203.341!Genome Evolution!

Lectures 21-22!!

Nielsen, 2005 Annual Review of Genetics 39:197-218!

Austen Ganley, October 5th, 2015

Genome Evolution •  Different parts of the genome can undergo

three different types of evolutionary behaviour:!•  Positive selection!•  Negative selection!•  Neutral evolution!

•  What are these, and importantly, how do we figure out which is at play?!

•  We are looking at genome evolution (i.e. evolution at the DNA level)!

Positive selection •  Where a region of the genome has been

selected for mutations that provide an advantage for the organism!

•  Positive selection is usually associated with adaptation!

•  If an organism that is not perfectly adapted to an environment happens to get a mutation that makes it more adapted, it will be more likely to contribute to the next generation!

Positive selection

•  The mean of the population for a certain trait shifts as a result of positive selection for an adaptive mutation!

•  Involves the adaptive allele sweeping to fixation in the population!

•  Normally, this happens on an ongoing basis!

Negative selection •  Where deleterious mutations compromise

the organism, therefore making it less likely to contribute to the next generation!

•  Negative selection is usually associated with maintenance of a useful function!

•  The more serious the effects of a non-permissible mutation, the stronger the selective effect against it!

Negative selection

•  Residues essential for organism survival will not tolerate mutations, and thus will be selected against!

•  Will manifest as highly conserved sites when comparing between species!

Neutral evolution •  Where mutations have neither a beneficial

nor a detrimental effect on the likelihood of contributing to the next generation!

•  Because neutral mutations are “unseen” by selection, they can either increase or decrease in frequency in a population!

•  Therefore, their frequency in a population is governed by genetic drift – chance dictates whether they increase or decrease in frequency!

Neutral evolution •  Neutral alleles

rise and fall in frequency through generations!

•  This is governed by chance – an individual may leave more or fewer offspring for reasons other than the neutral allele!

Other forms of selection

•  Stabilizing selection – where selection favours a narrow value for the trait and selects against individuals at either extreme (by negative selection)!

Other forms of selection

•  Disruptive selection – where selection favours extreme values for the trait over intermediate values, making populations with two distinct groups (also called diversifying selection)!

Other forms of selection

•  Balancing selection – where selection simultaneously favours both extreme values for the trait, thus maintaining multiple alleles. Usually occurs where there is heterozygous advantage!

Coef!cient of selection •  Different mutations have different

consequences – from very severe to very mild!

•  Therefore, we can think of mutations as falling on a continuum between 1 (lethal), 0 (completely neutral) and -1 (100% favoured)!

•  This is the coefficient of selection – how strongly, and in what direction, a mutation affects the fitness of individuals that have it!

Population size •  The size of the population dramatically affects

the strength of selection!•  Somewhat counter-intuitively, selection is much

more effective in large populations!•  The reason is that drift dominates in small

populations – chance events have a relatively large effect!

•  The smaller the population size, the greater the selection coefficient has to be to overcome genetic drift!

Selection effect •  The relationship between

population size (Ne) and the selection coefficient (s) can be graphed!

•  Above the line, selection rules for a mutation; below the line drift rules!

Detecting evolutionary history in the genome

•  A major goal of comparative genomics is to understand the evolutionary history of various parts of the genome!

•  This helps us to understand why things are the way they are!

•  The different forms of selective leave different patterns, and these help us determine what has happened!

•  We will look at ways of determining what selective force has been operating!

Detecting negative selection •  We will look at three methods for detecting

negative selection:!•  Unexpected abundance of low-frequency

polymorphisms (Tajima’s D)!•  Fewer non-synonymous than

synonymous mutations (Dn/Ds ratio)!•  Phylogenetic footprinting!

Low-frequency of polymorphisms •  If a region is under negative selection, we

expect to see fewer mutations in the population than a region that is not!

•  Therefore, relative to neutral regions, we are only likely to see occasional mutations that are present in few members of the population!

•  Tajima’s D is a measurement of the number of sites that are polymorphic and how polymorphic they are!

Low-frequency of polymorphisms

Limitations of Tajima’s D •  Tajima’s D is not specific to negative

selection – any force that results in such a shift in allele frequencies will be detected!

•  Importantly, positive selection has the same effect, so Tajima’s D only tells us that selection is important, not which type!

•  This pattern of reduced polymorphism is also expected when a population undergoes a rapid increase in size!

Codon Table

Synonymous to non-synonymouse mutation ratio

•  Therefore, based on this principle, we can use the ratio of non-synonymous to synonymous mutations to find evidence of negative selection!

•  This is called the dN/dS ratio (sometimes also the Ka/Ks ratio)!

•  The lower the ratio the more it suggests negative selection has removed non-synonymous mutations!

Calculating dN/dS ratio •  To calculate the dN/dS ratio, first you need at

least two DNA sequences (e.g. from two different species)!

•  These are aligned, and organised into codons!•  dN is the number of differences between the

two sequences per non-synonymous site!•  dS is the number of differences between the

two sequences per synonymous site !•  A ratio less than 1 suggests negative

selection!

Limitations of dN/dS ratio •  Only works on protein-coding regions of the

genome!•  Has limited sensitivity – if only a few sites

are undergoing negative selection, but the rest are not, the negative selection is very difficult to detect!

•  Need to take bias in mutations into account – not all mutations occur with equal frequency, and these can lead to an overestimate of dN!

Phylogenetic footprinting •  As we have seen, one hallmark of negative

selection is conservation of bases through evolution!

•  A way to reveal this is by phylogenetic footprinting!

•  For this, sequences (e.g. from several different species) are aligned, and the level of sequence conservation is plotted!

•  The regions undergoing negative selection stand out as “footprints” of sequence conservation!

Sequence Alignment

Phylogenetic Footprinting

Phylogenetic Footprinting

•  The evolutionary divergence of the species used is critical to success!

•  This in turn depends on the region being analysed!

Phylogenetic footprinting limitations

•  Relies on having sequences of your region of interest available for multiple species of the right evolutionary distances!

•  Detects regions, not individual bases, so has limited resolution (in the order of 10 bp)!

•  Measures relative conservation: if your region as a whole has anomalous conservation, you may be misled in your interpretations!