5.4: Cladistics

Terms in this set (25)

Define "clade."


Understanding: A clade is a group of organisms that have evolved from a common ancestor.
A clade is all of the organisms hypothesized to have evolved from a common ancestor. A "branch" on the tree of life.

In the example, crocodiles and birds are a in the same clade. Snakes and crocodiles are not in the same clade unless you also include birds, lizards and tuatara.
Define "cladistics."


Understanding: A clade is a group of organisms that have evolved from a common ancestor.
Cladistics is a way of classifying organisms into groups based on shared characteristics and common ancestry. Species in the same group (clade) are more closely related (share a more recent common ancestor) to members of the same group than to other organisms.
Outline the relationship between time, evolutionary relationships and biological sequences.


Understanding: Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein.
Mutations in the nucleotide base sequences of DNA, and therefore differences in the amino acid sequence of proteins, accumulate gradually over time.

Therefore, the more differences there are in biological sequences, the more time has passed for the differences to accumulate. The more time that has passed since organisms have shared a common ancestor, the less evolutionarily related the organism are to each other.

Visa versa: the less differences there are in biological sequences, the less time has passed for the differences to accumulate. The less time that has passed since organisms have shared a common ancestor, the more evolutionarily related the organism are to each other.
Summarize the use of DNA sequences as evidence for evolutionary relatedness between species.


Understanding: Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein.
The DNA base sequences of the same gene in different species is compared. Because mutations (differences) in the DNA sequence will accumulate over time, the species with more similarities in the base sequence are likely more closely related (meaning they have a more recent common ancestor; have diverged from their common ancestor more recently) than species with more differences in the base sequence. The percent similarity between species can be used as the basis for creating a cladogram of hypothesized evolutionary relationships.
Summarize the use of amino acid sequences as evidence for evolutionary relatedness between species.


Understanding: Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein.
The amino acid sequences of the same protein in different species is compared. Differences in the amino acid sequences are due to mutations of the DNA. Because DNA mutations (and in turn amino acid sequences) will accumulate over time, the species with more similarities in the amino acid sequence are likely more closely related (meaning they have a more recent common ancestor; have diverged from their common ancestor more recently) than species with more differences in the amino acid sequence. The percent similarity between species can be used as the basis for creating a cladogram of hypothesized evolutionary relationships.
Outline the use of a "molecular clock" to determine time since divergence between two species.


Understanding: Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor.​
The "molecular clock" is a technique that uses the rate of mutation of DNA sequences (or amino acid sequences of proteins) to estimate the time when two species diverged from a common ancestor. The molecular clock hypothesis states that DNA and protein sequences change at a rate that is relatively constant over time and among different organisms. A consequence of this constancy is that the genetic difference between any two species is proportional to the time since these species last shared a common ancestor.
State the source of differences between biological sequences (nitrogenous base or amino acid).


Understanding: Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor.​
Differences in DNA (and the resulting amino acid) sequences are due to mutation. A mutation is a change that occurs either due to mistakes when the DNA is replicated or as the result of environmental factors such as UV light and cigarette smoke.
Define "homologous structure."


Understanding: Traits can be analogous or homologous.​
A homologous structure is a biological structure (molecular or anatomical) that appears in different species of organisms. The commonality is evidence of descent from a common ancestor that also had the structure. DNA and protein sequences can be homologous.
State an example of a molecular homology.


Understanding: Traits can be analogous or homologous.​
Different species share molecular homologies as well as anatomical ones. Roundworms, for example, share 25% of their genes with humans. These genes are slightly different in each species, but their similarities are evidence of common ancestry.

The universal genetic code is a homology that links all life on Earth to a common ancestor. DNA and RNA possess a simple four-base code that provides the information for making proteins in all living things.
State an example of a homologous structure.


Understanding: Traits can be analogous or homologous.​
The wings of bats and the arms of primates are homologous. Although these two structures do not look similar or have the same function, they are due to inheritance of a limb structure found in their last shared ancestor.
Define "cladogram."


Understanding: Cladograms are tree diagrams that show the most probable sequence of divergence in clades.​
Cladograms are branching diagrams where each branch represents an evolutionary lineage (a clade). Cladograms are used to show the hypothesized sequence of divergence between organisms and common ancestor(s). The names of specific taxa are put at the end of each branch and the names of the clade to which those taxa belong is often placed at the intersection of branches (nodes).

A cladogram does not really have axes, but implied in one direction (x axis in this example) is some sort of evolutionary distance from each other and implied in the other direction (y axis in this example) is relative time (the first branch at the bottom happened long ago the latter branches higher up happened more recently).
Define "node" of a cladogram.


Understanding: Cladograms are tree diagrams that show the most probable sequence of divergence in clades.​
An internal node (branching point) is the hypothesized last common ancestor that speciated (split) to give rise to two or more daughter taxa.

Each internal node is also at the base of a clade, which includes the common ancestor (node) plus all its descendents.
Describe how knowledge of homologous traits are used in the formation of a cladogram.


Understanding: Cladograms are tree diagrams that show the most probable sequence of divergence in clades.​
To build a cladogram, heritable traits are compared across organisms, such as physical characteristics (morphology), genetic sequences, and behavioral traits.

Homologous traits can be used to group organisms into clades. Traits shared among the species or groups in a dataset tend to form nested patterns that provide information about when branching events occurred in the lineage.

For example, amphibians, turtles, lizards, snakes, crocodiles, birds and mammals all have (or had) four limbs. Four limbs is a homologous trait inherited from a common ancestor that helps set apart this particular clade from other vertebrates.
Outline how computer programs analyze biological sequence data to create cladograms.


Understanding: Cladograms are tree diagrams that show the most probable sequence of divergence in clades.​
With sequencing technology we can compare the sequences evolutionarily related genes or proteins. Each nucleotide of a gene or amino acid of a protein can be viewed as a separate characteristic. The amount of data available from sequence comparisons is much higher than when using physical traits. To analyze sequence data and identify the most probable cladogram, biologists typically use computer programs and statistical algorithms that are able to rapidly and accurate compare sequences, compute differences between sequences and analyze most likely divergence patterns between sequences.
Identify members of a clade given a cladogram.


Understanding: A clade is a group of organisms that have evolved from a common ancestor.
This cladogram tells you that all the animals listed are in the mammalia clade. The koala and kangaroo are more closely related to one another than to anything else on the diagram. Their branches intersect each other before they intersect any other lineage. This indicates that they diverged from each other more recently than they diverged from any of the other animals on the diagram. Furthermore, they both belong to the Marsupialia clade. Similarly, the bat and the lion are more closely related to each other than they are to either of the marsupials. They are both in the placental mammals (eutherians) clade.
Outline the role of technological advancements in the development of cladistics.


Understanding: Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species.​
Until the early twentieth century, biology focused on the processes of living organisms and almost always involved observation and experiments in laboratories and in the field. Then, with advancements in sequencing and computer technology, scientists started accumulating, storing and sharing DNA and protein sequence data at an exponential rate.

Computer based sequence alignment and comparison has become an essential tool for biologists. Its speed and sensitivity allow scientists to compare nucleotide and protein sequences in large databases. Most importantly, the technology has helped make information accessible to any researcher over the Internet.
Outline two limitations of only examining external morphology when hypothesizing evolutionary relationships.


Understanding: Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species.​
Historically, classification was based primarily on external morphological (shape) characteristics. Closely related species were thought to show similar structural features. However, there are closely related organisms can exhibit very different structural features (due to divergent evolution) and distantly related organisms can display very similar structural features (due to convergent evolution).
Outline an example of a difference in classification of a species in the traditional scheme compared to a cladistics based classification scheme.


Understanding: Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species.​
Scientific understanding of relationships among organisms has changed dramatically since the time of Linnaeus and classical taxonomy. For example, we now understand that the bird lineage shares a more recent ancestor with some modern reptiles (crocodiles) than with others (lizards). Yet both snakes and crocodiles are part of the same Linnaean Class (reptilia) and birds are in a separate Class (aves). Modern classification schemes seeks to represent taxa in a system that reflects an understanding of their evolutionary relationships.
Compare cladistics to traditional biological classification methods.


Understanding: Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species.​
Cladistic classification is based on evolutionary history, with a variable number of clades depending on how much divergence there has been in an evolutionary lineage. Additionally, cladistics does not "rank" organisms into a set number of groups. Linnaean classification forces organisms to fit into into set kingdoms, phyla, orders, etc.
Interpret a cladogram depicting primate species.


Application: Cladograms including human and other primates.
Humans belong to the biological group known as Primates. Besides similarities in anatomy and behavior, human relationship to other primate species is supported by DNA evidence.

Humans and chimpanzees are more closely related to one another than either is to gorillas or any other primate. The genetic difference between individual humans today is about 0.1%, on average. The same genes of the chimpanzee genome indicates a difference of about 1.2% with humans. The DNA difference between humans and gorillas is about 1.6%. Chimpanzees show this same amount of difference from gorillas. A difference of 3.1% distinguishes humans and the African apes from the Asian great ape, the orangutan. All of the great apes and humans differ from macaque and baboon monkeys by about 7% in their DNA sequences.
Analyze a cladogram to describe the evolutionary relationship between species.


Application: Reclassification of the figwort family using evidence from cladistics.
Butterflies and moths share a most recent common ancestor with flies.

Butterflies, moths and flies are all equally related to beetles.

Wasps are more closely related to butterflies, moths and flies than to beetles.

Ants share a more recent common ancestor with flies than they do with beetles.
Outline the reason and evidence for the reclassification of the figwort family.


Application: Reclassification of the figwort family using evidence from cladistics.
In traditional classification, Figworts were a family of flowering plants (angiosperms) grouped together based on morphology. However, scientists have used cladistics to reclassify the Figwort family. DNA analysis of three chloroplast genes revealed that the species in the Figwort family were not one clade but five clades that had been incorrectly grouped together into one family. Therefore, the entire figwort family was reclassified into six families, each composed of just one clade.
Discuss the use of cladograms as hypotheses of evolutionary relationships.


Application: Reclassification of the figwort family using evidence from cladistics.
Evolutionary trees are hypotheses that have been tested with evidence. Because they are supported by many lines of evidence, widely accepted cladograms are unlikely to have their branches rearranged (though new branches are likely to be added as species are discovered). However, a change in our understanding is always possible. If new evidence is discovered or old evidence is reinterpreted, adjustments to the evolutionary relationships depicted in a cladogram must be made in order to reflect the new information.
Outline the reason why biological theories may change with time.


Nature of Science: Falsification of theories with one theory being superseded by another- plant families have been reclassified as a result of evidence from cladistics.
Biological theories change over time as technology advances and human ability to observe and measure the natural world improves.
Summarize the changes in biological classification schemes over time.


Nature of Science: Falsification of theories with one theory being superseded by another- plant families have been reclassified as a result of evidence from cladistics.
Details of different classification schemes are beyond the scope of the IB biology curriculum. They are only included here to illustrate that ideas are superseded by others as knowledge improves over time.

In 1735, Linnaeus published Systema Naturae in which he proposed a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. Linnaeus's tree of life contained just two main branches for all living things: the animal and plant kingdoms.

In 1866, Haeckel, proposed another kingdom, Protista, for unicellular organisms. He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria.

In 1969, Whittaker proposed adding another kingdom—Fungi—in the tree of life. Whittaker's five-kingdom tree was considered the standard for many years.

In the 1970s, Woese created a tree with three Domains above the level of Kingdom: Archaea, Bacteria, and Eukarya.

Hennig developed cladistics in 1950. After scientists began using molecular data in classification, Hennig's cladistics approach to classification has become increasingly adopted.
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