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Chapter 4

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BIOL 359
Jonathan Witt

BIOL359 - Evolution Winter 2013 Chapter 4: Estimating Evolutionary Trees 4.1. The Logic of Phylogeny Inference - The most closely related taxa have the most traits in common o Nucleotide sequences, skeletal elements, embryonic development patterns etc. - Synapomorphies Identify Monophyletic Groups o Synapomorphy: Homologous trait shared among species, similar from a common ancestor “shared, derived traits” (Type of trait useful in estimating phylogenies) o Monophyletic group/Clade/Lineage: A group that includes an ancestor & all its descendants  Synapomorphies identifies between monophyletic groups (@ different taxonomic level)  Identifies the evolutionary branching points  Nested, each branching event adds one or more shared traits “each branch with unique derived traits” o Cladistic methods: Used to infer a phylogeny, determine which traits are more ancient and which are more derived  Outgroup analysis: The character state in the group of interest “ingroup” is compared to the state in very closely relatives that branched off earlier “outgroup” o Cladogram: Phylogenetic tree inferred by clustering synapomorphies as distinct branches  Synapomorphies are indicated on cladograms with bars across the branches  Limbs are derived from the limbs of common ancestors of tetrapods & lungfish  Moist skin is derived from the scaled skin of fish-like ancestors  Amniotic egg is derived from eggs similar to those in lungfish & amphibian - Problems in Reconstructing Phylogenies o Analyze homologous traits & identify characteristics that qualify as synapomorphies o Not All Similar Traits Are Homologous  Synapomorphies are reliable; homoplasy is misleading “interference”  Homoplasy: When similarity in traits are not due to homology “Parsimony – 2 changes”  Reversal “Back-mutations”: A mutation in DNA sequence results in having the same nucleotide as the ancestor. Common, only 4 possible choices (A, T, C, G) o Identical DNA sequences but was not inherited from the same ancestor  Convergent evolution: Natural selection favors similar structures as solutions to problems posed by similar environments (not homologous & are not synapomorphies) o E.g. Hippos vs. Crocodiles  Camera eyes  Hippos: Share fur, lactation with mammals  Crocs: Share array of synaptomorphies with reptiles  Both however have eyes located at the top of their skull instead of on the side o E.g. Octopus & vertebrate: camera eyes are not from a common ancestor, both linages evolved independently because both require eyesight to find food & avoid danger  Octopus: Layer of light-sensitive cells is oriented towards the opening where light enters the eye. Muscles move the lens back & forth & changes the shape of the eyeball  Vertebrate: Layer of light-sensitive cells is oriented in the opposite direction. Muscle changes the shape of the lens o E.g. Wings of bats & birds; steam-lined shapes of sharks & whales; elongated, limbless bodies of snakes & legless lizards  Homoplasy vs. Homology  Analyze many traits by reconstructing evolutionary relationships, instead of just one or a few traits BIOL359 - Evolution Winter 2013  Morphological traits that are similar due to shared ancestry should develop in similar ways during development  Resolving Conflicts in Data Sets: The Role of Parsimony  Parsimony: Simpler explanations > Complex explanations (Minimize homoplasy), preferred tree is the one that minimizes the total # of evolutionary changes o Logical way to distinguish homology from homoplasy & identify synapomorphies. Not infallible o Convergence & reversal will be rare relative to similarity from common ancestor, so they require more evolutionary changes 4.2. The Phylogeny of Whales - Whales, dolphins & porpoises: Lack of posterior limbs o Oldest fossil of whales: Mesonychians – Amphibious mammals, Himalayas, 53.5 million years old o Fossil record supports the hypothesis that whales evolved from ancestors that had hind limbs, but lack multiple direct transitional forms - Choosing Characters: Morphology and Molecules o Skeletal features and other morphological characteristics  Pro: Important in studying fossil species, especially well if homoplasy can be distinguished from homology by examining living representatives of the group  Con: Slow, painstaking work by a highly trained professional o DNA sequences and other molecular traits  Pro: Rapid analysis of large numbers of DNA sequences, can trace transitional forms with nucleotides before reversal to minimize homoplasy  Con: Homoplasy may be difficult to recognize, since there’s only 4 character states A, C, G & T, in DNA - Finding the Best Tree Implied by the Data o E.g. Parsimony with a Single Morphological Character  Ungluates “hoofed animals” contains 2x monophyletic groups  Perissodactyls: Horses & rhinos  Artiodactyls: Cows, deer, pigs, hippos, and camels o Astragalus “ankle bone”: both ends are smooth and pulley shaped, allows the foot to rotate in a wide arc around the end of the ankle “long stride”  Whales likely evolved from the artiodactyls group rather than the Hippo group (The only ungulate that spends a lot of time under water) o Whales are fully aquatic & Hippos are semi-aquatic o Fossil evidence: Some features of the pulley-shaped astragalus are found in the earliest whales (whales are descended from an artiodactyl ancestor) o Parsimony with Multiple Molecular Characters  Sequenced a milk-production protein – Beta-casesin  Look for variable but uniformative sites  Artiodactyla hypothesis  total of 47 nucleotide changes  Whale + Hippo hypothesis  total of 41 nucleotide changes  Parsimonious: Similarities in DNA sequence data from whales and hippos are
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