25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species...
-
Upload
constance-rose -
Category
Documents
-
view
221 -
download
2
Transcript of 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species...
![Page 1: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/1.jpg)
25Reconstructing and Using
Phylogenies
![Page 2: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/2.jpg)
25Phylogeny: the evolutionary history of a species
• Systematics: the study of biological diversity in an evolutionary context
• Taxonomy, a subdivision of systematics, is the theory and practice of classifying organisms.
• The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock
• Paleontologists: scientists who study fossils
![Page 3: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/3.jpg)
25The fossil record
• Sedimentary rock: rock formed from sand and mud that once settled on the bottom of seas, lakes, and marshes
• Dating:
• 1- Relative~ geologic time scale; sequence of species
• 2- Absolute~ radiometric dating; age using half-lives of radioactive isotopes
![Page 4: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/4.jpg)
25 Biogeography: the study of the past and present distribution of species
• Pangaea-250 mya √ Permian extinction
• Geographic isolation-180 mya
• √ African/South American reptile fossil similarities
• √ Australian marsupials
![Page 5: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/5.jpg)
25 Mass extinction
• Permian extinction (250 million years ago): 90% of marine animals; Pangea merge
• Cretaceous extinction (65 million years ago): death of dinosaurs, 50% of marine species; low angle comet
![Page 6: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/6.jpg)
25
![Page 7: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/7.jpg)
25 Phylogenetics
• The tracing of evolutionary relationships (phylogenetic tree)
• Linnaeus
• Binomial nomenclature
• Genus, specific epithet
• Homo sapiens
• Taxon (taxa)
![Page 8: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/8.jpg)
25 Phylogenetic Trees
• Cladistic Analysis: taxonomic approach that classifies organisms according to the order in time at which branches arise along a phylogenetic tree (cladogram)
• Clade: each evolutionary branch in a cladogram
• Types:
• 1- Monophyletic single ancestor that gives rise to all species in that taxon and to no species in any other taxon; legitimate cladogram
• 2- Polyphyletic members of a taxa are derived from 2 or more ancestral forms not common to all members; does not meet cladistic criterion
• 3- Paraphyletic lacks the common ancestor that would unite the species; does not meet cladistic criterion
![Page 9: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/9.jpg)
25 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 evolutionary changes in the traits of organisms.
![Page 10: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/10.jpg)
25 Phylogenetic Trees
• Systematists expect traits inherited from an ancestor in the distant 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.
![Page 11: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/11.jpg)
25 A Cladogram
![Page 12: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/12.jpg)
25 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.
![Page 13: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/13.jpg)
25 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 modified in the descendants.
• Two processes make this difficult:
Convergent evolution occurs when independently evolved features subjected to similar selective pressures become superficially similar.
Evolutionary reversal occurs when a character reverts from a derived state back to an ancestral state.
![Page 14: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/14.jpg)
Figure 25.2 The Bones Are Homologous, but the Wings Are Not
![Page 15: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/15.jpg)
25 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.
![Page 16: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/16.jpg)
25 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.
![Page 17: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/17.jpg)
25 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.
![Page 18: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/18.jpg)
25 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.
![Page 19: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/19.jpg)
25 Steps in Reconstructing Phylogenies
• Relationships between apes and humans 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.
![Page 20: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/20.jpg)
25 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.
![Page 21: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/21.jpg)
Table 25.1 Eight Vertebrates Ordered According to Unique Shared Derived Traits (Part 1)
![Page 22: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/22.jpg)
Table 25.1 Eight Vertebrates Ordered According to Unique Shared Derived Traits (Part 2)
![Page 23: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/23.jpg)
25 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.
![Page 24: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/24.jpg)
Figure 25.5 A Probable Phylogeny of Eight Vertebrates
![Page 25: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/25.jpg)
25 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 snakes, but these structures have been lost in the snake.
![Page 26: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/26.jpg)
25 Reconstructing a Simple Phylogeny
• Systematists use several methods to sort out the complexities of phylogenetic relationships.
• The most widely used method is the parsimony 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.
![Page 27: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/27.jpg)
25 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.
![Page 28: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/28.jpg)
Figure 25.8 Phylogeny and Classification (Part 1)
![Page 29: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/29.jpg)
Figure 25.8 Phylogeny and Classification (Part 2)
![Page 30: 25 Reconstructing and Using Phylogenies. 25 Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary.](https://reader035.fdocuments.us/reader035/viewer/2022062421/56649d0b5503460f949def84/html5/thumbnails/30.jpg)
25 Biological Classification andEvolutionary Relationships
• The traditional class Reptilia is paraphyletic 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.