BIOM 121 1nd Edition Exam 4 Study Guide Lectures 16 20 Lecture 16 Statistical Methods Linnean Taxonomy vs Phylogenetic Taxonomy Charles Linneaus phylogenetic trees I Linnean rigid hierarchy kingdom phylum etc a Sub groups for those that don t fit b No room for fossils c Required expert knowledge of groups II Phylogenetic a Phylogeny the course of evolution Basic Premise of Phylogenetics I All life can be grouped into a nested hierarchy by homologous characters a DNA structure is identical b Metabolism basically works the same in all animals c Nucleus organelles chromosomes II Most parsimonious simplest explanation to conclude that there were inherited from a common ancestor III The most closely related taxa should have the most traits in common Tree Terminology I Node points where one species split into two or more descendent species II Root common ancestor of all species on tree III Tips most recent species usually extant IV Sister taxon the hypothesized closest genealogical relative of a taxon exclusive of their most recent common ancestor V Taxon taxa a grouping given a proper name Monophyly vs Paraphyly I Monophyletic group natural clade a Single common ancestor b All of it s known descendants II Paraphyletic group a Single common ancestor b Does not include all descendants c Non avian dinosaurs Homology I Any similarity between species that is due to inheritance from a common ancestor Homoplasy II Similar character states that evolved independently III Examples loss of limbs fish whales snakes lizards streamlined morphology in sharks and dolphins etc All life can be grouped into a nested hierarchy by homologous characters I Types of Data Charcters Traits a Anatomy b Development c DNA RNA mtDNA etc d Behavior e Physiology II Making Trees a Use data to arrange organism by their ordered branching of evolutionary relationships b Goal identification ofmonophyletic groups natural groups or clades c Taxa mammalia canis familiaris are defined by characters d Parsimony i Fewest number of changes ii Maximum parsimony for many characters iii Lowest sum total number of changes e Objective not subjective i Not based on individual bias ii Assumes no a priori hypotheses of relationships III What defines monophyletic groups clades a Synapomorphies Shared derived characters i Ex 5 fingers fur feathers in birds must be unique to group b Must have the same character state c Must be homologous the same characters IV Character Polarity and Outgroups a Character state any trait value for a taxon b Polarity primitive vs derived directionality of how a character evolved i Jawless primitive jawed derived c Outgroup a more primitive group included to allow character polarity to be assessed all primitive V The Molecular Clock a How do we know when things happened i Geological timescale radiometric dating is used to date fossils ii Can we use molecular data to estimate the date of events not documented in fossils b Expected Patterns of Molecular Evolution from i Genetic drift constant rate of substitution that is equal to the mutation rate ii Use molecular traits that change at a steady rate timing and rate of evolution iii Date the common ancestor between two groups iv Date major evolutionary events v Especially useful when the fossil record is poor eg Flatworms viruses c Simple Molecular Clock Model i Changes at the molecular level accumulate at a constant rate ii Know rate iii Know number of changes iv Time v Molecular clocks must be calibrated Lecture 17 I II Synapomorphies Review a Synapomorphies define monophyletic groups b Derived trait character state is different than the ancestral state c Shared by the common ancestor and all members i BUT further modifications are okay ex Loss of limbs in snakes ii When there are reversals other synapomorphies place the group is that clade IN CLASS ACTIVITY Create a Candy Bar Phylogenetic Tree Lecture 18 I II The Comparative Method a A method for studying selection and adaptation b Compares species or populations c Tests for patterns across species i Correlations among traits ii Correlations between traits and features of the environment d Shows what has happened in past evolution e One of the most common methods for studying adaptation f Types of questions i Are large testes in bats an adaptation for sperm competition ii What are the respiratory adaptations to living in burrows iii What adaptations are associated with an aquatic lifestyle in mammals iv Does a reduced basal metabolic rate evolve in desert living animals Testes Size in Bats a Male bat testes size varies widely across species 0 12 8 5 of body mass b In primates the range is 0 02 0 75 c Larger testes larger ejaculates d Larger groups increases multiple mating e Is group size related to testes size III IV V VI i Do group size and testes size evolve in tandem ii Need to take phylogeny into account f Accounting for Phylogeny i There is variation among species in bother group size and relative testes mass ii Not all bats with large testes mass or large group size are in the same clade iii Why do we need to account for phylogeny Unit 6 Speciation and History of Life a Species i A group of interbreeding populations that are evolutionary independent of other populations ii The smallest evolutionary independent unit independent evolutionary trajectory iii A group that evolves independent of other groups The Biological Species Concept a Species a group of interbreeding populations that are reproductively isolated from other groups b Reproductive isolation defines evolutionary independence c Species do not exchange genes with one another no gene flow d Problems i Not relevant to asexual populations ii Cannot be used for fossils iii Boundary is sometimes blurry 1 Example Salamanders in California 2 Hybrid zones woodpeckers e Video on salamanders in California i Sometimes breed with each other but the offspring usually do not survive ii Reproductively isolated from one another 1 Either cannot mate at all or hybrids are unable to mate and reproduce The Phylogenetic Species Concept a Species a group of populations forming a monophyletic group b Must of diverged genetically and morphologically enough to show synapomorphies c Problems i Requires substantial resources to implement to sample etc ii May double the number of named species e g cryptic species Speciation a Formation of two or more daughter species from a single ancestral species b Key component genetic isolation i Allopatric speciation 1