character or trait in species A is homologous to a trait in species B if it can be demonstrated that the character was conserved in evolution, which means that it is primitive . In general, inferences of homology involve techniques to determine the &ldquoancestor state&rdquo of the character &ndash that is, if it was present or absent in the closest common ancestor of both species A and B. For example, cladistic analysis established that the ventral subpallial nuclei of teleosts is homologous to the septum of mammals (Wullimann and Mueller, 2004). However, it does not suffice to state homology as a relation between structures it is also necessary to state homology in relation to derivation. Consider the following example, found in Butler and Hodos (2005): the following statements are both true:

The wing of a bird is homologous to the wing of a bat

The wing of a bird is not homologous to the wing of a bat

The &ldquospecification&rdquo requirement is sufficient and necessary to distinguish the situations in which each statement is true. The wing of a bird is homologous to the wing of a bat as a deravative of the forelimb, which means that the common ancestors of birds and bats probably possessed forelimbs of a similar basic structure, and the wings of bats and birds are derivatives of those forelimbs. On the other hand, the wing of a bid is not homologous to the wing of a bat as a wing, because the forelimbs of the common ancestors of birds and bats were not wings. Citing Butler and Hodos (2005, pp. 8-9): &ldquoIn statements of homology, unless the specification is obvious and unmistakable, the specific characteristic being compared must be included in the statement for the statement to be meaningful&rdquo. Thus, in our example of Vl-Vv homologies with septum, it is necessary to define whether Vl-Vv and septum are homologous as septal areas or as derivatives of subpallial areas. In the first case, it is not yet possible to fully appreciate the ancestral state of the character as a septal area, because the Vl-Vv of the common ancestor of teleosts and mammals is not known. Statistical techniques, such as phylogenetic generalized least squares estimation of ancestor states (Martins and Hansen, 1999), are available to generate estimates for this trait, but there is still the problem of defining which properties of the trait should be included in the analysis.

The concept of homology as the relationship between two characters in two different species as inherited from a common ancestor is called historical homology. It is based mainly on a &ldquotransformational&rdquo approach, which states that a character A in species X is considered homologous to a character A' in species Y if it takes &ldquofewer steps to transform a into A' than it takes to transform A into A' than it takes to transform A into B'&rdquo (McKitrick, 1994). This &ldquotransformational&rdquo approach is superimposed by taxonomic considerations &ndash that is, the distribution of the character on a phylogenetical tree. The determination of historical homology is commonly based on the analysis of fossils however, in evolutionary neuroscience, one must face the problem of the impossibility of fossilization of the brain. Simpson (1961) proposed that other criteria should be used to establish historical homology hypotheses for neuroanatomical data. These include:

Similarity of axonal connections (hodology)

Similartiy in the relationships between the group of neurons in analysis to some consistent feature of the species analysed

Similarity of embriological derivation

Similarity in the morphological features of individual neurons that form the group

Similarity in the neurochemical attributes of the neurons that form the group

Similarity in the physiological properties of the neurons that form the group

Similartiy in the behavioral outcomes of neuronal activity

This is known as the &ldquorequirement of total evidence&rdquo epistemological principle (Fitzhugh, 2006), and gave rise to an endless controversy on whether the last two criteria &ndash being functional criteria &ndash should be included in homology analyses. Despite these controversies, &ldquothe more of these criteria that can be satisfied, the stronger the support for an hypothesis of historical homology&rdquo (Butler and Hodos, 2005, p. 9).

The opposite of historical homology is homoplasy, defined as the structural similarity between two traits in two species without phyletic continuity &ndash which is equivalent to saying that, even though the traits are similar, the common ancestor of species A and B did not present the trait. There are three different types of homoplasy: convergence, parallelism, and reversal. The first type refers to the evolution of similar traits in response to similar adaptive pressures, but not to similar genes and developmental processes an example of convergence can be found in the eletroreception of mormyrids and gymnotoids: while the organs responsible for this perceptual capacity are similar, they are not derived from a common ancestor. Parallelism occurs in closely related taxa, and is defined as the independent development of a descendant character that is not present on a common ancestor. Parallelism occurs when two taxa develop the same character after evolutionary divergence since the trait is absent in a common ancestor, but present in both descendant species, it is probable that the developmental genetics that produces the structures in the different taxa is the same, which means it was inherited from the common ancestor. Thus, there is homology between the developmental and genetic materials, but not on the final structure. Parallelism is the great challenge for statistical cladistic approaches, since they cannot detect whether the character was absent in the common ancestor without complementary approaches. Hennig (apud Butler and Hodos, 2005) stated an auxiliary principle that goes like this: &ldquoNever assume convergent or parallel evolution always assume homology in the absence of contrary evidence&rdquo. This is based on the &ldquotransformational&rdquo approach to parsimony. Reversals are instances of homoplasy in which a character appears, subsequently disappears, and later reappears along the descendants in one lineage. Statements of reversals, instead of parallelism and convergence, must be analysed through the &ldquotransformational&rdquo approach to parsimony.

There has been considerable debate on whether the historical homology concept is satisfactory to phylogenetical analyses. It has been argued that this concept is not capable of recognizing the importance of genetic and developmental continuity as bases for homology. Two alternatives to this approach appeared. Biological homology is defined as the morphological identity of characters. It focuses, thus, &ldquoon the developmental pathways and the behavior of morphogenetic fields [ie, discrete units of embryonary development] to account for the variability of character expression but does not define sameness by them&rdquo. Thus, a trait A in species A is considered homologous to a trait A' in species B if A and A' share a set of developmental constraints (Wagner, 1989). The requirement of similar phenotypic expression from historical homology is not taken as valid, and the requirement of phyletic continuity applies only to developmental units.

The concept of generative homology is a second alternative to historical homology, and proposed by Butler and Saidel (2000). It is defined as &ldquothe relationship of a given character in different taxa that is produced by shared generative pathways&rdquo (Butler and Saidel, 2000, p. 849), ie, shared genetic and/or morphogenetic basis. Generative homology encompases parallelism, reversals, and most cases of historical homology. It's opposite is convergence, and not all instances of homoplasy.

It must be noted that these different concepts of homology normally overlap, and are segregated only by different uses in different areas. While systematists are concerned with the reconstruction of phylogenetic relationships and the recognition of monophyletic groups &ndash thus relying on historical homology &ndash, evolutionary biologists are interested in the evolution of a trait, and rely on biological homology. Comparative developmental biologists, on the other hand, are concerned with evolution of generative pathways for traits, and, accordingly, use the concept of generative homology. Evolutionary neuroscience is normally interested in the evolution of a trait, and can sometimes be interested in the comparative developmental character of a trait thus, evolutionary neuroscientists normally rely on biological and generative homology concepts. This does not mean that the criteria for homology developed by Simpson (1961) should be discarded rather, they are complementary criteria for deciding on hypotheses of homology. A complete account of the evolution, generative status and cladistic status of a trait should refer to those criteria.

A considerable ammount of neuroscientists are not that interested in analysing form most of all, they are interested in the function of a given structure. This is specially relevant in the case of behavioral neuroscience &ndash the field from where I came. &ldquoYes, very neat, this structure is homologous in species A and B, and it presents such and such properties, but what does it do?&rdquo: this is the behavioral-neuroscientific equivalent of &ldquobut does it make coffee?&rdquo.

In contrast, evolutionary biologists are not that much worried about function. The concept of analogy was created to address functional questions in that field. Analogy refers to similarity of function, regardless of phyletic relationships. The rationale for identifying analogy as a different concept than homology is that structures that present different morphology and origin (be it phyletic or embryological) can have similar functions. As an illustration, let's return to the bat and bird example again. The wing of a bird and the wing of a bat are homoplastic as wings, but share the same function &ndash flying. This distinction is important, because it contains in itself the idea that relations between form and function are not always correlated to relations between form and phyletic relationships. The establishment of such relations must be made independently. A good strategy is to relate, via statistical analyses, the phylogenetic correlations between a given structure and a given function, which can be physiological or behavioral. It is teoretically sound that physiological functions will present greater correlations with morphological traits &ndash since it is a basic tenet of neuroscience that the physiological properties of a given structure are reducible (either literally or in form of supervenience) to the underlying organization. The relations between behavior and morphological traits, on the other hand, are less well established.

The field of behavioral phylogenetics is considerably new, and, so far, was not totally incorporated in evolutionary neuroscience. Its aim is to analyse the phylogenetical distributon of a given behavioral trait, using mainly statistical techniques. Phylogenetic questions about behavior is hindered by the fact that behavior patterns reflect individual variability, plasticity, and responses to environmental change thus, homology hypotheses on behavior should be rather weaek (Gittleman and Decker, 1994). However, diverse malleable patterns of behavior present some phylogenetic inertia (Wilson, 1975), because closely related species tend to evolve in similar niches, have similar genetic variance for selection to act upon, and have similar phenotypes, tending to respond to environmental change in a similar fashion (Harvey and Pagel, 1991). Ideally, statistical techniques could be used to analyse the rate of change and conservation in a given set of traits &ndash say, allometric data on amygdala and homologues and behavioral measures of fear. However, this is not enough to establish that a given analogous trait presents homology, be it historical, biological or generative. To my knowledge, there have been so far no studies attempting to correlate neural and behavioral traits in evolution. I may attempt to do so in the near future, as long as I can access a reliable data set.

That is it for today. Now, go away!

Butler AB, Saidel WM (2000). Defining sameness: Historical, biological and generative homology. BioEssays 22: 846-853.

Fitzhugh K (2006). The 'requirement of total evidence' and its role in phylogenetic systematics. Biology and Philosophy 21: 309-351.

Gittleman JL, Decker DM (1994). The phylogeny of behaviour. In: PJB Slater, TR Halliday (eds.), Behaviour and Evolution. Cambridge: Cambridge University Press.

Harvey PH, Pagel MD (1991). The Comparative Method in Evolutionary Biology . Oxford: Oxford University Press.

Martins EP, Hansen TF (1999). Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interespecific data. American Naturalist 149: 646-667.

McKitrick M (1994). On homology and the ontological relationships of parts. Systematic Biology 43: 1-10.

Simpson GG (1961). Principles of Animal Taxonomy . New York: Columbia University Press.

Wagner GP (1996). Homologues, natural kinds and the evolution of modularity. American Zoologist 36: 36-43.

Wilson DS (1975). Sociobiology: The New Synthesis. Cambridge: Harvard University Press.

Classification and differences between homologous, homoplastic, analogous, derived and ancestral traits? - Biology

The earth formed about 4.5 billion years ago and within a half billion years the first life originated. Everything alive today is descended from those first simple life forms. In the tree of life, some groups of living things branched out along different paths long ago and now have little in common, while others have branched only recently and are still very similar. In other words, some living things are close relatives, while others are distant cousins or near total strangers. It isn't always easy to see that family history because we can only look at species that are alive today (the living buds at the tips of the branches) while the rest of the tree is hidden in the past. Sometimes a fossil of an extinct species provides a clue, but fossils are rare and finding them requires hard work and a lot of luck! The science of Taxonomy uses the similarities and differences between organisms as clues to try to figure out the puzzle of relationships.

The following are all made of steel, and are all found in the toolbox. We will assume they are all living things derived from a common ancestor. Let's decide who is most closely related and who is more distantly related.

Homologous structures - structures which are similar because of common ancestry. Example - the front appendages of vertebrates are homologous. The flipper of a whale, the wing of a bat, the paw of a cat, the arm of a human, and the wing of a bird all have the same internal bone structure with only slight modifications in shape and size - they each contain a humerus, a radius, an ulna, carpals, metacarpals and phalanges.

Analogous structures - structures which perform similar functions but are based on completely independent designs. Example - the wing of an insect is analagous to the wing of a bird or the wing of an airplane.

Convergence - the process by which distantly related organisms come to resemble each other closely because they are adapting to the same environment and are under similar selection pressures. Example - the streamlined body and fins of dolphins and seals (both mammals) resemble those of fishes because swimming well requires these modifications.

Synapomorphy - a "shared-derived" trait. Synapomorphys are traits not found in the ancestors but which are shared by a group of descendants. Species which have shared-derived characteristics are probably closely related because the same structure rarely evolves more than once in separate lineages.

Dichotomous Tree of the Nuts and Bolts :

There appear to be four major groups - the bolts, the nuts, the screws and the nails. The group that is most different from the others is the nuts, because all the others are long and have a head. Within the three remaining groups, the nails are the most different because both the screws and bolts are threaded. Finally, the screws and bolts can be divided based on the pointed tips of the screws. Someone might argue that the nails and screws have more in common because they both have a pointed tip, and that "pointy tip" is a more important trait than "threading." This is a good argument. See if a third trait lends support for grouping them based on either the threading or the pointy tips.

Within each of the major groups, the branching continues. Bolts 3 and 5 could be grouped as closest relatives because 3 and 5 have identical heads and bolt diameters. Or you might argue that Bolts 2 and 3 are more closely related because they are the same length while Bolt 5 is longer. In the dichotomous (splitting into twos) tree of relationships shown below, it was decided that 3 and 5 were closer because head shape and bolt diameter are two traits that are shared between 3 and 5, while length is the only trait shared between 2 and 3. Note that the position of (3 and 5) could be switched with that of (2) without changing the meaning of the tree. 2, 3 and 5 are all equally distant from the pair of screws (4 and 7).

A Dichotomous Key to the Nuts and Bolts :

A key is useful when you find an organism and you want to identify it based on its characteristics. Here is a key based on the tree for the nuts and bolts. Start at Question 1a and read the description. If the answer to 1a is "Yes", you would be sent to Question 2a. If the answer to Question 1a is "No", you go to Question 1b, which then sends you to Question 3. Keep following the directions until you know the species by its identifying number.

7a. Body length twice the width of head

7b. Body length not twice the width of head

The identifying numbers have been removed from the nuts and bolts in the following picture. Use the key to identify them and write the correct species number in the blank next to each one.

Advanced Lesson - Classifying A Group of Imaginary Organisms

1) Carefully examine the imaginary animals (Caminalcules) or plants (Dendrogrammaceae). In both cases, these imaginary organisms represent separate species that are descended from a common ancestor. Some have remained much like the ancestral species, while others have adapted to different environments and have changed to better suit their new lifestyles. However, you will still see physical features in these species which indicate their relationship to each other. You must use those clues to determine who is most closely related to whom.

2) Cut out the creatures so that their identifying numbers remain with them. On a large surface, do some initial sorting of the creatures so you can compare them for similarities and differences. Try arranging them several different ways before you decide. When you think you have figured out the major groupings, get a blank piece of paper and draw a rough draft of your dichotomously branching tree (splitting from one branch into two) based on the similarities and differences between the organisms. Refer to the nuts and bolts tree as an example. The first branch of the tree should divide the organisms along the most distinctive lines, and subsequent branches should separate organisms based upon more and more subtle differences. Each time the tree splits (always from one branch into only two), write down the distinguishing characteristic you used. Choose your distinguishing characters so that they are unambiguous. Example: If you say "Big eye vs. little eye", you may run into problems. Big as compared to what? However if you said "Eye bigger than mouth", then you can look at the mouth and decide.

3) When your tree is complete and the creatures are all separated from each other (no further divisions are possible), glue all of the individuals down along the top of a new piece of paper according to your tree of groups and subgroups. Then redraw the branches of your relationship tree as in the nuts and bolts example.

4) Create a dichotomous key to the organisms using the example Nuts and Bolts key and your tree as a guide. The distinguishing characteristics you wrote will become the options in the key.