evoluciÓn: principios y cuantificaciÓn. human nuclear genome only 3% coding dna
TRANSCRIPT
The Evolutionary forces:
• Natural selection (Darwin, Bernardi)
• Neutral Theory: Genetic drift (Kimura)
• Small population sizes
• Mutation– Mutationalist theory (Sueoka)– Thermodynamic pressure theory (Zimic & Arévalo)
• Gene flow (migration), horizontal transfer
MUTATIONTHE ULTIMATE SOURCE OF NEW GENETIC VARIATION.
Mutation rates are in the general range of:
Approx 10-7 to 10-8 per nucleotide per generation
Approx 10-5 per gene per generation
Approx 10-3 per generation at microsatellites
Genomes, genes and molecular evolution
A G
TC
purines
pyrimidines
transversions
transitions
transitions
BZM210: E.Willassen
http://www.ncbi.nlm.nih.gov/index.htmlhttp://www.no.embnet.org/Interesting links:
Transitions - transversions
A G
TC
purines
pyrimidines
transversions
transitions
transitions
TS / TV ratios
mtDNA 9.0 and globins 0.66
Expected:
TS / TV = 4 / 8 = 0.5
GENE FLOWSPREAD OF VARIATION OVER SPACE BY MOVEMENT AND/OR INTERMARRIAGE AMONG PEOPLE (‘ADMIXTURE’)
INTRODUCES NEW VARIATION INTO A POPULATION
REDUCES VARIATION BETWEEN POPULATIONS
GENETIC DRIFT
ALLELE FREQUENCY CHANGE DUE TO CHANCE FACTORS IN SEGREGATION, SURVIVAL & REPRODUCTION IN FINITE POPULATIONS.
GENETIC DRIFTINVERSELY RELATED TO POPULATION SIZE
POSITIVELY RELATED TO TIME.
PROBABILITY OF ULTIMATE FIXATION OF AN ALLELE IS ITS CURRENT FREQUENCY
APPLIES TO WHOLE SPECIES, BECAUSE TIME IS LONG
Initial p=0.5, N=300, 100 generations
CHANGE IS SLOWER IN BIG POPULATIONS
Change is slower in larger populations
Drift reduces variation within populations due to fixation & loss of neutral alleles.
Drift increases variation between populations because different alleles are fixed in each populationLAS RAZAS HUMANAS EXISTEN?
Mean times to fixation and loss for selectively neutral alleles
Loss occurs more rapidly than fixation
Common alleles are generally old alleles
Geographically widespread alleles are usually old
GENE ‘TREES’
What happens to a DNA sequence over time?
. . . . . and why?(THINK OF THE DICE EXPERIMENT)
SPECIATIONA reduction in gene flow between populations accompagnied by divergent selection and/or
genetic drift, can lead to speciation.
Evolutionary history includes the transformation and divergens of lineages
Phylogenetic evolution or anagenesis
Mutations arise hierarchically
over time, generating a phylogeny
of cladistic (tree-like, branching)
DNA sequence relationships.
DNA sequences have a common ancestor and their variation reflects their descent history
Current sample of DNA sequences
ACTAA AATGA CGAAA CGAAG AGTAG
MRCA of all samples
MRCA of these 3 samples
Population history is reflected in
the pattern of sequence variation,
and the geographic location where
DNA sequence haplotypes are found.
• The great majority of mutations that are fixed are effectively neutral with respect to fitness, and are fixed by genetic drift
• polymorphism within populations is transient and due to the presence of selectively neutral alleles on their way to fixation or loss
The Neutral Theory
The Neutral Theory
• Adaptive Evolution is due to Natural Selection
• Advantageous mutations are rare
• most genetic variation at the molecular level is not selected within a population
• most genetic substitutions at the molecular level are not due to selection
• vertebrates
• fibrinopeptides
• hemoglobin
• cytochromes
• rates depend on functional constraints
Functional Constraint
millions of years since divergence
cytochrome c
hemoglobin
fibrinopeptide
• Mitochondrial gene in mammals
• uniform rate
• rate difference between silent and amino-acid replacement mutations
Functional Constraint
silent
replacement
Molecular Clock: observations
-hemoglobin in vertebrates
• plot amino acid differences against divergence time
• good linear approximation
1 What use is the molecular clock?
• date divergence in phylogeny
• as a first approximation
Molecular Clock
Rates of Nucleotide Substitution
Rate: number of substitutions K between two homologous sequences divided by twice the time of divergence t
Ancestral sequence
Sequence 1 Sequence 2
t t
• Number of substitutions
Rates of Nucleotide Substitution
1 lineageK = r t
2 lineagesfrom splitK = 2 r t
• molecular clock is used to put a time to phylogenies
• construct phylogeny first by clock independent method
• clock based on well established partial phylogenies
• rate tests on reference set and subsets
• estimate times on total data base
Molecular Clock
Orthologous genes or not?
•orthologous - same gene copy
Well matching sequences may not be directly homologous
•paralogous - duplicate gene copy
•xenologous - introgressed gene copy(hybridization, virus) Horizontal transfer
v (3rd)
tran
sversio
ns
F84 distance
0.01
0.03
0.04
0.05
0.07
0.08
0.10
0.11
-0.0581 0.0000 0.0581 0.1163 0.1744 0.2326 0.2907 0.3489
’Multiple hits’ and ’saturation’
Time
Bas
e pa
ir d
iffe
renc
es
AD BCE
G>T
A>T
T>A
G - T - A - T
Reversal to a previous state may be detected as homoplasy. True phylogenetic signal would be masked with time and give false synapomorphies.
Signal depends on mutation rates, r.
v (3rd)
tran
sversio
ns
F84 distance
0.01
0.03
0.04
0.05
0.07
0.08
0.10
0.11
-0.0581 0.0000 0.0581 0.1163 0.1744 0.2326 0.2907 0.3489
Adjusted sequence change
Time
Bas
e pa
ir d
iffe
renc
es
different models have been made with intention to correct for multiple hits by converting observed distances between sequences to actual (expected) distances (under the particlar model)
’correction factor’
We can use genetic differences among populations or species to reconstruct
evolutionary history
Infering on likely evolutionary history from genetic differences
Amino acid sequences of hemoglobin alpha chains No. of Taxa : 6 Gaps/Missing data : Complete Deletion Distance method : Amino: Poisson correction No. of Sites : 140 d : Estimate
1 2 3 4 5 6 [1] Human -[2] Horse 0.13 -[3] Cow 0.13 0.13 -[4] Kangaroo 0.21 0.23 0.20 -[5] Newt 0.57 0.64 0.60 0.64 -[6] Carp 0.66 0.65 0.62 0.71 0.75 -
Human Horse
Cow Kangaroo
Newt Carp
0.1
Divergence can be used for grouping
Molecular clock
Kimura (1968,1983): •if sequence divergence between humans and horses is scaled for time using fossils •and estimated evolutionary rate, r, is applied to all known protein coding loci•one amino acid substitution has been fixed every second year on average
Interpretation: This is too much for selection to have been influential during evolution of the vertebrates
Zuckerkandl & Pauling (1965): rate of amino acid change appears constant through time
the fate of mutations
mutations can be neutral
mutations can be advantageous and subject to positive selection
mutations can be disadvantageous and subject to purifying selection
selection can be detected by testing sequences against the predictions of neutral theory(for instance synonymous vs non-synonymous codons)
Mutations can be driven by thermodynamic pressure
Evolutionary constraints on DNAs
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
Base position
Ent
ropy
G A A G A C C C U AUA A AGC U U
U AUAUUUUAUAUUUA
UUUUUUAUAAAGA A U AUUU
AAAAUU
UU
AUUUAAUUAAAUAU U U
UGUU
GGGG
UGAC
CAUAAGAU
UUAA UA
AA
CUCUUAUAAAUAUUUAACAUUG
AUUAAUG
AA
UUAUUGAUC
CGGUUUU
AUCGAUUAAAAA
UU
UAAGUU
ACUUUAGG
GA
Constraints are associated with functionality, for instance the need for rRNA to base pair and form helices in a secondary molecular structure
helix
loop
Transcription and translation
Translation requires available tRNA with appropriate anticodons to match with each codon on mRNA
codon
anticodon
Anopheles gambiaeAAcid Codon FractionGly GG G 0.14Gly GG A 0.56Gly GG T 0.27Gly GG C 0.03
Glu GA G 0.02Glu GA A 0.98Asp GA T 0.95Asp GA C 0.05
Val GT G 0.02Val GT A 0.50Val GT T 0.45Val GT C 0.02
Ala GC G 0.00Ala GC A 0.28Ala GC T 0.64Ala GC C 0.08
codon bias: all codons are not equally frequentCodon usage
Codon redundancy:synonomous (silent) substitutions give the same amino acids.
synonomous substitutions do not affect the translation product and thus should be neutral in expressed genes
However, availability of specific tRNAs may make some codons more ’fit’
Synonymous codons are expected to be neutral, are expected to occur in equal frequency
Expect 50/50 frequency for two phenylalanine codons
5. Anomalous DNA composition
for instance: codons xxC and xxU can be read by the same anticodon, xxG
Translational efficiencydepends on tRNA availability
some tRNAs may pair with different codons due to: •’wobbles’ on the anticodon •modified nucleotides on the anticodon(possibility of G-U-pairing, Inosine (G’) pairs with A,C and U
codon
anticodonxxG xxGxxC xxU
Consequently some genomes do well with reduced number of tRNA types in the genome: 22 in vertebrate mitochondrial (mtDNA).
Factor Analysis of codon usage of B. subtilis genes reveals three classes of genes
Class 3 (13%) genes that were apparently horizontally transferred.
Class 1 comprises the majority of the B. subtilis genes (82%)
Class 2 (5%) genes that are highly expressed under exponential growth conditions
Because some of the genes in this group showed clear relationships with bacteriophage genes, the hypothesis has been proposed that all these genes were alien and have been acquired horizontally from various sources.
Kunst, F et al. Nature (1997) 390 249-256
Mozner I. Current Opinion in Microbiology 1999, 2:524–528
Why do horizontally transferred genes use the genetic code differently?
Rocha EP. Trends Genet 2002 Jun;18(6):291-4
Bacterial species display a wide degree of variation in their overall G+C content
• Distribution of A + T-rich islands along the chromosome of B. subtilis.
• Location of genes from class 3 according to codon usage analysis is indicated by dots at the bottom of the graph.
• Known prophages (PBSX, SPb and skin) are indicated by their names, and prophage-like elements are numbered from 1 to 7.
However, most genes have roughly the same GC content within a genome
Kunst, F et al. Nature (1997) 390 249-256
Synonimous substitutions are not necessarily neutral
lowly expressed genes highly expressed genes
strong selection for translational efficiency
weak selection for translational efficiency
fewer tRNAs usedmore tRNAs used
strong codon biasweak codon bias
high rates of silent (neutral) mutations
low rates of silent mutations:
i.e. synonomous mutations
are not necessarily neutral!purifying selection
Redundancy and rates on codon positions
Code Table: StandardMethod: Nei-Gojobori (1986)S = No. of synonymous sitesN = No. of nonsynonymous sites----- No of Sites Redundancy----- for codon Pos Pos PosCodon S N 1st 2nd 3rdTTT (F) 0.333 2.667 0 0 2 TTC (F) 0.333 2.667 0 0 2 TCT (S) 1.000 2.000 0 0 4 TCC (S) 1.000 2.000 0 0 4 TCA (S) 1.000 2.000 0 0 4 TCG (S) 1.000 2.000 0 0 4 TAA (*) 0.000 3.000 0 0 0 TAG (*) 0.000 3.000 0 0 0TGA (*) 0.000 3.000 0 0 0TGT (C) 0.500 2.500 0 0 2 TGC (C) 0.500 2.500 0 0 2 TGG (W) 0.000 3.000 0 0 0 CTT (L) 1.000 2.000 0 0 4 CTC (L) 1.000 2.000 0 0 4 CTA (L) 1.333 1.667 2 0 4TTA (L) 0.667 2.333 2 0 2 TTG (L) 0.667 2.333 2 0 2
With codon redundancy we would expect less selective constraints on 3rd codon positions.
1st and 2nd position should be under stronger selective pressure.
Consequently evolution rates on 3rd codon positions are usually found to be higher than on 1st and 2nd positions
Even the sacred of sacreds of phylogenetic taxonomy can be violoated:
The problem: different molecules can yield different trees AND may still be telling the truth
ArchaeBacteria
Gene tree A Gene tree B Gene tree C
Kingdoms are not monophyletic in gene tree B and C
HGT possesses two ingredients sure to cause a controversy
1. Challenges the traditional tree-based view of evolution2. Is difficult to prove unambiguously
The solution: Horizontal Gene Transfer (HGT)
The significance of horizontal transfer was first recognized in the 1950’s resistance to multiple antibiotics could be transferred simultaneously from Shigella to Escherichia coli
“Infectious heredity”
Xenologs arise by horizontal transfer
SpeciationOrthologs
DuplicationParalogs
Horizontal TransferXenologs
Ancestral geneti
me
organisms
Xenologs
Paralogs – homologs related by duplicationOrthologs – homologs related by speciation
Xenologs – homologs related by horizontal transfer
1) Transformation – prokaryotes can take up free DNA from their surroundings
2) Conjugation – (bacterial sex) an organism builds a tube-like structure known as the pilus, joins it to its ‘‘mate’’, and transfers a plasmid through the tube. E. coli has been shown to conjugate with cyanobacteria, AND EVEN with S. cerevisiae!
3) Transduction – genes can be moved from one prokaryote species to another via viruses.
Mechanisms of horizontal transfer (also referred to as lateral transfer)
Base composition differences are mostly due to third position of codonsLawrence and Ochman. J Mol Evol (1997) 44:383–397
Horizontally transferred genes retain the sequence characteristics of the donor
genome
4. Conservation of gene order
Gene order is not generally conserved in microbial genomes
E. coli
B. subtilis
V. cholerae
• The presence of three or more genes in the same order in distant genomes is extremely unlikely unless these genes form an operon.
• Each operon typically emerges only once during evolution and is maintained by selection ever after.
• Therefore, when an operon is present in only a few distantly related genomes, horizontal gene transfer seems to be the most likely scenario.