Reconstructing and Using Phylogenies

Reconstructing and Using Phylogenies

21.1 All of Life Is Connected through Its Evolutionary History
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 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. 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.

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.

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.

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
Evolutionary relationships among organisms can be represented in a treelike diagram.

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)
(A) Phylogenetic trees can be produced with time scales, as shown here, or with no indication of time. If no time scale is shown, then the trees are only meant to depict the relative order of divergence events. (B) Lineages can be rotated around a given node, so the vertical order of taxa is largely arbitrary.

Figure 21.2 How to Read a Phylogenetic Tree (Part 2)
(A) Phylogenetic trees can be produced with time scales, as shown here, or with no indication of time. If no time scale is shown, then the trees are only meant to depict the relative order of divergence events. (B) Lineages can be rotated around a given node, so the vertical order of taxa is largely arbitrary.

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
All clades are subsets of larger clades, with all of life as the most inclusive taxon. In this example, the groups called mammals, amniotes, tetrapods, and vertebrates represent successively larger clades. Only a few species within each clade are represented on the tree.

Sister species: Two species that are each other’s closest relatives. Sister clades: Two clades that are each other’s closest relatives.

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.

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.

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.

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.

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.)

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
The supporting bone structures of both bat wings and bird wings are derived from a common four-limbed ancestor and are thus homologous. However, the wings themselves—an adaptation for flight—evolved independently in the two groups.

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.

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.

Similar traits generated by convergent evolution and evolutionary reversals are called homoplastic traits or homoplasies.

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 phylogenetic tree and explain the biological interpretation of each part. Make inferences and predictions about evolutionary groups based on a phylogenetic tree.

Explain how homoplasies (convergences and reversals of character states) are accounted for when reconstructing phylogenetic relationships.

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: 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.

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 Traits

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.

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
This phylogenetic tree was constructed from the information in Table 21.1 using the parsimony principle. Each clade in the tree is supported by at least one shared derived trait, or synapomorphy.

Phylogenetic trees are typically constructed using hundreds or thousands of traits. How are synapomorphies and homoplasies determined?

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.

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.

Morphology Most species have been described by morphological data.

Limitations of morphological analyses Some taxa show few morphological differences. Difficult to compare distantly related species. Some morphological variation is caused by environment.

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 Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates (Part 1) Figure Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates All chordates—a taxonomic group that includes sea squirts and frogs—have a notochord at some stage of their development. The larvae share similarities that are not apparent in the adults. Such similarities in development can provide useful evidence of evolutionary relationships. The notochord is lost in adult sea squirts. In adult frogs, as in all vertebrates, the vertebral column replaces the notochord as the support structure.

Paleontology Fossils provide information about morphology of past organisms and where and when they lived. Fossils help determine derived and ancestral traits and when lineages diverged. Limitations: Fossil record is fragmentary and missing for some groups.

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.

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.

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.

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.

Experiments with living organisms and computer simulations are used to test the accuracy of phylogenetic reconstructions. In one experiment, a culture of bacteriophage T7 was manipulated so that nine different lineages evolved.

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 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
Original Paper: Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux Experimental phylogenetics: Generation of a known phylogeny. Science 255: 589–592. To test whether analysis of gene sequences can accurately reconstruct evolutionary phylogeny, we must have an unambiguously known phylogeny to compare against the reconstruction. Will the observed phylogeny match the reconstruction?

Analyze a phylogenetic tree to identify synapomorphies, homoplasies, and relationships among taxa. Reconstruct a phylogenetic tree from a data matrix of characters.

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 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
The evolutionary relationships of immunodeficiency viruses show that these viruses have been transmitted to humans from two different simian hosts: HIV-1 from chimpanzees and HIV-2 from sooty mangabeys. (SIV stands for simian immunodeficiency virus.)

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
This phylogenetic analysis demonstrated that strains of HIV present in a victim (shown in red) were a phylogenetic subset of viruses isolated from a physician’s patient (shown in blue). This analysis was part of the evidence used to show that the physician drew blood from his HIV-positive patient and injected it into the victim in an attempt to kill her. A jury found the physician guilty of attempted murder.

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
The tail extension of male swordtails (genus Xiphophorus) apparently evolved through sexual selection, as females mated preferentially with males that had long “swords.” Phylogenetic analysis reveals that Priapella split from the swordtails before the evolution of the sword. The independent finding that female Priapella prefer male Priapella with an artificial sword further supports the idea that this appendage evolved as a result of a preexisting preference in females.

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.

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.

Leptosiphon species have a variety of breeding systems. Outcrossing species have long petals and are self-incompatible. Self-pollinating 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)
Self-compatibility apparently evolved independently three times among these species of the plant genus Leptosiphon. Because the appearance and structure of the flowers converged in the three selfing lineages, taxonomists mistakenly thought they were varieties of the same species.

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.

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)

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.

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
Amino acid replacements in hemoglobin have occurred at a relatively constant rate over nearly 500 million years of evolution. The graph shows the relationship between the time of divergence and the proportion of amino acids that have changed for 13 pairs of vertebrate hemoglobin proteins. The average rate of change represents the molecular clock for hemoglobin in vertebrates.

Molecular clocks must be calibrated using independent data, such as the fossil record, known divergences, or biogeographic dates.

A molecular clock helped determine when HIV-1 entered the human population from chimpanzees. The clock can be calibrated using samples taken during the 1980s and s, and then tested using samples from the 1950s.

Figure 21.12 Dating the Origin of HIV-1 in Human Populations (Part 1)
(A) A phylogenetic tree for samples of the main group of HIV-1 virus. The dates indicate the years in which the samples were taken. (For clarity, only a small fraction of the samples that were examined in the original study are shown.) (B) A plot of sample year versus genetic divergence from the common ancestor provided an average rate of divergence, or a molecular clock. (C) The molecular clock was used to date a sample taken in 1959 (as a test of the clock) and to estimate the date of origin of the HIV-1 main group (about 1930). Branch length from a common ancestor represents the average number of substitutions per nucleotide.

Figure 21.12 Dating the Origin of HIV-1 in Human Populations (Part 2)
(A) A phylogenetic tree for samples of the main group of HIV-1 virus. The dates indicate the years in which the samples were taken. (For clarity, only a small fraction of the samples that were examined in the original study are shown.) (B) A plot of sample year versus genetic divergence from the common ancestor provided an average rate of divergence, or a molecular clock. (C) The molecular clock was used to date a sample taken in 1959 (as a test of the clock) and to estimate the date of origin of the HIV-1 main group (about 1930). Branch length from a common ancestor represents the average number of substitutions per nucleotide.

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.

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 started by Swedish biologist Carolus Linnaeus in the 1700s. Binomial nomenclature gives every species a unique, unambiguous name.

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

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).

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.

Families are grouped into orders; orders into classes; classes into phyla; phyla into kingdoms. Application of these levels is somewhat subjective.

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.

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
Monophyletic groups are the basis of taxa in modern biological classifications. Polyphyletic and paraphyletic groups are not appropriate for use in classifications because they do not accurately reflect evolutionary history.

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.

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)
All three of these distinct plant species are called “Indian paintbrush.” Binomial nomenclature allows us to avoid the ambiguity of such common names and communicate exactly what is being described. (A) Asclepias tuberosa is a perennial milkweed native to eastern North America. (B) Castilleja coccinea is also native to eastern North America, but is a member of a very different group of plants called scrophs. (C) Hieracium aurantiacum is a European species of aster that has been widely introduced into North America.

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.

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
Mikhail Matz and his colleagues used phylogenetic analysis to reconstruct the sequences of fluorescent proteins that were present in the extinct ancestors of modern corals. They then expressed these proteins in bacteria and plated the bacteria in the form of a phylogenetic tree to show how the colors evolved over time.

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.

Reconstructing and Using Phylogenies

Similar presentations

Presentation on theme: "Reconstructing and Using Phylogenies"— Presentation transcript:

Similar presentations

About project

Feedback

Log in

Auth with social network:

Reconstructing and Using Phylogenies

Similar presentations

Presentation on theme: "Reconstructing and Using Phylogenies"— Presentation transcript:

Similar presentations

About project

Feedback