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25 Reconstructing and Using Phylogenies 25 Reconstructing and Using Phylogenies • 25.1 What Is Phylogeny? • 25.2 How Are Phylogenetic Trees Constructed? • 25.3 How Do Biologists Use Phylogenetic Trees? • 25.4 How Does Phylogeny Relate to Classification? 25.1 What Is Phylogeny? Phylogeny is a description of the evolutionary history of relationships among organisms. This is portrayed in a diagram called a phylogenetic tree. Each split or node represents the point at which lineages diverged. The common ancestor of all organisms in the tree is the root. Figure 25.1 How to Read a Phylogenetic Tree (Part 1) Figure 25.1 How to Read a Phylogenetic Tree (Part 2) 25.1 What Is Phylogeny? The timing of divergences is shown by the position of nodes on a time or divergence axis. Lineages can be rotated around nodes; the vertical order of taxa is largely arbitrary. 25.1 What Is Phylogeny? A taxon (plural taxa) is any group of species that we designate (e.g., vertebrates). A taxon that consists of all the descendents of a common ancestor is called a clade. 25.1 What Is Phylogeny? Two species that are each other’s closest relatives are sister species. Two clades that are each other’s closest relatives are sister clades. Phylogenetic trees were used mainly in systematics (study of biodiversity); but are now used in nearly all fields of biology. 25.1 What Is Phylogeny? One of the greatest unifying concepts in biology is that all life is connected through evolutionary history. The “Tree of Life” is the complete, 4billion-year history of life. Knowledge of evolutionary relationships is essential for making comparisons in biology. 25.1 What Is Phylogeny? 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. 25.1 What Is Phylogeny? 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. 25.1 What Is Phylogeny? A trait that differs from the ancestral trait is called derived. A trait that was present in the ancestor of a group is ancestral. 25.1 What Is Phylogeny? Derived traits that are shared among a group and are viewed as evidence of the common ancestry of the group are known as synapomorphies. The vertebral column is a synapomorphy of all vertebrates. 25.1 What Is Phylogeny? 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 Figure 25.2 The Bones Are Homologous; the Wings Are Not 25.1 What Is Phylogeny? • Evolutionary reversal—a character reverts from a derived state back to the ancestral state. Example: Most frogs do not have lower teeth, but the ancestor of frogs did. One frog genus has regained teeth in the lower jaw. 25.1 What Is Phylogeny? Traits that are similar for reasons other than inheritance from a common ancestor are called homoplastic traits or homoplasies. Traits may be ancestral or derived, depending on the point of reference in phylogeny. Bird feathers are ancestral in birds, but derived when considering all living vertebrates. 25.2 How Are Phylogenetic Trees Constructed? Constructing a phylogenetic tree using eight vertebrate animals: Assume no convergent evolution; and no derived traits have been lost. Lampreys are the outgroup—any species or group outside the group of interest. The group of interest is the ingroup. Comparison with the outgroup shows which traits of the ingroup are derived and which are ancestral. Table 25.1 (Part 1) Table 25.1 (Part 2) 25.2 How Are Phylogenetic Trees Constructed? Chimpanzees and mice share two derived traits—fur and mammary glands. Assume these traits evolved only once; 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 25.3 Inferring a Phylogenetic Tree 25.2 How Are Phylogenetic Trees Constructed? Phylogenetic trees are typically constructed using hundreds or thousands of traits. How are synapomorphies and homoplasies determined? 25.2 How Are Phylogenetic Trees Constructed? The parsimony principle: the simplest explanation of observed data is the preferred explanation. Minimize 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. 25.2 How Are Phylogenetic Trees Constructed? Computer programs are now used to analyze traits and construct trees. All kinds of traits—morphological, fossil, developmental, molecular, behavioral— are used by systematists to construct phylogenies. 25.2 How Are Phylogenetic Trees Constructed? Morphology Most species have been described on the basis of morphological data, such as features of the skeletal system in vertebrates, or floral structures in plants. Limitations: comparing distantly related species; some morphological variation is caused by environment; some species show few morphological differences. 25.2 How Are Phylogenetic Trees Constructed? Development Similarities in development patterns may reveal evolutionary relationships. Example: Sea squirts and vertebrates all have a notochord at some time in their development. Figure 25.4 A Larva Reveals Evolutionary Relationships 25.2 How Are Phylogenetic Trees Constructed? Paleontology Fossils provide information about the morphology of past organisms, and where and when they lived. Important in determining derived and ancestral traits, and when lineages diverged. Limitations: fossil record is fragmentary and missing for some groups. 25.2 How Are Phylogenetic Trees Constructed? Behavior 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. 25.2 How Are Phylogenetic Trees Constructed? Molecular data DNA sequences have become the most widely used data for constructing phylogenetic trees. Mitochondrial and chloroplast DNA is used as well as nuclear DNA. Gene product information, such as amino acid sequences, are also used. 25.2 How Are Phylogenetic Trees Constructed? Mathematical models are used to describe DNA changes over time. Models can be used to compute maximum likelihood solutions, the probability of the observed data evolving on the specified tree. Most often used for molecular data, models of evolutionary change are easier to develop. 25.2 How Are Phylogenetic Trees Constructed? Testing the accuracy of phylogenetic reconstructions: experiments with living organisms and computer simulations. Cultures of bacteriophage T7 were grown in the presence of a mutagen and allowed to evolve in the laboratory. Figure 25.5 A Demonstration of the Accuracy of Phylogenetic Analysis (Part 1) Figure 25.5 A Demonstration of the Accuracy of Phylogenetic Analysis (Part 2) 25.2 How Are Phylogenetic Trees Constructed? At the end of the experiment, genomes of the endpoints were sequenced and investigators built phylogenetic trees that accurately reflected the known evolutionary history of the cultures. 25.2 How Are Phylogenetic Trees Constructed? Phylogenetic methods can be used to reconstruct traits or nucleotide sequences for ancestral species. Example: Reconstruction of opsin (pigment involved in vision) in the ancestral archosaur (last common ancestor of birds, crocodiles, and dinosaurs). 25.2 How Are Phylogenetic Trees Constructed? 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 animal may have been nocturnal. 25.2 How Are Phylogenetic Trees Constructed? Molecular clock hypothesis: Rates of molecular change are constant enough to predict timing of evolutionary divergence. Among closely related species, a given gene usually evolves at a reasonably constant rate, and can be used to determine time elapsed since a divergence. 25.2 How Are Phylogenetic Trees Constructed? Molecular clocks must be calibrated using independent data, such as the fossil record, and known divergences or biogeographic dates (e.g., from continental drift). Example: 500 species of cichlid fishes of Lake Victoria. 25.2 How Are Phylogenetic Trees Constructed? Mitochondrial DNA sequences were used to construct a phylogenetic tree of the cichlids. It has been suggested that the ancestors came from the older Lake Kivu, and they colonized Lake Victoria on two occasions. Molecular clock analysis suggested that some endemic cichlid lineages split at least 100,000 years ago. 25.2 How Are Phylogenetic Trees Constructed? The analyses suggest that Lake Victoria did not dry up completely between 15,600 and 14,700 years ago, and many species survived in rivers and in the remnants of the lake during the dry period. Figure 25.6 Origins of the Cichlid Fishes of Lake Victoria (Part 1) Figure 25.6 Origins of the Cichlid Fishes of Lake Victoria (Part 2) 25.3 How Do Biologists Use Phylogenetic Trees? Most flowering plants reproduce by outcrossing or mating with another individual. Other plants are selfing, which requires that they be self-compatible. Phylogenetic analysis can show how often self-compatibility has evolved. 25.3 How Do Biologists Use Phylogenetic Trees? The genus Linanthus has a variety of breeding systems. Outcrossing species have long petals and are self-incompatible. Selfcompatible species have short petals. A phylogeny was constructed using ribosomal DNA. Self-incompatibility is the ancestral state. Figure 25.7 Phylogeny of a Section of the Plant Genus Linanthus (Part 1) Figure 25.7 Phylogeny of a Section of the Plant Genus Linanthus (Part 2) 25.3 How Do Biologists Use Phylogenetic Trees? Phylogenetic analysis can be important in understanding zoonotic diseases (infectious organisms are transmitted to humans from another animal host). Example: HIV was acquired from chimpanzees and sooty mangabeys. Figure 25.8 Phylogenetic Tree of Immunodeficiency Viruses 25.3 How Do Biologists Use Phylogenetic Trees? Reproductive success of male swordtails is associated with long “swords” (sexual selection). Evolution of the sword may result from a preexisting bias of female sensory systems—sensory exploitation hypothesis. Phylogenetics identified platyfishes as the closest relatives. 25.3 How Do Biologists Use Phylogenetic Trees? Artificial swords were attached to platyfish males. Female platyfish preferred males with the artificial swords, supporting the idea that females had a preexisting bias even before the swords evolved. Figure 25.9 The Origin of a Sexually Selected Trait in the Fish Genus Xiphophorus 25.3 How Do Biologists Use Phylogenetic Trees? Rate of evolution of influenza virus is high. Phylogenetic analysis indicates there is a strong selection by the human immune system for most strains. Only strains with the greatest number of substitutions on hemagglutinin (surface protein recognized by the immune system) are likely to leave descendents. Figure 25.10 Model of Hemagglutinin, a Surface Protein of Influenza 25.3 How Do Biologists Use Phylogenetic Trees? Phylogenetic analysis helps biologists predict which of the currently circulating strains are most likely to survive and leave descendents. This information is then used to formulate influenza vaccines. 25.4 How Does Phylogeny Relate to Classification? The biological classification system was started by Swedish biologist Carolus Linnaeus in the 1700s. Binomial nomenclature gives every species a unique, unambiguous name. Figure 25.11 Many Different Plants Are Called Bluebells 25.4 How Does Phylogeny Relate to 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 is often included. Example: Homo sapiens Linnaeus 25.4 How Does Phylogeny Relate to 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). 25.4 How Does Phylogeny Relate to Classification? Families are grouped into orders Orders into classes Classes into phyla Phyla into kingdoms Application of these levels is somewhat subjective. 25.4 How Does Phylogeny Relate to Classification? Biological classifications are used to express the evolutionary relationships of organisms. Taxa are expected to be monophyletic: a taxon contains an ancestor and all descendents of that ancestor, and no other organisms. Also known as a clade. 25.4 How Does Phylogeny Relate to Classification? But 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. 25.4 How Does Phylogeny Relate to Classification? A true clade or monophyletic group can be removed from the tree by making a single “cut.” Taxonomists agree that polyphyletic and paraphyletic groups are not appropriate taxonomic units. These groups are gradually being eliminated and taxonomic classifications revised. Figure 25.12 Monophyletic, Polyphyletic, and Paraphyletic Groups 25.4 How Does Phylogeny Relate to Classification? Explicit rules govern the use of scientific names. Ensures that there is only one correct scientific name for any taxon. Different taxonomic rules have been developed for zoology, botany, and microbiology, but taxonomists are now working towards common sets of rules.