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BCB 444/544. Lecture 29 Phylogenetics #29_Oct31. Required Reading ( before lecture). Mon Oct 29 - Lecture 28 Promoter & Regulatory Element Prediction Chp 9 - pp 113 - 126 Wed Oct 30 - Lecture 29 Phylogenetics Basics Chp 10 - pp 127 - 141 Thurs Oct 31 - Lab 9

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Bcb 444 544

BCB 444/544

Lecture 29

Phylogenetics

#29_Oct31

BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


Required reading before lecture

Required Reading (before lecture)

MonOct 29- Lecture 28

Promoter &Regulatory Element Prediction

  • Chp 9 - pp 113 - 126

    Wed Oct 30 - Lecture 29

    Phylogenetics Basics

  • Chp 10 - pp 127 - 141

    Thurs Oct 31 - Lab 9

    Gene & Regulatory Element Prediction

    Fri Oct 30 - Lecture 29

    Phylogenetic Tree Construction Methods & Programs

  • Chp 11 - pp 142 - 169

BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


Assignments announcements

Assignments & Announcements

Mon Oct 29 - HW#5

HW#5 = Hands-on exercises with phylogenetics

and tree-building software

Due: Mon Nov 5 (not Fri Nov 1 as previously posted)

BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


Bcb 544 team projects

BCB 544 "Team" Projects

Last week of classes will be devoted to Projects

  • Written reports due:

    • Mon Dec 3(no class that day)

  • Oral presentations (20-30') will be:

    • Wed-Fri Dec 5,6,7

    • 1 or 2 teams will present during each class period

  • See Guidelines for Projects posted online

  • BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Bcb 544 only new homework assignment

    BCB 544 Only: New Homework Assignment

    544 Extra#2

    Due: √PART 1 - ASAP

    PART 2 - meeting prior to 5 PM Fri Nov 2

    Part 1 - Brief outline of Project, email to Drena & Michael

    after response/approval, then:

    Part 2 - More detailed outline of project

    Read a few papers and summarize status of problem

    Schedule meeting with Drena & Michael to discuss ideas

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Seminars this week

    Seminars this Week

    BCB List of URLs for Seminars related to Bioinformatics:

    http://www.bcb.iastate.edu/seminars/index.html

    • Nov 1 Thurs - BBMB Seminar 4:10 in 1414 MBB

      • Todd YeatesUCLATBA -something cool about structure and evolution?

    • Nov 2 Fri - BCB Faculty Seminar 2:10 in 102 ScI

      • Bob Jernigan BBMB, ISU

        • Control of Protein Motions by Structure

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Chp 10 phylogenetics

    Chp 10 - Phylogenetics

    SECTION IV MOLECULAR PHYLOGENETICS

    Xiong: Chp 10 Phylogenetics Basics

    • Evolution and Phylogenetics

    • Terminology

    • Gene Phylogeny vs. Species Phylogeny

    • Forms of Tree Representation

    • Why Finding a True Tree is Dificult

    • Procedure of Building a Phylogenetic Tree

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Evolution and phylogenetics

    Evolution and Phylogenetics

    • Evolution – the development of biological form from other preexisting forms

    • Evolution proceeds by natural selection

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Natural selection

    Natural Selection

    • Species can produce more offspring than the environment can support. This leads to competition for resources. Genetic variations exist in a population that give some individuals an advantage, others a disadvantage, leading to differential reproductive success.

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Phylogenetics

    Phylogenetics

    • Phylogenetics is the study of the evolutionary history of living organisms

    • Uses tree like diagrams to represent the pedigrees of the organisms

    • Similarities and differences seen in a multiple sequence alignment are easier to make sense of in a phylogenetic tree

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Data used in phylogenetics

    Data Used in Phylogenetics

    • Fossil records - morphology and timeline of divergence

      • Limitations - not available for all species in all areas, morphology determined by multiple genetic factors, fossils for microorganisms are especially rare

    • Molecular data - DNA and protein sequences - molecular fossils

      • Advantages - lots of data, easy to obtain

      • Limitations - can be difficult to get sequences from extinct species

    • Physical, behavior, and developmental characteristics can also be used in phylogenetics

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Molecular phylogenetics

    Molecular Phylogenetics

    • Molecular phylogenetics is the study of evolutionary relationships of genes and other biological macromolecules by analyzing their sequences

    • Sequence similarity can be used to infer evolutionary relationships

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Assumptions in molecular phylogenetics

    Assumptions in Molecular Phylogenetics

    • Sequences used are homologous, i.e. share a common ancestor

    • Phylogenetic divergence is bifurcating, i.e. parent branch splits into two daughter branches

    • Each position in a sequence evolved independently

    • Molecular Clock – sequences evolve at constant rates (only used in some methods)

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Terminology

    Terminology

    A

    B

    C

    D

    E

    F

    G

    H

    Taxa (terminal nodes)

    Internal node

    Branch

    Root

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Terminology1

    Terminology

    A

    B

    C

    D

    E

    F

    G

    H

    • Clade = group of taxa descended from a common ancestor

    • Lineage = branch path depicting ancestor-descendant relationship

    • Paraphyletic group = group of taxa that share more than one closest common ancestor

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Tree topology

    Tree Topology

    • Tree topology is the branching pattern in a tree

    Dichotomy

    Bifurcation

    Polytomy

    Multifurcation

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Rooted vs unrooted trees

    Rooted vs. Unrooted Trees

    Rooted Tree

    C

    A

    B

    D

    Unrooted Tree

    C

    A

    B

    D

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Rooted vs unrooted trees1

    Rooted vs. Unrooted Trees

    • Unrooted trees have no root node – do not assume knowledge of a common ancestor, just relationships

    • Can convert between unrooted and rooted, but first need to determine where the root is

    • Two ways to define the root:

      • Use an outgroup

      • Midpoint rooting – midpoint of the two most divergent groups is assigned to be the root

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    Outgroups

    Outgroups

    • Outgroup is a sequence related to the sequences being studied, but is more distantly related

    • Must be distinct from the ingroup, but not too distant

    • If outgroup is too distantly related, it can lead to errors in tree construction

    • Trick is to find the closest related sequence that is removed from the ingroup

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Gene phylogeny vs species phylogeny

    Gene Phylogeny vs. Species Phylogeny

    • When using molecular data, we are technically building a phylogeny for just that sequence, not for the species from which the sequences came

    • Species evolution is the result of mutations in the entire genome

    • Your gene may have evolved differently than other genes in the genome

    • To obtain a species phylogeny, we need to use a variety of gene families to construct the tree

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    Forms of tree representation

    Forms of Tree Representation

    Phylogram

    Branch lengths represent amount of evolutionary divergence

    Cladogram

    Branch lengths are meaningless, only topology matters

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    Forms of tree representation1

    Forms of Tree Representation

    • Newick format – text format for use by computer programs

    • Example: (((B,C),A),(D,E))

    • Can also have branch lengths

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    Consensus trees

    Consensus Trees

    Multiple trees that are equally optimal – build consensus tree by collapsing disagreements into a single node

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    Why finding a true tree is difficult

    Why Finding a True Tree is Difficult

    Number of rooted trees

    • The number of possible trees grows exponentially with the number of species (or sequences)

    • Nr = (2n -3)!/2(n-2)(n-2)!

    • Nu = (2n -5)!/2(n-3)(n-3)!

    • To find the best tree, you must explore all possibilities (or must you?)

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    Tree building procedure

    Tree Building Procedure

    • Choose molecular markers

    • Perform MSA

    • Choose a model of evolution

    • Determine tree building method

    • Assess tree reliability

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Choice of molecular markers

    Choice of Molecular Markers

    • Very closely related organisms - nucleic acid sequence will show more differences

    • For individuals within a species - faster mutation rate is in noncoding regions of mtDNA

    • More distantly related species - slowly evolving nucleic acid sequences like ribosomal RNA or protein sequences

    • Very distantly related species - use highly conserved protein sequences

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    Advantages of protein sequences

    Advantages of Protein Sequences

    • More highly conserved - mutations in DNA may not change amino acid sequence

    • Third position in a codon especially can vary - violates our assumption of independent evolution of all positions in a sequence

    • DNA sequences can be biased by codon usage differences between species - causes variations in sequence that are not attributable to evolution

    • In alignments, DNA sequences that are not related can show a lot of similarity due to only 4 letters in alphabet, proteins do not have this problem (at least not as much)

    • Introducing gaps in alignments of DNA sequences can cause frameshift errors, making alignment biologically meaningless

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Advantages of dna sequences

    Advantages of DNA Sequences

    • Better for closely related species

    • Show synonymous and non-synonymous mutations, which allows analysis of positive and negative selection events

      • Lots of nonsynonymous mutations may mean positive selection for new functions of protein with different amino acid sequence

      • Lots of synonymous mutations may mean negative selection - changed amino acid sequence is detrimental

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Multiple sequence alignment

    Multiple Sequence Alignment

    • Most critical step in tree building - cannot build correct tree without correct alignment

    • Should build alignments with multiple programs, then inspect and compare to identify the most reasonable one

    • Most alignments need manual editing

      • Make sure important functional residues align

      • Align secondary structure elements

      • Use full alignment or just parts

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


    Automatic editing of alignments

    Automatic Editing of Alignments

    • Rascal and NorMD – correct alignment errors, remove potentially unrelated or highly divergent sequences

    • Gblocks – detect and eliminate poorly aligned positions and divergent regions

    BCB 444/544 F07 ISU Terribilini #29- Phylogenetics


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