Lecture 5 Systematics and Phylogeny PDF

Systematics and Phylogeny BIO 110 SYSTEMATICS UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Outline I. Characters A....

Systematics and Phylogeny BIO 110 SYSTEMATICS UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Outline I. Characters A. Intrinsic VS Extrinsic B. Genotypic VS Phenotypic II. Homology (Homology Assessment) Ontogeny, Tokogeny, Phylogeny III. Divergent and Convergent IV. Tree Interpretation A. Phylogenetic Trees B. Assumption about Trees UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Objectives At the end of the class, the student must be able to: 1.Familiarize oneself with characters; 2.Understand the relationship of characters and homology; and 3.Interpret phylogenetic trees. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  I. CHARACTERS Fundamental Unit of systematic analysis Characters are theory-laden objects Could be used for comparison, but we usually limit ourselves to those features that are intrinsic and heritable. Character = Property/Component/Feature UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  A. Intrinsic VS Extrinsic INTRINSIC EXTRINSIC Morphology Population size Behavior Geographic location Biochemistry Environmental conditions Intrinsic features are the more frequent sources of systematic information. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  B. Genotypic VS Phenotypic GENOTYPIC PHENOTYPIC the most obvious clearly more similar in appropriate source of parents and offspring comparative variation. than they are to other All changes are creatures. heritable. anatomy, behavior, overall shape, and size. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  How about Character States? UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  How about Character States? States can be: Binary (Yes/No) or Multistate (Number of Teeth) Quantitative (Weight) or Qualitative (Spotted) Discrete (Number of legs) or Continuous (Weight) Character: Character States: Eye color Blue, Brown, Green Mammary Glands Present, Absent Number of Legs 0, 2, 4, 8, etc. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  What is Homology? UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  II. HOMOLOGY (Homology Assessment) similarities in traits or features that are the result of a common evolutionary ancestry may have different functions in different species but share similar underlying structures used to infer evolutionary relationships and to study the evolution of traits over time UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Homology requires common origin at THREE LEVELS! Organism Level ONTOGENY: developmental stages. Population Level TOKOGENY: within a sexually reproducing species. Species Level PHYLOGENY: across taxa or groups. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Homology requires common origin at THREE LEVELS! Organism Level ONTOGENY: developmental stages. How? via Organogenetic studies same cell lineage: ORGANS same tissue position: TISSUE same precursor molecule: MOLECULES same initial sequence: GENES UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Homology requires common origin at THREE LEVELS! Analogy Do not share a common origin. Orthology similar at certain sub-levels Serialogy repeated structures, within an individual, are similar at certain sub-levels. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Homology requires common origin at THREE LEVELS! Population Level TOKOGENY: within a sexually reproducing species. How? Study features such as: Phenotype Chromosome number Phylogeography etc. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Homology requires common origin at THREE LEVELS! Xenology transfer from one lineage to another belonging to a different species via hybridization (Horizontal Gene Transfer) Genealogy transfer from one generation to another (same species) Paralogy are different characters UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Homology requires common origin at THREE LEVELS! Species Level PHYLOGENY: across taxa or groups. How? Character compatibility Parsimony Bayesian Likelihood Analysis UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  III. DIVERGENT AND CONVERGENT Divergent two or more species that share a common ancestor evolve and develop differing characteristics or traits over time. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  IV. DIVERGENT AND CONVERGENT Convergent unrelated or distantly related species independently evolve similar features or traits in response to similar environmental or ecological conditions. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  TAXA Collections of organisms Two organism “Species” “Terminal entities” ≠ single creature as taxon Since all groups (size > 1) are arbitrary in their level (although “real” in the sense of monophyly), “higher taxa” are arbitrary Operational Taxonomic Units (OTUs) & Hypothetical Taxonomic Units (HTUs) UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  V. TREE INTERPRETATION Central objects of systematic analysis Cladograms (Hennig) – nested sister-group relationships Trees – series of ancestors–descendants statements Scenario – endowed with explanation in terms of evolution, ecology, or other biological or geological factors of the changes. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  CLADOGRAM, TREE, SCENARIO UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic Trees A gene tree that models a genealogy of a gene. Incorporates branch lengths, which represent the estimated amount of genetic or evolutionary change that has occurred over time Branch lengths – represent the number of character changes Nodes – points where the different taxon deviate / speciate Root Outgroup – basal taxon / farthest relative Ancestors Descendants Clade / Cluster / Group – group of organisms with a common ancestors UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  How do we read and interpret trees? UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  TOPOLOGY Figure 1. Examples of trees with the same (top box) and different (lower box) topologies. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  TOPOLOGY Figure 2. Branch length representations. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  NODES Figure 3. A cartoon diagram of a tree indicating types of nodes. Image courtesy of Andrew Rambaut. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  ROOT Figure 4. Rooting a tree: before (left) and after (right). NB: The branch lengths are not drawn to scale. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  ROOT Figure 5. Rooting a tree: before (left) and after (right). NB: The branch lengths are not drawn to scale. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  ROOT UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  CONFIDENCE Confidence Uncertainty in phylogenetics. several approaches that are commonly used to estimate our confidence in the inferred tree topology including bootstraps, likelihood and Bayesian Figure 6. Example of confidence in Phylogeny. approaches. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  CONFIDENCE UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic Trees UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic Trees Figure 7. The cladogram exhibits roles of extant and extinct species in grouping phylogenies in stem and crown groups (Retrieved from: https://bioone.org/journals/Paleobiology/volume- 31/issue-4/04028.1/Saving-the-stem-groupa- contradiction-in-terms/10.1666/04028.1.short). UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic a.) Trees b.) UNIVERSITY OF THE PHILIPPINES BAGUIO Figure 7. Sample of a a.) Diagonal type, and a b.) Bracket type of College of Science – Department of Biology phylogenetic tree (Image source: Dee et al., 2018).  CLARIFICATIONS! Figure 8. Reading phylogenetic trees from ancestors to descendants. (Retrieved from http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_05). UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  CLARIFICATIONS! UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Figure 9. (I) Cladogram, (II) Phylogram, and (III) Dendrogram. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic Trees Phylogenetic classification Naming species Understand life history Learn about the evolution of complex features To make predictions about poorly-studied species UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Assumptions about Trees Apomorphy: specialized or derived character state Synapomorphy: derived trait shared by two or more groups Autapomorphy: derived trait that is unique to one group Symplesiomorphy: primitive or ancestral trait UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic Trees Monophyletic (scheme=Hennig,1950; term=Haeckel, 1868) more closely related to every other taxon in the group than to any taxon that is classified outside the group group must contain all descendants of a common ancestor “Reptilia,” not including Aves, but including its sister- taxon Crocodilia Recognized and defined, by synapomorphy and are the only “natural” (i.e. phylogenetic = directed subtree) groups. UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic Trees Paraphyletic groups are those based on symplesiomorphy (shared primitive features) primitive features (often absence-based) Polyphyletic groups on convergence Functional, convergent similarity is mistaken for similarity based on descent UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology  Phylogenetic Trees UNIVERSITY OF THE PHILIPPINES BAGUIO College of Science – Department of Biology