Reconstructing and Using Phylogenies
Reconstructing and Using Phylogenies
• Phylogenetic Trees
• Steps in Reconstructing Phylogenies
• Reconstructing a Simple Phylogeny
• Biological Classification and Evolutionary Relationships
• Phylogenetic Trees Have Many Uses
Phylogenetic Trees
• Systematics, the scientific study of the ________ of organisms, reveals the evolutionary relationships between organisms.
• Taxonomy, a subdivision of systematics, is the theory and practice of classifying organisms.
• Information about evolutionary relationships can be of great value, as in the control of the disease schistosomiasis.
Phylogenetic Trees
• A phylogeny is a hypothesis proposed by a systematist that describes the history of descent of a group of organisms from their common ancestor.
• A phylogenetic tree represents that history.
• A lineage is represented as a branching tree, in which each split or node represents a speciation event.
• Systematists reconstruct phylogenetic trees by analyzing________ changes in the traits of organisms.


Phylogenetic Trees
• Systematists expect traits inherited from an ancestor in the ________ past to be shared by a large number of species.
• Traits that first appeared in a more recent ancestor should be shared by fewer species.
• These shared traits, inherited from a common ancestor, are called ancestral traits.
Phylogenetic Trees
• Any features (DNA sequences, behavior, or anatomical feature) shared by two or more species that descended from a common ancestor are said to be homologous.
• For example, the vertebral column is homologous in all vertebrates.
• A trait that differs from its ancestral form is called a derived trait.
Phylogenetic Trees
• To identify how traits have changed during evolution, systematists must infer the state of the trait in an ancestor and then determine how it has been ________ in the descendants.
• Two processes make this difficult:
§ ________ evolution occurs when independently evolved features subjected to similar selective pressures become superficially similar.
§ Evolutionary ________ occurs when a character reverts from a derived state back to an ancestral state.

Phylogenetic Trees
• Convergent evolution and evolutionary reversal generate homoplastic traits, or homoplasies: Traits that are similar for some reason other than inheritance from a common ancestor.
Phylogenetic Trees
• The distinction between ancestral and derived traits is very important in reconstructing phylogenies.
• A particular trait may be ancestral or derived, depending on the group of interest.
• In a phylogeny of rodents, continuously growing incisors are an ancestral trait because all rodents have them.
• In a phylogeny of mammals, continuously growing incisors are a derived trait unique to the rodents.
Phylogenetic Trees
• Distinguishing derived traits from ancestral traits may be difficult because traits often become very dissimilar.
• An outgroup is a lineage that is closely related to an ingroup (the lineage of interest) but has branched off from the ingroup below its base on the evolutionary tree.
• Ancestral traits should be found not only in the ingroup, but also in outgroups. Derived traits would be found only in the ingroup.

Steps in Reconstructing Phylogenies
Creating a phylogeny:
§ Select a group of organisms to classify (the ________ ) and an appropriate outgroup.
§ Choose the characters that will be used in the analysis and identify the possible forms (traits) of the character.
§ Determine the ancestral and derived traits.
§ Distinguish ________ from homoplastic traits.
Steps in Reconstructing Phylogenies
• Systematists use many characters to reconstruct phylogenies, including physiological, behavioral, molecular, and structural characters of both living and fossil organisms.
• The more traits that are measured, the more inferred phylogenies should converge on one another and on the actual evolutionary pattern.
Steps in Reconstructing Phylogenies
• An important source of information for systematists is morphology, which describes the sizes and shapes of body parts.
• Early developmental stages of many organisms reveal similarities to other organisms, but these similarities may be lost in adulthood.
• The notochord of larval sea squirts is an example.
• The fossil record provides much morphological data and reveals when lineages diverged.

Steps in Reconstructing Phylogenies
• Molecular traits are also useful for constructing phylogenies.
• The molecular traits most often used in the construction of phylogenies are the structures of nucleic acids (DNA and RNA) and proteins.
Steps in Reconstructing Phylogenies
• Comparing the primary structure of proteins:
§ Homologous proteins are obtained and the number of amino acids that have changed since the lineages diverged from a common ancestor are determined.
• DNA base sequences:
§ Chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) have been used extensively to study evolutionary relationships.
Steps in Reconstructing Phylogenies
• Relationships between ________ and ________ were investigated by sequencing a hemoglobin pseudogene (a nonfunctional DNA sequence derived early in primate evolution by duplication of a hemoglobin gene).
• The analysis indicated that chimpanzees and humans share a more recent common ancestor with each other than they do with gorillas.
Reconstructing a Simple Phylogeny
• A simple phylogeny can be constructed using eight vertebrates species: lamprey, perch, pigeon, chimpanzee, salamander, lizard, mouse, and crocodile.
• The example assumes initially that a derived trait evolved only once during the evolution of the animals and that no derived traits were lost from any of the descendant groups.
• Traits that are either present (+) or absent (–) are used in the phylogeny.


Reconstructing a Simple Phylogeny
• Examining the table reveals that the chimpanzee and mouse share two traits: mammary glands and fur.
• Since mammary glands and fur are absent in the other animals, the traits can be attributed to a common ancestor of the mouse and chimpanzee.
• Using similar reasoning, the remaining traits are assigned to common ancestors of the other animals until the phylogenetic tree is complete.
• Note that the group that does not have any derived traits (the lamprey) is designated as an outgroup.

Reconstructing a Simple Phylogeny
• The example phylogeny was simplified by the assumption that derived traits appear only once in a lineage and were never lost after they appeared.
• If a snake were included in the group of animals used in the phylogeny, the assumption that traits are never lost would be violated.
• Lizards, which have limbs and claws, are the ancestors of ________ but these structures have been lost in the snake.
Reconstructing a Simple Phylogeny
• Systematists use several methods to sort out the complexities of phylogenetic relationships.
• The most widely used method is the ________ principle.
• This principle states that one should prefer the simplest hypothesis that explains the observed data.
• In reconstruction of phylogenies, this means minimizing the number of evolutionary changes that need to be assumed over all characters in all groups in the tree.
• In other words, the best hypothesis is one that requires fewest homoplasies.
Reconstructing a Simple Phylogeny
• The maximum likelihood method is used primarily for phylogenies based on molecular data and requires complex computer programs.
• Determining the most likely phylogeny for a given group can be difficult. For example, there are 34,459,425 possible phylogenetic trees for a lineage of only 11 species.
• A consensus tree is the outcome of merging multiple likely phylogenetic trees of approximately equal length. In a consensus tree, groups whose relationships differ among the trees form nodes with more than two branches.
Biological Classification and
Evolutionary Relationships
• The system of biological classification used today was developed by Carolus Linnaeus in 1758.
• His two-name system is referred to as binomial nomenclature.
• The first name identifies the genus; the other name identifies the species.
• Using this system, scientists throughout the world can refer unambiguously to the same organisms by the same names.
Biological Classification and
Evolutionary Relationships
• The name of the taxonomist who first proposed the species is often added to the name.
• Homo sapiens Linnaeus is the name of the modern human species.
• The generic name is always capitalized, whereas the specific name is not, and both names are italicized.
Biological Classification and
Evolutionary Relationships
• Abbreviations:
§ For references to more than one species in a genus, the abbreviation "spp." is used in place of the names of all the species (Drosophila spp. means more than one species of the genus Drosophila).
§ If the identity of the species is uncertain, the abbreviation "sp." may be used (Drosophila sp.).
§ If an organism is referred to numerous times, the genus is abbreviated (D. melanogaster for Drosophila melanogaster).
Biological Classification and
Evolutionary Relationships
• Any group of organisms that is treated as a unit is called a________ (plural, taxa).
• In the Linnaean system species and genera are further grouped into higher taxonomic categories.
• The category above genus is family. Family names end with the suffix "-idae" for animals and "-aceae" for plants.
• Families in turn are grouped into orders, classes, phyla, and kingdoms.

Biological Classification and
Evolutionary Relationships
• Biological classification systems and unique names are important for several reasons.
§ They are aids to memory and precise communication.
§ They improve the ability to infer relationships among organisms, and are also useful for predictions in scientific investigations.
q The discovery of precursors of cortisone in some yam species of the genus Dioscorea stimulated a successful search for higher concentrations of the drug in other species of Dioscorea.
Biological Classification and
Evolutionary Relationships
• Most taxonomists today believe that biological classification systems should reflect evolutionary relationships and that taxonomic units should be________
• A monophyletic group (or clade) contains all the descendants of a particular ancestor and no other organisms.



• A polyphyletic taxon contains members with more than one recent common ancestor.
• A paraphyletic group contains some, but not all, of the descendants of a particular ancestor.

Biological Classification and
Evolutionary Relationships
• Some systematists believe that classification systems should also reflect degrees of difference among organisms.
• Certain paraphyletic groups have undergone rapid evolutionary change and should be retained. The groups are called grades.
• Recent molecular evidence suggests, for example, that birds, turtles, and crocodilians share a more recent ancestor than crocodilians and turtles share with snakes and lizards.


Biological Classification and
Evolutionary Relationships
• The traditional class Reptilia is ________ because it does not include all descendants of its common ancestor; birds are excluded.
• This emphasizes that birds have evolved unique derived traits since they separated from reptiles, and are thus a distinct grade.
• The current tendency is to change classifications to eliminate paraphyletic groups; however, some of the familiar taxonomic categories (such as reptiles) are paraphyletic and will probably remain in use.
Phylogenetic Trees Have Many Uses
• Studies of a genus in the phlox family (Linanthus) illustrate how phylogenetic analyses can determine how many times a trait has evolved.
• Some species can reproduce by self-pollination (they are self-compatible).
• A nuclear ribosomal DNA sequence was used to construct the phylogeny of the Linanthus plants.
• Self-incompatibility is the ancestral state.
• Self-compatibility has evolved three times within the Linanthus lineage.

Phylogenetic Trees Have Many Uses
• Studies of characiform fishes illustrate how phylogenetic analyses can help determine when lineages split.
• The 1,400 species of these freshwater fishes vary greatly in size, shape, and diet.
• Closely related species have been found on both sides of the Atlantic Ocean.
• Genetic differences in the rRNA of both groups are great enough to be consistent with a split caused by the separation of Africa from South America, about 90 million years ago.

Phylogenetic Trees Have Many Uses
• A plausible phylogeny enables biologists to answer a variety of questions about the history of the group.
• For example, molecular and geological data have been used to reconstruct a phylogeny of Lake Victoria's cichlid fishes.
• Initially, the radiation that produced more than 500 species was assumed to have occurred over a period of about 750,000 years.
• Recent geological evidence suggests, however, that the lake dried up completely between 15,600 and 14,700 years ago.
Phylogenetic Trees Have Many Uses
• Biologists determined that the hundreds of diverse cichlids could not have evolved in such a short time.
• A new phylogeny of the cichlids of Lake Victoria and other lakes in the region was developed using 300 mtDNA sequences.
• This phylogeny suggested that the ancestors of the Lake Victoria cichlids came from the much older lake Kivu.
• The phylogeny also indicated that some of the cichlid lineages found only in Lake Victoria split at least 100,000 years ago, suggesting that the lake did not completely dry up about 15,000 years ago.