Molecular evidence for endosymbiosis

1
Molecular evidence for endosymbiosis

• Perform blastp to investigate sequence similarity
  among domains of life
• Found yeast nuclear genes exhibit more sequence
  similarity (closer in evolutionary time) with
  archaeal genes
• Found yeast mitochondrial genes exhibit more
  sequence similarity with eubacterial genes

2
t-test and significance

• t-test determines if the data come from the same
  population or if there are significant
  differences
• Calculate the mean of data, standard deviation of
  each data set, derive a weighted standard
  deviation to be used in t-test
• Compare to t-critical value obtained from t-table
  or software

3
Origins of eukaryotic cells
4
Martin-Muller hypothesis
Martin and Muller hypothesis
5
Evidence from phylogenetic relationships
6
Leprae vs. tuberculosis

• Leprae (3.2Mb) is 50 coding, contrasted with
  4.4 Mb and 91 coding for tuberculosis
• Comparing genomes using Mummer
• http//www.tigr.org/tigr-scripts/CMR2/webmum/mumpl
  ot

7
How Mummer works

• Uses suffix trees to create an internal
  representation of a genome sequence
• Identify maximal unique matches (MUM) version
  2.0 uses streaming whereas 1.0 adds sequence 2 to
  suffix tree for sequence 1
• Alignment via Smith-Waterman

8
Origin of species

• Mitochondrial DNA and human evolution
• Evolution of pathogens

9
Phylogeny data mining by biologists

• Molecular phylogenetics is using clustering
  techniques to discern relationships between
  different biological sequences

10
Why phylogenetics?

• Understand evolutionary history
• Map pathogen strain diversity for vaccines
• Assist in epidemiology (Dentist and HIV)
• Aid in prediction of function of novel genes
• Biodiversity
• Microbial ecology

11
Changes can occur
12
Observing differences in nucleotides

• The simplest measure of distance between two
  sequences is to count the of sites where the
  two sequences differ
• If all sites are not equally likely to change,
  the same site may undergo repeated substitutions
• As time goes by, the number of differences
  between two sequences becomes less and less an
  accurate estimator of the actual number of
  substitutions that have occurred

13
The relationship between time and substitutions
is non-linear
14
Various models have been generated to more
accurately estimate distance and evolution

• All use the following framework

Probability matrix pAC is the probability of a
site starting with an A had a C at the end of
time interval t, etc.
Base composition of sequence fa frequency of A
15
Jukes-Cantor Model

• Distance between any two sequences is given by
  d -3/4 ln(1-4/3p)
• p is the proportion of nucleotides that are
  different in the two sequences
• All substitutions are equally probable
• Each position in matrix a except diagonal
  1-Sa

16
Kimuras two parameter model

• d ½ ln1/(1-2P-Q) ¼ ln1/1-2Q)
• P and Q are proportional differences between the
  two sequences due to transitions and
  transversions, respectively.
• Accounts for transition bias in sequences
  (transversions more rare)

17
Evolutionary models
18
Implementing models and building trees
19
Rooted vs. unrooted

• Root ancestor of all taxa considered
• Unrooted relationship without consideration of
  ancestry
• Often specify root with outgroup
• Outgroup distantly related species (ie. mammals
  and an archaeal species)

20
Tree building

• Get protein/RNA/DNA sequences
• Construct multiple sequence alignment
• Compute pairwise distances (if necessary)
• Build tree topology and distances
• Estimate reliability
• Visualize

21
Distance methods

• UPMGA
• Neighbor joining

22
Unweighted pair-group method using arithmetic
averages (UPGMA)

• Assumes a constant rate of gene substitution,
  evolution
• Clustering algorithm that measures distances
  between all sequences, merges the closest pair,
  recalculates that node as an average, then merges
  the next closest pair, re-iterate
• Usually gives a rooted tree

23
Testing the reliability of trees

• Interior branch test or Bootstrap analysis
• Bootstrap analysis subsequences or sequence
  deletion or replacement re-draw trees how many
  times do you get some branching? Bootstrap
  values of 70 (95) or greater are normally
  considered reliable

24
Homework due on 10/6

• Discovery questions in Chapter 2
• 4, 25-27