Gene Evolution 1

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

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 can transport DNA segments from flanking regions

Integrase DNA transposons can insert promoters in new genomic locations Protease Repetitive DNA from “dead” transposable elements encourages duplication by recombination

Gene duplication Gene families evolve on a range of scales

• Single genes • Chromosomal segments (a few genes) • Partial chromosomes • Entire chromosomes • Whole genome duplication

20 Complete and partial chromosomal duplications are almost always deleterious

nichd.nih.gov e.g. Down’s syndrome

Gene duplication Gene families evolve on a range of scales

• Single genes • Chromosomal segments (a few genes) • Partial chromosomes • Entire chromosomes • Whole genome duplication

21 Autopolyploidy

Project goals

Allopolyploidy

Paramecium

http://en.wikipedia.org/wiki/Paleopolyploidy Ref: Adams & Wendel, 2005; Cui et. al, 2006; Wolfe, 2001.