Genomes-L11- Social Genome: Modern Human Diversity

how do you compare homologous sequences?

• taking single nucleotide variants ie A and C and comparing their frequencies

• with this- you can measure the minor allele freuency- ie

what is homology?

similarity due to shared common ancestry

what is MAF?

minor allele frequency- tells you how likely it is you’ll pick 2 people and they’ll differ in the genome

• if a MAF is greater than 1%- single nucleotide variance is called a single nucleotide polymorphism

• the lower the MAF- the rarer the allele- the lower the chance of varying at that nucleotide

what is the 1000 genomes project?

sequenced 2500 human genomes from 36 countries

• found 88m variants- 84m of these were single nucleotide variants

• 60k- had deletions, variations etc

• 12m variants have a MAF>1%

what is genetic diversity? where are there the highest diversity?

amount of genetic variation within a population or species- many ways to measure this

• africa has the highest diversity- higher number of variance

how do we measure genetic diversity?

1. segregating sites- measure number of polymorphic sites

2. allelic richness- average number of alleles per locus but sensitive to sample size

3. expected heterozygosity-the probability that two alleles randomly selected from the population are different

how is genetic diversity maintained?

1. mutation- creates new alleles- can go extinct due to genetic drift

   • if neutral- decided by fate

2. genetic drift- random change in allele frequency due to random chance

   • impacted by pop size- stronger in small populations- larger

3. population bottle neck- only small no. of offspring reproduced- increase sampling error and increase drift

types of genetic drift

1. small group of population breaks off and becomes isolated- founder effect

2. reduction in population size due to stress such as famine- population bottleneck

what is true about diversity and distance?

• as you move away from Africa- allele richness decreases from distance from Ethiopia

• linguistic diversity decreases too

how do we measure genetic distance?

1. by measured evolutionary distance- time since divergence from last common ancestor

2. observed degree of genetic differentiation between 2 samples ie proportion of alleles shared

example of comparing individuals and measuring genetic distance

11/20 alleles shared= 0.55

genetic distance would be 0.45

how would we compare population genetic distances?

compare allele frequencies for different populations at each locus- using the F2 statistic matrix

• to construct trees representing population relationships

what are the issues with using F2 statistic to measure population relationships?

1. tree diagrams- not an ideal representation due to GENE FLOW- intermixing and sharing genetic material

   • trees usually represent isolated populations

2. genetic distances don’t represent evolutionary history- we don’t know mutation rates

3. costs money to completely sequence- we just look at SNPs and MAF- don’t have full genetic data

other ways of visualising genetic relationships that are more useful

1. admixture moidelling- use allele frequencies to assign someones ancestral composition- % of ancestry

2. admixture clines- gradual transitions in genetic composition between populations as you move across geographic regions