Gene evolution 1 03‐327/727 Lecture 3 Fall 2013 Review of character state analysis Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes • Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly • Relatedness: common ancestry, no similarity • Classification, cladistics, and phylogenetics 1 Character •A heritable trait or "well defined feature that … can assume one or more mutually exclusive states“* Gorilla Chimp Human Fur Yes Yes No Wt Heavy Light Light Tool No Yes Yes use * Graur and Li, Molecular Evolution, 2000 Use parsimony to infer • Ancestral character states (states on internal nodes) • Character state transitions (on branches) Parsimony: • Thrifty, stingy • The hypothesis that requires the fewest changes to explain the data is the best Gorilla Chimp Human hypothesis. Fur Yes Yes No Wt Heavy Light Light Tool No Yes Yes use 2 Use parsimony to infer furry, light • Ancestral character states (states on internal nodes) gain: tool use • Character state transitions gain: (on branches) body mass furry, light, tool use loss: fur Parsimony: • Thrifty, stingy • The hypothesis that requires the fewest changes to explain the data is the best Gorilla Chimp Human hypothesis. Fur Yes Yes No Wt Heavy Light Light Tool No Yes Yes use • Ancestral (basal) states: furry, light • Low body mass (~50kg) • Fur • Doesn’t use tools gain: tool use gain: furry, light body mass tool use loss: fur Character state transitions Gorilla Chimp Human • Derived states Fur Yes Yes No • High body mass (~175kg) • No fur Wt Heavy Light Light Tool • Tool use No Yes Yes use 3 Review • Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly • Relatedness: common ancestry, no similarity • Classification, cladistics, and phylogenetics Homoplasy: A two‐state character (trait) is homoplastic with respect to a tree, if it cannot be explain by a single state transition. These traits are not homoplastic because only one state change occurred. 4 A two‐state character (trait) is homoplastic, if it cannot be explain by a single state transition. Homoplasy can arise through a reversal. Example: larval form in salamanders Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution, Wake, Wake and Specht. Science 25 February 2011: Vol. 331 no. 6020 pp. 1032‐1035 A two‐state character (trait) is homoplastic, if it cannot be explain by a single state transition. Homoplasy can arise through parallel or convergent evolution. Example: body elongation Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution, Wake, Wake and Specht. Science 25 February 2011: Vol. 331 no. 6020 pp. 1032‐1035 5 A two‐state character (trait) is homoplastic, if it cannot be explain by a single state transition. Homoplasy can arise through parallel or convergent evolution. Example: elongation of individual vertebrae Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution, Wake, Wake and Specht. Science 25 February 2011: Vol. 331 no. 6020 pp. 1032‐1035 Monphyly, paraphyly and polyphyly Monophyly Polyphyly The species possessing the The species possessing the orange orange trait form a monophyletic trait are not monophyletic, group. Note: Orange is the because of homoplasy derived state. Paraphyly The species possessing the orange trait are not monophyletic, because orange is the ancestral state. Data: A single character with two states: orange and blue. 6 Review • Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes • Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly Relatedness: common ancestry, no similarity • Classification, cladistics, and phylogenetics Common ancestry versus similarity • Crocodiles are similar to lizards because the share basal characters (green) • Crocodiles differ from birds due to derived characters (pink)unique to birds • Derived characters shared by birds and Similarity due to shared basal crocodiles (yellow) support the characters can be misleading. monophyly of birds and crocodiles. Birds Crocs Lizards Turtles scales, shell, External feathers skin skales, skin skin Body temp warm cold cold cold Legs two four four four Gait upright semi-erect sprawling sprawling Antorbital fenestra yes yes no no Mandibular fenestra yes yes no no Builds/defends nests yes yes no no 7 Review • Inferring character evolution on a tree –Characters and character states –Ancestral and derived characters –The parsimony criterion – Inferring state changes • Properties of characters – Homoplasy, monophyly, paraphyly, polyphyly • Relatedness: common ancestry, no similarity Classification, cladistics, and phylogenetics Cladistic approach to evolutionary trees •Gather data on characters to be used • Establish the character states • Determine which states are ancestral (polarize the characters) • Select outgroup(s) with all ancestral states • Apply the principle of parsimony to obtain a hierarchical organization of taxa that minimizes state transitions 8 Example: Deuterostomes are monophyletic The traits mapped onto the phylogeny were carefully chosen to be derived states that define these groups. Classification, cladistics, and phylogenetics • Classification: traditionally based on similarity •Darwin: Evolution by descent from a common ancestor with modification • Cladistics: Attempts to unify classification and evolution by focusing on shared, derived characters –Construct trees based on shared, derived characters –In a classification based on such a tree, groups will share common ancestry and similar derived characters •Elegant solution, but too restrictive for most cases of interest today – Requires that the data satisfy strict criteria (no homoplasy) –More suited to morphoplogical characters, than sequence data –Not suited to data with conflicting phylogenetic signal – Cannot take advantage of more powerful statistical approaches. 9 Molecular Phylogenetics What are the processes we are trying to reconstruct? • Species evolution – Morphological characters –Molecular characters Gene evolution Outline •A motivating example: Hemoglobin evolution •Gene family evolution: Today – Mechanisms of new gene origination –Models of functional differentiation •Gene trees – Properties of gene trees –What they are good for • More terminology: Homology, orthology, paralogy • Multigene families 10 Vertebrate and globins arose via duplication of an ancestral globin gene in a vertebrate ancestor beta alpha Duplication Differentiation via mutation alpha beta Migration to separate chromosomes Chromosome 11 Chromosome 16 Additional duplication gave rise to the human globin family beta alpha alpha beta 11 Additional duplication gave rise to the human globin family Additional duplication gave rise to the human globin family beta alpha What is the benefit of having several copies of the globins? alpha beta 12 beta alpha Functional roles of the globins alpha beta , 0 wks 8 wks birth Embryo Fetus Adult Sickle cell disease beta alpha alpha beta 13 beta But fetal β globin (γ) can partially compensate for alpha the sickle cell mutation in adult fetal β globin! alpha beta In some individuals, fetal globin continues to , be expressed into adulthood 0 wks 8 wks birth Embryo Fetus Adult Outline •A motivating example: Hemoglobin evolution •Gene family evolution: – Mechanisms of new gene origination –Models of functional differentiation •Gene trees – Properties of gene trees –What they are good for • More terminology: Homology, orthology, paralogy • Multigene families 14 Gene duplication Gene families evolve on a range of scales • Single genes • Chromosomal segments a few genes) • Partial chromosomes • Entire chromosomes • Whole genome duplication Gene duplication Gene families evolve on a range of scales • Recombination • Single genes • Unequal crossing over • Chromosomal segments • Retrotransposition (a few genes) • Transposition • Non‐homologous End • Partial chromosomes Joining • Entire chromosomes • …. • Whole genome duplication 15 Tandem duplication and gene loss via unequal crossing over Tandem duplication and gene loss via unequal crossing over 16 OrthologousExamples relationships of tandem among duplications: the HBZ (A) and HBA (B)The genes globins of anthropoid primates, as inferred from an analysis of 5′ and 3′ flanking sequence. Hoffmann F G et al. Mol Biol Evol 2008;25:591-602 © The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: [email protected] Examples of tandem duplications: The globins 17 Examples of tandem duplications: The HOX cluster Examples of tandem duplications: The HOX cluster 18 Transposable elements Vestigial viruses that reside in the genome Endonuclease Reverse transcriptase •RNA transposons aka Retrotransposons Protease Integrase –Copy and Paste •DNA transposons Long terminal repeats –Cut and Paste TE families vary from genome to genome Retrotransposition integration of cDNA transcription cDNA RNA splicing reverse transcriptase ribosome 19 Transposable elements: Relevance to duplication Duplication by retrotransposition Endonuclease Reverse transcriptase DNA transposons