21 Reconstructing and Using Phylogenies Chapter 21 Key

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21 Reconstructing and Using Phylogenies

21 Reconstructing and Using Phylogenies

Chapter 21 Key Concepts 21. 1 All of Life Is Connected through Its Evolutionary

Chapter 21 Key Concepts 21. 1 All of Life Is Connected through Its Evolutionary History 21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms 21. 3 Phylogeny Makes Biology Comparative and Predictive 21. 4 Phylogeny Is the Basis of Biological Classification

Investigating Life: Using Phylogeny to Improve a Genetic Tool The evolutionary history (phylogeny) of

Investigating Life: Using Phylogeny to Improve a Genetic Tool The evolutionary history (phylogeny) of fluorescent proteins in corals was determined from gene sequences in different species. This aided development of fluorescent pigments for research. How are phylogenetic methods used to resurrect protein sequences from extinct organisms?

Key Concept 21. 1 Focus Your Learning • Phylogenetic trees represent evolutionary relationships. •

Key Concept 21. 1 Focus Your Learning • Phylogenetic trees represent evolutionary relationships. • Phylogenies enable biologists to compare organisms and make predictions and inferences based on similarities and differences in traits. • Only homologous traits are used in reconstructing phylogenetic trees.

21. 1 All of Life Is Connected through Its Evolutionary History All of life

21. 1 All of Life Is Connected through Its Evolutionary History All of life is related through a common ancestor. Phylogeny: The evolutionary history of relationships among organisms. Phylogenetic tree: A diagrammatic reconstruction of the evolutionary history of species, populations, and genes.

21. 1 All of Life Is Connected through Its Evolutionary History Phylogenetic trees have

21. 1 All of Life Is Connected through Its Evolutionary History Phylogenetic trees have been constructed based on physical structures, behaviors, and biochemical attributes. Now, genome sequencing allows biologists to reconstruct the history of life in ever greater detail.

21. 1 All of Life Is Connected through Its Evolutionary History A series of

21. 1 All of Life Is Connected through Its Evolutionary History A series of ancestor and descendant populations is a lineage, which is depicted as a line drawn on a time axis. When a lineage divides into two, it forms a node. New traits arise in the new lineages. As lineages split over time, a branching tree is formed.

Figure 21. 1 The Components of a Phylogenetic Tree

Figure 21. 1 The Components of a Phylogenetic Tree

21. 1 All of Life Is Connected through Its Evolutionary History The common ancestor

21. 1 All of Life Is Connected through Its Evolutionary History The common ancestor of all organisms in the tree forms the root. Timing of splitting events is shown by the position of nodes on a time axis. Lineages can be rotated around nodes; the vertical order of lineages in the tree is largely arbitrary.

Figure 21. 2 How to Read a Phylogenetic Tree (Part 1)

Figure 21. 2 How to Read a Phylogenetic Tree (Part 1)

Figure 21. 2 How to Read a Phylogenetic Tree (Part 2)

Figure 21. 2 How to Read a Phylogenetic Tree (Part 2)

21. 1 All of Life Is Connected through Its Evolutionary History Taxon (plural, taxa):

21. 1 All of Life Is Connected through Its Evolutionary History Taxon (plural, taxa): Any species or group of species that we designate or name (e. g. , vertebrates). A taxon that consists of all the evolutionary descendants of a common ancestor is called a clade.

Figure 21. 3 Clades Represent an Ancestor and All of Its Evolutionary Descendants

Figure 21. 3 Clades Represent an Ancestor and All of Its Evolutionary Descendants

21. 1 All of Life Is Connected through Its Evolutionary History Sister species: Two

21. 1 All of Life Is Connected through Its Evolutionary History Sister species: Two species that are each other’s closest relatives. Sister clades: Two clades that are each other’s closest relatives.

21. 1 All of Life Is Connected through Its Evolutionary History Phylogenetic trees were

21. 1 All of Life Is Connected through Its Evolutionary History Phylogenetic trees were used mainly in systematics (study and classification of biodiversity) but are now used in nearly all fields of biology. Evolutionary relationships, as represented in the tree of life, form the basis for biological classification.

21. 1 All of Life Is Connected through Its Evolutionary History Biologists determine traits

21. 1 All of Life Is Connected through Its Evolutionary History Biologists determine traits that differ within a group of interest, then try to determine when these traits evolved. Often we wish to know how the trait was influenced by environmental conditions or selection pressures.

21. 1 All of Life Is Connected through Its Evolutionary History Features shared by

21. 1 All of Life Is Connected through Its Evolutionary History Features shared by two or more species that were inherited from a common ancestor are homologous. • Example: The vertebral column is homologous in all vertebrates.

21. 1 All of Life Is Connected through Its Evolutionary History An ancestral trait

21. 1 All of Life Is Connected through Its Evolutionary History An ancestral trait was present in the ancestor of a group. A trait found in a descendent that differs from the ancestral trait is called a derived trait.

21. 1 All of Life Is Connected through Its Evolutionary History Synapomorphies: Derived traits

21. 1 All of Life Is Connected through Its Evolutionary History Synapomorphies: Derived traits shared among a group; they are viewed as evidence of the common ancestry of the group. The vertebral column is a synapomorphy of all vertebrates (a shared, derived trait). (The ancestral trait was an undivided supporting rod. )

21. 1 All of Life Is Connected through Its Evolutionary History Similar traits can

21. 1 All of Life Is Connected through Its Evolutionary History Similar traits can develop in unrelated groups of organisms: • Convergent evolution: Independently evolved traits subjected to similar selection pressures may become superficially similar. § Example: The wings of bats and birds are not homologous.

Figure 21. 4 The Bones Are Homologous, the Wings Are Not

Figure 21. 4 The Bones Are Homologous, the Wings Are Not

21. 1 All of Life Is Connected through Its Evolutionary History The wing bones

21. 1 All of Life Is Connected through Its Evolutionary History The wing bones of bats and birds are homologous, they were inherited from a common tetrapod ancestor. § But the wings are not homologous; functionally similar structures that have independent origins are called analogous characters. §

21. 1 All of Life Is Connected through Its Evolutionary History • Evolutionary reversal:

21. 1 All of Life Is Connected through Its Evolutionary History • Evolutionary reversal: A character reverts from a derived state back to the ancestral state. § Example: Ancestors of whales and dolphins returned to the ocean, and cetacean limbs evolved to once again resemble their ancestral state—fins.

21. 1 All of Life Is Connected through Its Evolutionary History Similar traits generated

21. 1 All of Life Is Connected through Its Evolutionary History Similar traits generated by convergent evolution and evolutionary reversals are called homoplastic traits or homoplasies.

21. 1 All of Life Is Connected through Its Evolutionary History A trait may

21. 1 All of Life Is Connected through Its Evolutionary History A trait may be ancestral or derived, depending on the point of reference. • Example: Feathers are an ancestral trait for any group of modern birds. • But in a phylogeny of all vertebrates, feathers would be a derived trait, and thus is a synapomorphy of the birds.

Key Concept 21. 1 Learning Outcomes • Draw and label the parts of a

Key Concept 21. 1 Learning Outcomes • Draw and label the parts of a phylogenetic tree and explain the biological interpretation of each part. • Make inferences and predictions about evolutionary groups based on a phylogenetic tree.

Key Concept 21. 1 Learning Outcomes • Explain how homoplasies (convergences and reversals of

Key Concept 21. 1 Learning Outcomes • Explain how homoplasies (convergences and reversals of character states) are accounted for when reconstructing phylogenetic relationships.

Key Concept 21. 2 Focus Your Learning • Modern phylogenetic methods employ the principle

Key Concept 21. 2 Focus Your Learning • Modern phylogenetic methods employ the principle of parsimony and mathematical models (when appropriate) to analyze morphological, developmental, paleontological, behavioral, and molecular data.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Constructing a phylogenetic tree:

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Constructing a phylogenetic tree: The group of primary interest is the ingroup. The ingroup is compared with an outgroup, a closely related species or group known to be outside the group of interest. The root of the tree is located between the ingroup and the outgroup.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms In the following example,

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms In the following example, we assume no convergent evolution and that no derived traits have been lost.

Table 21. 1 Eight Vertebrates and the Presence or Absence of Some Shared Derived

Table 21. 1 Eight Vertebrates and the Presence or Absence of Some Shared Derived Traits

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms A trait present in

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms A trait present in both ingroup and outgroup must have evolved before the ingroup and thus must be ancestral for the ingroup. Lampreys (jawless fishes) arose before the lineage leading to other vertebrates —they are the outgroup.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Chimpanzees and mice share

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Chimpanzees and mice share two derived traits not present in the other groups—fur and mammary glands. They are synapomorphies for this group. Keratinous scales are a synapomorphy of the crocodile, pigeon, and lizard. Information about the synapomorphies allows construction of the tree.

Figure 21. 5 Constructing a Phylogenetic Tree

Figure 21. 5 Constructing a Phylogenetic Tree

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Phylogenetic trees are typically

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Phylogenetic trees are typically constructed using hundreds or thousands of traits. How are synapomorphies and homoplasies determined?

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Parsimony principle: The simplest

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Parsimony principle: The simplest explanation of observed data is the preferred explanation. This minimizes the number of evolutionary changes that must be assumed—the fewest homoplasies. Occam’s razor: The best explanation fits the data with the fewest assumptions.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Computer programs are now

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Computer programs are now used to analyze traits and construct trees. Any trait that is genetically determined can be used in a phylogenetic analysis. All kinds of traits—morphological, fossil, developmental, molecular, behavioral— are used to construct phylogenies.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Morphology Most species have

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Morphology Most species have been described by morphological data.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Limitations of morphological analyses

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Limitations of morphological analyses • Some taxa show few morphological differences. • Difficult to compare distantly related species. • Some morphological variation is caused by environment.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Development Similarities in developmental

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Development Similarities in developmental patterns may reveal evolutionary relationships. • Example: Sea squirts and vertebrates all have a notochord at some time in their development.

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part 1)

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part 2)

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part 3)

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part

Figure 21. 6 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part 4)

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Paleontology Fossils provide information

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Paleontology Fossils provide information about morphology of past organisms and where and when they lived. Fossils help determine derived ancestral traits and when lineages diverged. Limitations: Fossil record is fragmentary and missing for some groups.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Behavior can be inherited

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Behavior can be inherited or culturally transmitted. Bird songs are often learned and may not be a useful trait for phylogenies. Frog calls are genetically determined and can be used in phylogenetic trees.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Molecular data DNA sequences

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Molecular data DNA sequences have become the most widely used data for constructing phylogenetic trees. Nuclear, mitochondrial, and chloroplast DNA is used. Gene product information, such as amino acid sequences, is also used.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Mathematical models are now

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Mathematical models are now used to describe DNA changes over time. Models can account for multiple changes at a given sequence position and different rates of change at different positions.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Maximum likelihood methods identify

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Maximum likelihood methods identify the tree that most likely produced the observed data. • Most often used for molecular data. • They incorporate more information than parsimony methods and are easier to treat in a statistical framework.

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Experiments with living organisms

21. 2 Phylogeny Can Be Reconstructed from Traits of Organisms Experiments with living organisms and computer simulations are used to test the accuracy of phylogenetic reconstructions. In one experiment, a culture of bacteriophage T 7 was manipulated so that nine different lineages evolved.

Investigating Life: Testing the Accuracy of Phylogenetic Analysis Hypothesis: A phylogeny reconstructed by analyzing

Investigating Life: Testing the Accuracy of Phylogenetic Analysis Hypothesis: A phylogeny reconstructed by analyzing the DNA sequences of living organisms can accurately match the known evolutionary history of the organisms. Method: Lineages in the ingroup were split after every 400 generations. Mutagens were added to the cultures.

Investigating Life: Testing the Accuracy of Phylogenetic Analysis The 9 lineages were then sequenced

Investigating Life: Testing the Accuracy of Phylogenetic Analysis The 9 lineages were then sequenced by researchers who did not know the history of the lineages. Phylogenetic methods were used to reconstruct the known history correctly.

Investigating Life: Testing the Accuracy of Phylogenetic Analysis, Experiment

Investigating Life: Testing the Accuracy of Phylogenetic Analysis, Experiment

Key Concept 21. 2 Learning Outcomes • Analyze a phylogenetic tree to identify synapomorphies,

Key Concept 21. 2 Learning Outcomes • Analyze a phylogenetic tree to identify synapomorphies, homoplasies, and relationships among taxa. • Reconstruct a phylogenetic tree from a data matrix of characters.

Key Concept 21. 3 Focus Your Learning • Biologists use phylogenetic trees to investigate

Key Concept 21. 3 Focus Your Learning • Biologists use phylogenetic trees to investigate living organisms, explore instances of convergent evolution, and reconstruct ancestral states. • The timing of an evolutionary event can be estimated using the average rate of change for a given gene or protein and known calibration dates.

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenetic trees can help reconstruct past

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenetic trees can help reconstruct past events. For zoonotic diseases (transmitted to humans from another animal host), it is important to understand where, how, and when it entered humans. • Example: HIV was acquired from chimpanzees and sooty mangabeys.

Figure 21. 7 Phylogenetic Tree of Immunodeficiency Viruses

Figure 21. 7 Phylogenetic Tree of Immunodeficiency Viruses

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenetic analysis in forensics: • A

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenetic analysis in forensics: • A physician was accused of injecting blood from an HIV-positive patient into his former girlfriend. • Phylogenetics revealed that the HIV strains in the girlfriend were a subset of those in the physician’s patient.

Figure 21. 8 A Forensic Application of Phylogenetic Analysis

Figure 21. 8 A Forensic Application of Phylogenetic Analysis

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenies to compare living organisms: •

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenies to compare living organisms: • Reproductive success of male swordtail fish is associated with long tails (sexual selection). • Evolution of the sword may result from a preexisting bias of female sensory systems—the sensory exploitation hypothesis.

Figure 21. 9 The Origin of a Sexually Selected Trait

Figure 21. 9 The Origin of a Sexually Selected Trait

21. 3 Phylogeny Makes Biology Comparative and Predictive • Phylogenetics identified Priapella as the

21. 3 Phylogeny Makes Biology Comparative and Predictive • Phylogenetics identified Priapella as the closest relative, which split from the swordtails before the evolution of the sword. • When artificial swords were attached to Priapella males, the females preferred these males, supporting the idea that females had a preexisting bias even before the swords evolved.

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenies can reveal convergent evolution: •

21. 3 Phylogeny Makes Biology Comparative and Predictive Phylogenies can reveal convergent evolution: • In many flowering plants, individuals produce both male and female gametes. Self-incompatible species have mechanisms to insure outcrossing with other individuals. • Other species are self-fertilizing, and their gametes are self-compatible.

21. 3 Phylogeny Makes Biology Comparative and Predictive • Leptosiphon species have a variety

21. 3 Phylogeny Makes Biology Comparative and Predictive • Leptosiphon species have a variety of breeding systems. • Outcrossing species have long petals and are self-incompatible. Selfpollinating species have short petals. • A phylogeny was constructed using ribosomal DNA. • Self-incompatibility is the ancestral state.

Figure 21. 10 Phylogeny Reveals Convergent Evolution (Part 1)

Figure 21. 10 Phylogeny Reveals Convergent Evolution (Part 1)

Figure 21. 10 Phylogeny Reveals Convergent Evolution (Part 2)

Figure 21. 10 Phylogeny Reveals Convergent Evolution (Part 2)

Figure 21. 10 Phylogeny Reveals Convergent Evolution (Part 3)

Figure 21. 10 Phylogeny Reveals Convergent Evolution (Part 3)

21. 3 Phylogeny Makes Biology Comparative and Predictive • The reconstructed phylogeny suggests that

21. 3 Phylogeny Makes Biology Comparative and Predictive • The reconstructed phylogeny suggests that self-compatibility evolved three times, accompanied by reduced petal size. • The three self-compatible species had been described as one species based on the similarity of the flowers.

21. 3 Phylogeny Makes Biology Comparative and Predictive Ancestral states can be reconstructed. •

21. 3 Phylogeny Makes Biology Comparative and Predictive Ancestral states can be reconstructed. • Example: Reconstruction of an opsin protein (a pigment involved in vision) in the ancestral archosaur (the most recent common ancestor of birds, dinosaurs, and crocodiles)

21. 3 Phylogeny Makes Biology Comparative and Predictive • Analysis of opsin from living

21. 3 Phylogeny Makes Biology Comparative and Predictive • Analysis of opsin from living vertebrates was used to estimate the amino acid sequence of opsin in the archosaur. • A protein of this sequence was constructed in the laboratory and then wavelengths of light it absorbs were measured. • Activity in the red range indicated that the archosaur may have been nocturnal.

21. 3 Phylogeny Makes Biology Comparative and Predictive Timing of evolutionary splits: • Molecular

21. 3 Phylogeny Makes Biology Comparative and Predictive Timing of evolutionary splits: • Molecular clock hypothesis: Rates of molecular change are constant enough to predict timing of evolutionary divergence. • Molecular clock: Average rate at which a gene or protein accumulates changes.

Figure 21. 11 A Molecular Clock for the Protein Hemoglobin

Figure 21. 11 A Molecular Clock for the Protein Hemoglobin

21. 3 Phylogeny Makes Biology Comparative and Predictive • Molecular clocks must be calibrated

21. 3 Phylogeny Makes Biology Comparative and Predictive • Molecular clocks must be calibrated using independent data, such as the fossil record, known divergences, or biogeographic dates.

21. 3 Phylogeny Makes Biology Comparative and Predictive • A molecular clock helped determine

21. 3 Phylogeny Makes Biology Comparative and Predictive • A molecular clock helped determine when HIV-1 entered the human population from chimpanzees. • The clock can be calibrated using samples taken during the 1980 s and 1990 s, and then tested using samples from the 1950 s.

Figure 21. 12 Dating the Origin of HIV-1 in Human Populations (Part 1)

Figure 21. 12 Dating the Origin of HIV-1 in Human Populations (Part 1)

Figure 21. 12 Dating the Origin of HIV-1 in Human Populations (Part 2)

Figure 21. 12 Dating the Origin of HIV-1 in Human Populations (Part 2)

Key Concept 21. 3 Learning Outcomes • Use a phylogenetic tree to formulate a

Key Concept 21. 3 Learning Outcomes • Use a phylogenetic tree to formulate a hypothesis about the origins of an epidemic. • Calculate the rate of a molecular clock from a graph that shows change over time.

Key Concept 21. 4 Focus Your Learning • Only monophyletic groups are considered appropriate

Key Concept 21. 4 Focus Your Learning • Only monophyletic groups are considered appropriate taxonomic units. • Classifications are used to organize and name groups on the tree of life.

21. 4 Phylogeny Is the Basis of Biological Classification The biological classification system was

21. 4 Phylogeny Is the Basis of Biological Classification The biological classification system was started by Swedish biologist Carolus Linnaeus in the 1700 s. Binomial nomenclature gives every species a unique, unambiguous name.

21. 4 Phylogeny Is the Basis of Biological Classification Every species has two names:

21. 4 Phylogeny Is the Basis of Biological Classification Every species has two names: the genus (group of closely related species) to which it belongs and the species name. The name of the taxonomist who first described the species may be included. • Example: Homo sapiens Linnaeus

21. 4 Phylogeny Is the Basis of Biological Classification A taxon is any group

21. 4 Phylogeny Is the Basis of Biological Classification A taxon is any group of organisms that is treated as a unit—such as a genus, or all insects. Species and genera are further grouped into a hierarchical classification system. Genera are grouped into families (e. g. , the family Rosaceae includes the genus Rosa and its close relatives).

21. 4 Phylogeny Is the Basis of Biological Classification Animal family names end in

21. 4 Phylogeny Is the Basis of Biological Classification Animal family names end in “-idae. ” Family names are based on the name of a member genus; Formicidae (all ants) is based on the genus Formica. Plant family names end in “-aceae, ” as in Rosaceae.

21. 4 Phylogeny Is the Basis of Biological Classification Families are grouped into orders;

21. 4 Phylogeny Is the Basis of Biological Classification Families are grouped into orders; orders into classes; classes into phyla; phyla into kingdoms. Application of these levels is somewhat subjective.

21. 4 Phylogeny Is the Basis of Biological Classification Biological classifications express evolutionary relationships.

21. 4 Phylogeny Is the Basis of Biological Classification Biological classifications express evolutionary relationships. Taxa should be monophyletic: a taxon contains an ancestor and all descendents of that ancestor and no other organisms. A taxon is a clade.

21. 4 Phylogeny Is the Basis of Biological Classification Detailed phylogenetic information is not

21. 4 Phylogeny Is the Basis of Biological Classification Detailed phylogenetic information is not always available. A group that does not include its common ancestor is polyphyletic. A group that does not include all descendents of a common ancestor is paraphyletic.

Figure 21. 13 Monophyletic, Polyphyletic, and Paraphyletic Groups

Figure 21. 13 Monophyletic, Polyphyletic, and Paraphyletic Groups

21. 4 Phylogeny Is the Basis of Biological Classification A true clade or monophyletic

21. 4 Phylogeny Is the Basis of Biological Classification A true clade or monophyletic group can be removed from the tree by making a single “cut. ” Polyphyletic and paraphyletic groups are inappropriate as taxonomic units because they do not correctly reflect evolutionary history.

21. 4 Phylogeny Is the Basis of Biological Classification Explicit rules govern the use

21. 4 Phylogeny Is the Basis of Biological Classification Explicit rules govern the use of scientific names. This ensures that there is only one correct scientific name for any taxon. There may be many common names for an organism in different languages, or the same common name may refer to more than one species.

Figure 21. 14 Same Common Name, Not the Same Species (Part 1)

Figure 21. 14 Same Common Name, Not the Same Species (Part 1)

Figure 21. 14 Same Common Name, Not the Same Species (Part 2)

Figure 21. 14 Same Common Name, Not the Same Species (Part 2)

Figure 21. 14 Same Common Name, Not the Same Species (Part 3)

Figure 21. 14 Same Common Name, Not the Same Species (Part 3)

Key Concept 21. 4 Learning Outcomes • Use a phylogeny to build a classification

Key Concept 21. 4 Learning Outcomes • Use a phylogeny to build a classification for a group of organisms. • Analyze a classification and phylogenetic tree to identify monophyletic, polyphyletic, and paraphyletic groups.

Investigating Life: Using Phylogeny to Improve a Genetic Tool How are phylogenetic methods used

Investigating Life: Using Phylogeny to Improve a Genetic Tool How are phylogenetic methods used to resurrect protein sequences from extinct organisms? Gene sequences of extinct species can be reconstructed if there is enough genomic information about their descendents. This is how fluorescent proteins from the extinct ancestors of modern corals were resurrected.

Figure 21. 15 Evolution of Fluorescent Proteins of Corals

Figure 21. 15 Evolution of Fluorescent Proteins of Corals

Investigating Life: Using Phylogeny to Improve a Genetic Tool Biologists have reconstructed protein sequences

Investigating Life: Using Phylogeny to Improve a Genetic Tool Biologists have reconstructed protein sequences in the common ancestor of life. The sequences were made into proteins and tested for temperature optima. The optimal range was 55– 65 C, consistent with the hypothesis that life originated in high-temperature environments.