molecular phylogenetics and patterns of floral evolution in the ericales
A Brief of Molecular Evolution & Phylogenetics
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Transcript of A Brief of Molecular Evolution & Phylogenetics
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A Brief of
Molecular
Evolution &
Phylogeneti
cs
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Aims of the course:• To introduce to the practice
phylogenetic inference from molecular data.
• To known applications and computer programmes to practice phylogenetic inference.
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Two Concepts of Two Concepts of Molecular EvolutionMolecular Evolution
• Ortologous vs Paralogous genes
– Genes & species trees
• Molecular clock
– Substitution rates
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Homologous genes
• Orthologous genesDerived from a process of new
species formation (speciation)
• Paralogous genesDerived from an original gene
duplication process in a single biological species
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• Paralogous genes of Globin
(Glob), Myo y Leg haemoglobin, each originated by duplication from an ancestral gene
Species trees vs Gene Species trees vs Gene treestrees
Orthologous genes of Cytochrome Each one is present in a biological species
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Species trees and Gene trees
We often assume that gene trees give us species trees
a
b
c
A
B
D
Gene tree Species tree
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Orthologues and paralogues
a A*b* c BC*
Ancestral gene
Duplication to give 2 copies = paralogues on the same genome
orthologousorthologous
paralogousA*C*b*
A mixture of orthologues and paralogues sampled
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The malic enzyme gene tree contains a mixture of orthologues and
paralogues
Anas = a duck!
Schizosaccharomyces
Saccharomyces
Giardia lamblia
Ascaris suum
Homo sapiens 1
Anas platyrhynchos
Homo sapiens 2
Zea mays
Flaveria trinervia
Populus trichocarpa
Lactococcus lactis
100
100
100
97100 Cyt
Mit
Ch
Trichomonas vaginalisHyd
Solanum tuberosum
Amaranthus
75 100
Cyt
Mit
ChCh
Mit
Mit
Neocallimastix
Cyt
Hyd
Gene duplication
Plant chloroplast
Plant mitochondrion
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Is there a molecular clock?
• The idea of a molecular clock was initially suggested by Zuckerkandl and Pauling in 1962
• They noted that rates of amino acid replacements in animal haemoglobins were roughly proportional to time - as judged against the fossil record
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The molecular clock for alpha-globin:
Each point represents the number of substitutions separating each animal from humans
0
20
40
60
80
1000
100
200
300
400
500
Time to common ancestor (millions of years)
nu
mb
er
of
su
bsti
tuti
on
s
cow
platypuschicken
carp
shark
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Rates of amino acid replacement in different
proteins
Protein Rate (mean replacements per siteper 10 9 years)
Fibrinopeptides 8.3Insulin C 2.4Ribonuclease 2.1Haemoglobins 1.0Cytochrome C 0.3Histone H4 0.01
• Evolutionary rates depends on functional constraints of proteins
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There is no universal clock• The initial proposal saw the clock as a
Poisson process with a constant rate• Now known to be more complex - differences
in rates occur for:
– different sites in a molecule– different genes– different base position (synonimous-
nonsynonymous)
– different regions of genomes– different genomes in the same cell– different taxonomic groups for the same
gene
• Molecular Clocks Not Exactly Swiss
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Phylogenetic Trees
A B C D E F G H I J
ROOTROOT
polytomypolytomy
terminal branchesterminal branches
interior interior branchesbranches
node 1node 1 node 2node 2
LEAVESLEAVES
A CLADOGRAM
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Trees - Rooted and Unrooted
ROOTA
B
C
D E
F
GH
I
J
A B C D E F GH I J
ROOT
A B C D E F G H I J
ROOT
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Rooted by outgroup
Rooting using an outgroup
archaea
archaea
archaea
eukaryote
eukaryote
eukaryote
eukaryote
bacteria Outgroup
root
eukaryote
eukaryote
eukaryote
eukaryote
Unrooted tree
archaea
archaea
archaea
Monophyletic Ingroup
MonophyleticIngroup
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Some Common Phylogenetic Methods
Types of Data
DistancesSites
(nucleotides, aa)
Tree buildi
ng meth
od
Cluster Algorithm
s
UPGMANJ
Optimality Criteria
Minimum Evolution
Least Square
ParsimonyMaximum LikelihoodBayesian Inference
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• Distance Estimates attempt to estimate the mean number of changes per site since 2 species (sequences) split from each other.
• Simply counting the number of differences may underestimate the amount of change - especially if the sequences are very dissimilar - because of multiple hits.
• We therefore use a model which includes parameters which reflect how we think sequences may have evolved.
Distance Methods
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1 2 obs real sustitución:
A A A A 0 0 no
A A A C 1 1 simple
A C A G 1 2 coincidente
A A A C G 1 2 múltiple
A C A C 0 2 paralela
A C A G C 0 3 convergente
A A A C A 0 2 reversa
Cálculo de distancias:
observación y realidad
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The simplest model : Jukes & Cantor:
dxy = -(3/4) Ln (1-4/3 D)
• dxy = distance between sequence x and sequence y expressed as the number of changes per site
• (note dxy = r/n where r is number of replacements and n is the total number of sites. This assumes all sites can vary and when unvaried sites are present in two sequences it will underestimate the amount of change which has occurred at variable sites)
• D = is the observed proportion of nucleotides which differ between two sequences (fractional dissimilarity)
• Ln = natural log function to correct for superimposed substitutions
• The 3/4 and 4/3 terms reflect that there are four types of nucleotides and three ways in which a second nucleotide may not match a first - with all types of change being equally likely (i.e. unrelated sequences should be 25% identical by chance alone)
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The natural logarithm ln is used to correct for superimposed changes at
the same site
• If two sequences are 95% identical they are different at 5% or 0.05 (D) of sites thus:
– dxy = -3/4 ln (1-4/3 0.05) = 0.0517
• Note that the observed dissimilarity 0.05 increases only slightly to an estimated 0.0517 - this makes sense because in two very similar sequences one would expect very few changes to have been superimposed at the same site in the short time since the sequences diverged apart
• However, if two sequences are only 50% identical they are different at 50% or 0.50 (D) of sites thus:
– dxy = -3/4 ln (1-4/3 0.5) = 0.824
• For dissimilar sequences, which may diverged apart a long time ago, the use of ln infers that a much larger number of superimposed changes have occurred at the same site
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Distance models can be made more parameter rich to increase their
realism 1
• It is better to use a model which fits the data than to blindly impose a model on data
• The most common additional parameters are:– A correction for the proportion of sites which are
unable to change– A correction for variable site rates at those sites
which can change – A correction to allow different substitution rates
for each type of nucleotide change
• PAUP will estimate the values of these additional parameters for you.
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A gamma distribution can be used to model site rate
heterogeneity
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Exchangeability parameters from two common empirical models of amino acid sequence evolution are presented. The parameter value for each amino acid pair is indicated by the areas of the bubbles, and discounts the effects of amino acid frequencies.
(a) The JTT model (Jones, D.T. et al. 1992CABIOS 8, 275–282) derived from a wide variety of globular proteins.
(b) The mtREV model (Yang, Z. et al. 1998 Mol. Biol. Evol. 15, 1600–161) derived from mammalian mitochondrial genes that encode various transmembrane proteins.
Exchangeability parameters for two models of amino acid replacement.
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• Fast - suitable for analysing data sets which are too large for ML
• A large number of models are available with many parameters - improves estimation of distances
• Use ML to test the fit of model to data
Distances: advantages:
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• Information is lost - given only the distances it is impossible to derive the original sequences
• Only through character based analyses can the history of sites be investigated e,g, most informative positions be inferred.
• Generally outperformed by Maximum likelihood methods in choosing the correct tree in computer simulations
Distances: disadvantages:
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• T(i) = (2i-5) :: T(unrooted), i>3 1,3,15,105,945,10395,135135
• For 10 taxa there are 2 x 106
unrooted trees• For 50 taxa there are 3 x 1074
unrooted trees• How can we find the best tree ?
Numbers of possible trees for N taxa:
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Cluster Analysis
UPGMA y NJ
Se unen recursivamente el par de elementos más cercanos. Se recalcula la matriz de distancias (*) y se analiza el par unido como un nuevo elemento
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Human
Monkey
MosquitoRice
Spinach
Unrooted Neighbor-Joining Tree
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A perfectly additive tree
A B C DA - 0.4 0.4 0.8B 0.4 - 0.6 1.0C 0.4 0.6 - 0.8D 0.8 1.0 0.8 -
A
B
C
D
0.1
0.10.3
0.6
0.2
The branch lengths in the matrix and the tree path lengths match perfectly - there is a single unique
additive tree
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Distance estimates may not make an
additive tree
Thermus
Deinococc
ruber
Bacillus
Aquifex
0.0560.017
0.145
0.079
0.057
0.119
0.217
Jukes-Cantor distance matrixProportion of sites assumed to be invariable = 0.56;identical sites removed proportionally to base frequencies estimated from constant sites only
1 2 4 5 6 1 ruber - 2 Aquifex 0.38745 - 4 Deinococc 0.22455 0.47540 - 5 Thermus 0.13415 0.27313 0.23615 - 6 Bacillus 0.27111 0.33595 0.28017 0.28846 -
Aquifex > Bacillus (0.335)
Aquifex > Thermus (0.33)
Thermus > Deinococcus (0.218)
Some path lengths are longer and others shorter than appear in the matrix
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Obtaining a tree using pairwise distances
• Stochastic errors will cause deviation of the estimated distances from perfect tree additivity even when evolution proceeds exactly according to the distance model used
• Poor estimates obtained using an inappropriate model will compound the problem
• How can we identify the tree which best fits the experimental data from the many possible trees
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Obtaining a tree using pairwise distances
• Use statistics to evaluate the fit of tree to the data (goodness of fit measures)– Fitch Margoliash method - a least squares
method
– Minimum evolution method - minimises length of tree
• Note that neighbor joining while fast does
not evaluate the fit of the data to the tree
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• Minimises the weighted squared deviation of the tree path length distances from the distance estimates
Fitch Margoliash Method 1968:
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Thermus
Deinococc
ruber
Bacillus
Aquifex
0.0590.006
0.148
0.077
0.051
0.129
0.207
Deinococc
Thermusruber
Bacillus
Aquifex
0.139
0.0230.0580.076
0.0400.132
0.204
Optimality criterion = distance (weighted least squares with power=2)Score of best tree(s) found = 0.12243 (average %SD = 11.663)Tree # 1 2Wtd. S.S. 0.13817 0.12243APSD 12.391 11.663
Tree 2 - best
Tree 1
Fitch Margoliash Method 1968:
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Minimum Evolution Method:
• For each possible alternative tree one can estimate the length of each branch from the estimated pairwise distances between taxa and then compute the sum (S) of all branch length estimates. The minimum evolution criterion is to choose the tree with the smallest S value
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Tree 2
Tree 1 - best
Minimum Evolution
Optimality criterion = distance (minimum evolution) Score of best tree(s) found = 0.68998Tree # 1 2ME-score 0.68998 0.69163
Thermus
Deinococc
ruber
Bacillus
Aquifex
0.0560.017
0.145
0.079
0.057
0.119
0.217
Deinococc
Thermusruber
Bacillus
Aquifex
0.152
0.0120.0530.081
0.0580.119
0.217
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Parsimony analysis
• Parsimony methods provide one way of choosing among alternative phylogenetic hypotheses
• The parsimony criterion favours hypotheses that maximise congruence and minimise homoplasy (convergence, reversal & parallelism)
• It depends on the idea of the fit of a character to a tree
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Parsimony
Seq 1 ...ACCT...
Seq 2 ...AACT...
Seq 3 ...TACT...
Seq 4 ...TCCT...T
T
A
1
C
A
C
2 0 0 = 3
1(C)
2(A)
3(A)
4(C)A
2 mutations
3(A)
2(A)
1(C)
4(C)A
1 mutation
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Maximum Likelihood - goal
• To estimate the probability that we would observe a particular dataset, given a phylogenetic tree and some notion of how the evolutionary process worked over time.
– P(D/H)
Probability of given
a b c d
b a e f
c e a g
d c f a
a ,c,g,t
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Maximum likelihood
1
2
5 63
4V5
V1
V2
V3
V4
)()()()()( 43521 46366525155vPvPvPvPvPgl xxxxxxxxxxxk
)()()()()( 43521 46366525155
65
vPvPvPvPvPgL xxxxxxxxxxxxx
k Since we do not know x5 and x6 we sum over all the possible nucleotides
Where:
gx0prior probability that node 0 has
nucleotide x (relative frequency)
)1()(
)1()(v
iij
viiii
egvP
eggvP
(if gi=1/4, model becomes JC)
Summing over all sites:
n
kkLL
1
lnln lnL is maximized changing Vi’s
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Bayes’ rule
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Bayes’ theorem
dXlp
XlpXf
)|()(
)|()()|(
Posteriordistribution
Prior distribution
Likelihood function
Pr [Tree/Data] = (Pr [Tree] x Pr [Data/Tree]) / Pr [Data])Pr [Tree/Data] = (Pr [Tree] x Pr [Data/Tree]) / Pr [Data])
Unconditional probab.
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A B C
Prior probabilitydistributionpr
obab
ility 1.0
Posterior probabilitydistributionpr
obab
ility 1.0
Data (observations)
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Markov Chain Monte Carlo (MCMC)
parameter space
pro
babili
ty
)|()( Xlp
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Bootstrap
...ahdfhgkhkafkdgg...
...rhdfkgkhkaykdgg...
...ahdfhgk-kafkdgg...
...ahdfhgk-kafkdgg...
...ghdfhg--kafkdht...
...ahdfhg--kafaddg...
...hhdfhg--kafaddg...
...ahdfpgchka-kwgg...
...ahhfhgkhkafdggg...
...rhhfkgkhkaydggg...
...ahhfhgk-kafdggg...
...ahhfhgk-kafdggg...
...ghhfhg--kafdhtt...
...ahhfhg--kafddgg...
...hhhfhg--kafddgg...
...ahhfpgchka-wggg...
...adfhgkkaffkdgg...
...rdfkgkkayykdgg...
...adfhgkkaffkdgg...
...adfhgkkaffkdgg...
...gdfhg-kaffkdht...
...adfhg-kaffaddg...
...hdfhg-kaffaddg...
...adfpgcka--kwgg...
....
90
50
7065
75
86
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Aplicaciones de la filogenia:
Trazar el origen de una cepa
Fechar la introducción de una
cepa
Estudio de la función
Estudios evolutivos
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Trazando el origen
Europa
América
Asia
Europa
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Datos epidemiológicos
1926
1970
a
b
c
d
t0
t1
(1926-t0)*v=a
(1970-t1)*v=c+d
...
Virus RNA: alta tasa de evolución
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Función
A ...ahgfhgkhkafkdggggcatgcgayhhks...
B ...rfgfkgkhkaykdggggcatgcgayhhks...
C ...ahdfhgkrkafkdggcccatgcgayhhks...
D ...ahdfhgkrkafkdglcccatgcgayhhks...
E ...ghdfhg-rkafkdhtcccatgcgayhhks...
Estados Ancestrales
Función1
Función2
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PHYLIPhttp://evolution.genetics.washington.edu/phylip.html
DNA
DNAPARS. Estimates phylogenies by the parsimony method using nucleic acid sequences.
DNAMOVE. Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by parsimony and compatibility
DNAPENNY. Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search.
DNACOMP. Estimates phylogenies from nucleic acid sequence data using the compatibility criterion,
DNAINVAR. For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants,
DNAML. Estimates phylogenies from nucleotide sequences by maximum likelihood.
DNAMLK. Same as DNAML but assumes a molecular clock.
DNADIST. Computes four different distances between species from nucleic acid sequences.
Proteins
PROTPARS. Estimates phylogenies from protein sequences using the parsimony method.
PROTDIST. Computes a distance measure for protein sequences
Restriction
RESTML. Estimation of phylogenies by maximum likelihood using restriction sites data
FITCH. Estimates phylogenies from distance matrix data under the "additive tree model".
KITSCH. Estimates phylogenies from distance matrix data under the "ultrametric" model.
NEIGHBOR. An implementation of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method.
Continuous
CONTML. Estimates phylogenies from gene frequency data by maximum likelihood.
GENDIST. Computes one of three different genetic distance formulas from gene frequency data.
Discrete characters
MIX. Wagner parsimony method and Camin-Sokal parsimony method,
MOVE. Interactive construction of phylogenies from discrete character Evaluates parsimony and compatibility criteria.
PENNY. Finds all most parsimonious phylogenies
DOLLOP. Estimates phylogenies by the Dollo or polymorphism parsimony criteria.
DOLMOVE. Interactive DOLLOP.
DOLPENNY. branch-and-bound method
CLIQUE. Finds the largest clique of mutually compatible characters,
SEQBOOT. Reads in a data set, and produces multiple data sets from it by bootstrap resampling..
CONSENSE. Computes consensus trees by the majority-rule consensus tree method,
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