A derived trait is not necessarily an entirely new trait. More often it is a modified form of an ancestral trait. For example, birds evolved feathers from the scales that were already present in their reptile ancestor. Similarly, mammals evolved fur from the scales of their reptile ancestor.
More than one possible cladogram usually can be created from the same set of data. In fact, the number of possible cladograms increases exponentially with the number of species included in the analysis. Only one cladogram is possible with two species. More than 100 cladograms are possible with five species. With nine species, more than two million cladograms are possible! Figure below shows just six of the many possible cladograms that can be generated for five species.
Six Possible Cladograms for Five Hypothetical Species
Figure 14.11
The same set of data on five related species may generate over 100 possible cladograms. Just six are shown here. In cladogram 1 (top, left), D and E share a more recent common ancestor than either shares with C. In cladogram 2 (top, middle), C and D share a more recent common ancestor than either shares with E. Compare how each of the remaining cladograms differs from the others.
How do scientists know which of many possible cladograms is the “right” one? There is no right or wrong cladogram. However, some cladograms fit the facts better than others. Statistical methods can be used to determine which cladogram best fits a particular data set. An important deciding factor is parsimony. Parsimony means choosing the simplest explanation from among all possible explanations. In cladistics, parsimony usually means choosing the cladogram with the fewest branching points.
A cladogram shows just one of many possible phylogenies for a group of organisms. It can provide insights about how evolution occurred. However, a cladogram should not be considered a model of actual evolutionary events. It does not necessarily show what really happened. It just shows what could have happened.
Phylogenetic Classification
A cladogram shows how species may be related by descent from a common ancestor. A classification of organisms on the basis of such relationships is called a phylogenetic classification. A phylogenetic classification involves placing organisms in a clade with their common ancestor. Consider the cladogram in Figure below. It groups birds in the same clade as reptiles, because a variety of evidence suggests that birds evolved from a reptile ancestor. The cladogram places mammals in a separate clade, because evidence suggests that mammals evolved from a different ancestor.
Figure 14.12
. This cladogram represents the evolutionary history of reptiles, birds, and mammals. The reptile clade includes birds. Mammals are in a separate clade.
Figure below shows the phylogenetic classification of reptiles, birds, and mammals based on the cladogram in Figure below. Birds are grouped with reptiles in one clade, called the Sauropsids. Mammals and their reptile-like ancestor are grouped in a separate clade, called the Synapsids. Compare this phylogenetic classification with the Linnaean classification, also shown in Figure below. In the Linnaean classification, reptiles, birds, and mammals are all placed in separate classes based on differences in physical traits. This classification artificially separates both birds and mammals from their reptilian ancestors. It also illustrates the difficulty of showing evolutionary relationships with Linnaean taxonomy.
Phylogenetic and Linnaean Classifications of Reptiles, Birds, and Mammals
Figure 14.13
The cladistic classification on the right assumes that mammals and birds evolved from different reptile ancestors. Mammals are placed in one clade, and birds are placed in another clade (with modern reptiles). Compare this classification with the Linnaean classification on the left. Why are birds and reptiles placed in separate classes in the Linnean taxonomy
Both phylogenetic and Linnaean classification systems have advantages and drawbacks (see the point by point comparison in the two lists, below). As an overall approach, most biologists think that phylogenetic classification is preferable to Linnaean classification. This is because it is based on evolutionary relationships and not just similarities in physical traits that may or may not have evolutionary significance. However, both approaches have a place in the classification of organisms. Linnaean binomial names are still needed to identify species, because phylogenetics does not include a method for naming species. In addition, many higher taxa in the Linnaean system, such as birds and mammals, remain useful in phylogenetic classifications. This is because they are also clades.
Phylogenetic Classification
Treats all levels of a cladogram as equivalent.
Places no limit on the number of levels in a ladogram.
Primary goal is to show the process of evolution.
It is limited to organisms that are related by ancestry.
Does not include a method for naming species.
Linnaean Classification
Treats each taxa uniquely and has a special name or each (e.g., genus, species).
Has fixed numbers and types of taxa.
Primary goal is to group species based on similarities in physical traits.
Can include any organisms without regard to ancestry.
Has a method for giving unique names to species.
Phenetics is an older method to classify organisms. Phenetics is based on overall similarity, usually in morphology or other observable traits, regardless of their evolutionary relation. Phenetics has largely been replaced by cladistics for research into evolutionary relationships among species. Phenetic techniques include various forms of clustering and ordination of traits. These are sophisticated ways of reducing the variation displayed by organisms to a manageable level. Phenetic analyses do not distinguish between traits that are inherited from an ancestor and traits that evolved anew in one or several lineages. Consequently, phenetic analyses can be misled by convergent evolution and adaptive radiation.
Evidence for Evolutionary Relationships
Traditionally, evidence for evolutionary relationships included similarities in physical traits of form or function. For example, in Linnaean taxonomy, homeothermy (warm-bloodedness) is one of the traits used to separate both birds and mammals from other animals (see Figure above). However, this trait is not suitable for showing evolutionary relationships between birds and mammals. This is because birds and mammals did not inherit the trait of homeothermy from a common ancestor. Both groups independently evolved the trait. The presence of homeothermy in both birds and mammals is an example of convergent evolution (see the History of Life chapter). In general, convergent evolution may make two groups seem to be more closely related than they really are. Using such traits for phylogenetic analysis can lead to misleading phylogenetic classifications.
Similarities among nucleic acid base sequences provide some of the most direct evidence of evolutionary relationships (see the Evolutionary Theory chapter). Nucleic acids directly control genetic traits and copies of nucleic acids are actually passed from parents to offspring. Therefore, similarities in these traits are likely to reflect shared ancestry. By the 1960s, scientists had found ways to sequence the bases in nucleic acids. This coincided with the growing popularity of cladistics. In cladistic analysis, similar nucleic acid base sequences are assumed to indicate descent from a common ancestor. The more similar the sequences, the more recently two groups are assumed to have shared a common ancestor.
Many base sequence comparisons have confirmed genetic relationships that were assumed on the basis of similarities in physical traits. For example, 96 percent of the DNA in humans and chimpanzees is the same. This agrees, in general, with the Linnaean classification of chimpanzees as close human relatives (see Lesson 14.1).
Most biologists interested in taxonomy now use nucleic acid sequences or other related molecular data to classify organisms. However, using nucleic acid base sequences for phylogenetic analysis is not without its drawbacks. Two of the drawbacks are:
Data on nucleic acids can rarely be obtained for extinct
species. This is true even for species represented by fossils. Fossil DNA and RNA generally are not sufficient in quantity or quality to be useful for such analyses.
Base sequence data may be influenced by horizontal gene transfer. This occurs when an organism passes DNA to an unrelated organism. First discovered in bacteria in 1959, it is now known to be common in bacteria and some other microorganisms. Horizontal gene transfer can make species seem more closely related than they really are.
Because of horizontal gene transfer, some biologists have started to question whether phylogenetic trees are the best way to show evolutionary relationships. This is especially true for those biologists that are interested in classifying bacteria. An entirely new process of determining evolutionary relationships may be needed in order to include horizontal gene transfer.
Lesson Summary
Phylogeny is the evolutionary history of a group of genetically related organisms. It is usually represented by a diagram called a phylogenetic tree.
Cladistics is the most widely used method of generating phylogenetic trees. It is based on evolutionary ancestry and generates trees called cladograms. Cladistics also identifies clades, which are groups of organisms that include an ancestor species and its descendants.
Classifying organisms on the basis of descent from a common ancestor is called phylogenetic classification. Phylogenetic classification may or may not agree with Linnaean taxonomy, which is based on similarities in physical traits regardless of ancestry.
The most direct evidence for evolutionary relationships is similarity in base sequences of the nucleic acids DNA and RNA. The more similar the base sequences of two species, the more closely related the species are assumed to be.
Review Questions
What is a phylogeny?
Define cladistics.
What does phylogenetic classification involve?
Why are nucleic acid base sequences directly related to evolution?
In cladogram 6 of Figure above, explain how the five species are related to one.
Identify an ancestral trait and a derived trait in mammals. Explain your answer.
Explain why a cladogram represents only one hypothesis about how evolution occurred.
Compare the advantages of Linnaean and phylogenetic classification systems.
Further Reading / Supplemental Links
http://evolution.berkeley.edu/evolibrary/article/0_0_0/phylogenetics_01
D.Graham Burnett, Trying Leviathan: The Nineteenth-Century Court Case that Put the Whale on Trial and Challenged the Order of Nature. Princeton University Press, 2007.
Jan Sapp (ed.) http://evolution.berkeley.edu/evolibrary/article/0_0_0/phylogenetics_01 Jan Sapp (ed.)
Microbial Phylogeny and Evolution: Concepts and Controversies. Oxford University Press, 2005.
N. R. Scott-Ram http://evolution.berkeley.edu/evolibrary/article/0_0_0/phylogenetics_01 N. R. Scott-Ram
Transformed Cladistics, Taxonomy, and Evolution. Cambridge University Press, 2009.
http://evolution.berkeley.edu/evolibrary/article/0_0_0/phylogenetics_01-08
http://mansfield.osu.edu/~sabedon/biol3005.htm
http://news.nationalgeographic.com/news/2005/08/0831_050831_chimp_genes.html
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Taxonomy.html
http://www.genome.gov/12514316
http://www.palaeos.com/Systematics/Cladistics/incompatable.html
Vocabulary
ancestral traits
Traits inherited from a common ancestor.
clade
Group of organisms that includes an ancestor species and all of its descendants.
cladistics
Method of making evolutionary trees based on comparisons of traits of ancestor and descendant species.
cladogram
Diagram showing evolutionary relationships within one or more clades.
common ancestor
Last ancestral species that two descendant species shared before they took different evolutionary paths.
derived traits
Traits that evolved since two groups shared a common ancestor.
parsimony
Choosing the simplest explanation from among all possible explanations.
phylogenetic classification
Classification of organisms on the basis of evolutionary relationships.
phylogenetic tree
Diagram representing a phylogeny.
phylogeny
Evolutionary history of a group of genetically related organisms.
Points to Consider
When Linnaeus developed his classification system in the early 1700s, he knew almost nothing about microorganisms (microscopic organisms). Therefore, he did not include microorganisms in his taxonomy.
How do you think microorganisms should be classified?
Where do you think microorganisms should be placed in Linnaean taxonomy?
Do you think a new taxon might be needed for microorganisms?
Lesson 14.3: Modern Classification Systems
Lesson Objectives
Identify the four new kingdoms that were added to the original Linnaean taxonomy.
Describe the three domains of the three-domain system of classification.
Explain why the three-domain system may need revision in the future.
Introduction
Linnaeus established two kingdoms of organisms in his classification system: Plantae (the plant kingdom) and Animalia (the animal kingdom). Since then, scientists have repeatedly revised the Linnaean system. They have added several new kingdoms and other taxa. These changes were necessary as scientists learned more about life on Earth.
New Kingdoms
Between 1866 and 1977, a total of four new kingdoms were added to the original plant and animal kingdoms identified by Linnaeus. The new kingdoms include Protista (protists), Fungi, Monera (eubacteria), and Archaea (archaebacteria). Table below identifies the scientists who introduced the kingdoms and the dates the kingdoms were introduced. The table starts with the two-kingdom system introduced by Linnaeus in 1735.
Kingdoms in the Classification of Organisms Number of Kingdoms Two Three Four Five Six
Scientist Linnaeus Haeckel Copeland Whittaker Woese
Date 1735 1866 1956 1969 1977
Names of Kingdoms Animalia
Plantae
Protista
Animalia
Plantae
Monera
Protista
Animalia
Plantae
Monera
Fungi
Protista
Animalia
Plantae
Archaea
Monera
Fungi
Protista
Animalia
Plantae
(Source: http://en.wikipedia.org/wiki/Kingdom_%28biology%29, License: GNU Free Documentation)
The Protist Kingdom
When Linnaeus created his taxonomy, microorganisms were almost unknown. As scientists began studying single-celled organisms under the microscope, they generally classified them as either plants and or animals. For example, bacteria are single-celled organisms, some of which make their own food. They were classified as plants, which also make their own food. Protozoa are single-celled organisms that can move on their own. They were classified as animals, which are organisms that have independent movement.
As more single-celled organisms were identified, many didn’t seem to fit in either the plant or the animal kingdom. As a result, scientists could not agree on how to classify them. To address this problem, in 1866, biologist Ernst Haeckel created a third kingdom for all single-celled organisms. He called this kingdom Protista. Figure below shows drawings that Haeckel made of several different types of protists as they looked under a microscope. The drawings show some of the diversity of microorganisms.
Figure 14.14
. Biologist Ernst Haeckel made these drawings of various types of single-celled organism
s as viewed under a microscope. Based on his extensive knowledge of the diversity of microorganisms, Haeckel introduced a new kingdom just for single-celled life forms, called the protist kingdom. This was the first major change in the original Linnaean taxonomy.
The Bacteria Kingdom
Haeckel’s protist kingdom represented all known single-celled organisms, including both bacteria and protozoa. In the early 1900s, scientists discovered that bacterial cells are very different not only from plant and animal cells but also from the cells of protists, such as protozoa. Figure below shows a bacterial cell, a protozoan cell, and an animal cell. When you compare the three cells, what differences do you see? The major difference is that, unlike the protozoan and animal cells, the bacterial cell does not contain a nucleus surrounded by a nuclear membrane. Instead, its DNA is found in the cytoplasm of the cell. Organelles in the bacterial cell also lack surrounding membranes.
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