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Chapter 4

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University of Waterloo
BIOL 359
Jonathan Witt

BIOL 359 Lecture 7 Janice Wong Evolution Phylogeny Chapter 4: Estimating Evolutionary Trees 4.1| The Logic of Phylogeny Inference Synapomorphies Identify Monophyletic Groups • Recall: homology: similarity in traits that is due to descent from a common ancestor • Types of homologies that are useful in estimating phylogenies are called synapomorpies • Synapomorphy: a homologous trait that is shared among certain species and is similar because it was modified in a common ancestor. They are shared, derived traits. • Monophyletic group: any group that includes an ancestor and all of its descendents • Not all homologous traits are synapomorphies, but all synapomorphies are homologous • 1. Synapomorphies are important because they identify monophyletic groups, and evolutionary branch points o Speciation starts when two populations become genetically isolate, meaning that gene flow is reduced or absent o Some of the homologous traits in each population undergos changes due to mutation, selection, and drift • 2. Synapomorphies create a nested hierarchy o As described by synapomorphies also describes the hierarchy of branching events • Cladistic methods: phylogeny inference methods that use these principles. • Cladogram: a phylogenetic tree inferred by clustering synapomorphies • Synapomorphies are indicated on cladograms with bars across the branches and then described with labels Problems in Reconstructing Phylogenies Not All Similar Traits are Homologous • Convergent evolution: similarity between species that is caused by a similar, but evolutionarily independent, response to a common environment • Occurs when natural selection favours similar structures as solutions to problems proposed by similar environments • If convergent evolution has occurred, then similar traits are not homologous and do not qualify as synapomorphies • Ex. Octopuses and vertebrates did not inherit their camera eyes from a common ancestor • The two lineages independently evolved camera eyes because both depend on eyesight to find food and avoid danger • Ex. Wings of bats and birds, streamlined shapes of sharks and whales, the elongated, limbless bodies of snakes and legless lizards Reversal complicate phylogeny inference (Fig.4.5) • Evolution at the molecular level entails changes in nucleotide sequence due to mutation • New nucleotide sequences are inherited by descendant lineages as shared derived traits • A mutations occurred and changed the fifth base in the sequence from an A to a T • Ancestral DNA sequence: TGCTATT 1 BIOL 359 Lecture 7 Janice Wong Evolution Phylogeny • However, later on another mutation occurred, and changed the fifth position back to A • Descendant DNA sequence: from TGCTTTT to TGCTATT • They did not inherit this sequence from the same ancestor, the similar bases are not homologous • If a reversal has occurred, then similar traits are not homologous and do not qualify as synapomorphies • Convergence and reversal are lumped under the term homoplasy o Similarities in traits that are not due to homology Distinguishing Homology from Homoplasy • The essence of phylogeny inference is to maximize the use of reliable information while minimizing the impact of misleading information • Synapomorphies are reliable; homoplasy is misleading • Slide 26 o The evolution of the camera eye is not a result of homology, but convergence o Tree a) assumes that the octopus eye and vertebrate eye are homologous, and therefore it evolved at the base of the tree. The eye would then have to be lost from 6 other points o Tree b) assumes that the octopus eye and the vertebrate eye resulted from convergent evolution, so there are just two changes • Structural homologies result from developmental homologies, which result from genetic homologies • Homoplasy implies that species are closely related, when they are not Resolving Conflicts in Data Sets: The Role of Parsimony • Parsimony is a general logical criterion, provides one way to identify which branching pattern minimizes the effects of homoplasy • Parsimony is a logical way to distinguish homology from homoplasy and identify synapomorphies. • When applied to phylogeny inference, the preferred tree is the one that minimizes the total amount of evolutionary change that has occurred • This will also minimize homoplasy 4.2| The Phylogeny of Whales Choosing Characters: Morphology and Molecules • Morphological traits o Essential when studying species that exists only as fossils o Convincing when homoplasy can be distinguished from homology o Slow & a lot of work • Molecular traits o Analyzing DNA sequences are easier nowadays thanks to techonology o Homoplasy can be difficult to recognize in molecular data
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