lecture 12 Flashcards
Can FST be high for some genes but low for others?
What would be a possible biological interpretation?
*something about the ecology of the top left population where natural selection favors purple allele
chance events
genetic drift
chance events and genetic drift happens over all genes
but with selection is not expected to affect all genes in the same way
Results on the graph with Fst and position along the chromosome
A, B, and D all have low Fst
- So they are a really good reflection of the baseline amount of genetic variation of genetic structure and of gene flow in your species
- doesn’t mean that there isn’t genetic variation.
It means that Fst is low so it means that there’s lots of gene flow because you’ve got those different alleles moving around across all these different populations
C gene has a very high Fst value bc the purple C allele is only found in one popualtion
what are genes with Fst values useful for
genes with Fst values that are
outliers compared to the rest of the genome.
We can use those as strong indicators that there has been positive selection (=adaptation)
Tracking footprints of artifcial selection in the dog genome
- genotyped ≈21,000 autosomal SNPs (single nucleotide polymorphisms) in 10 diverse dog breeds
- get a baseline of how all the genes and alleles were distributed among dogs
- looking for signatures of positive selection: significant deviations from what Fst vales look like around the genome
- each has their own history of effects
Let’s zoom in on Shar-peis
- di = deviation in FST for breed i, relative to the genome-wide average
- SNPs that lie above the dashed red line indicate statistically-significant outliers
- dash line was discovery rate
- the ones above are significant outliers that are different than the baseline due to chance events
what does the section of chromosome 13 of the Shar-pei genome have?
unusual levels of differentiation (relative to the rest of the genome)
this section contains 3 genes, including HAS2 (hyaluronan synthase)
Hyaluronan (hyaluronic acid)
found throughout the body, including joints, eyes, and skin, produced by hyaluronan synthases (mostly HAS2)
Helps skin stretch, increases wound healing
HAS2 (hyaluronan synthase) expression in Shar-peis
HAS2 (hyaluronan synthase) expression is elevated in Shar-peis (more protein too)
Naked mole rats and HAS2 gene
Naked mole rats secrete very high molecular mass hyaluronan & their HAS2 gene has evolved unique amino acid substitutions
Rare human case and HAS2 gene
Rare human case of cutaneous mucinosis and very high levels of hyaluronan
How might you infer that a gene (or other part of the genome) is essential, just by sequence analysis?
how much genetic variation there is
little variation it means its very important, if you tinker with it it will be removed by natural selection, strength of purifying selection
How much data would you need?
about population samples or across species samples
highly conserved regions of the gemeone indicate strong purifying selection
- comparing the amount of nonsynonymous to synonymous variation (or of ant type of variation) is very informative
- dN and dS describe nonsynonymous and sysnomous variation within species
dS is bigger than dN
- kA and kS describe nonsynonymous (amoino acid) and synonymous divergence (substitiuation) between species
- if there is strong functional constriant (strong puryfing selection), than kA/kS (or dN/dS) ratio will be close to zero
nonsynonymous mutations (polymorphisms, substitution)/ synonymous (polymorphisms, substitution)
Human and yeast ubiquitin proteins
are almost identical!
Amino acid sequence of human and yeast ubiquitin proteins
73/76 = 96% similar
Nucleotide sequence of human and yeast ubiquitin proteins
170/228 = 75% similar
