DNA Basics
A difference at a single DNA base is called what?
A SNP: single-nucleotide polymorphism.
Which method summarizes many genetic variants into principal components to visualize population structure?
PCA: Principal Component Analysis.
What is our professors name?
Daniel Matute
Which two countries supplied the 350 newly sequenced genomes?
Angola and Mozambique.
Approximately how many SNPs were novel relative to dbSNP155?
2.9 million SNPs.
What makes a variant a singleton in this dataset?
Its variant allele occurs on only one sampled chromosome.
Which analysis looks for DNA segments that individuals inherited from a common ancestor?
IBD: identity by descent.
Where’s Matute From
Colombia 🇨🇴
In what African region did the Bantu Expansion begin, and approximately when?
Central-West Africa, approximately 5,000-6,000 years ago.
What is the process of predicting untyped genotypes using a reference panel called?
Genotype imputation.
What is a run of homozygosity, or ROH?
An extended region where an individual is homozygous across many consecutive markers.
Which program uses haplotype-sharing patterns to estimate ancestry sources and their proportions?
SOURCEFIND.
What tiny organism is the main model system used by the Matute Lab to study how new species form?
Drosophila / fruit flies 🪰
Which geographic feature may have helped separate southwestern and southeastern dispersal patterns?
The Kalahari semi-desert.
Why did the researchers hide known sequenced genotypes before imputing them?
So they could compare the predictions with the original known genotypes and measure accuracy.
Why do shorter IBD segments generally point to older shared ancestry?Why do shorter IBD segments generally point to older shared ancestry?
More generations give recombination more chances to break inherited segments into smaller pieces.
Which program estimates admixture dates using haplotype patterns shaped by recombination?
fastGLOBETROTTER.
What evolutionary process is the major focus of the Matute Lab?
Speciation
Match the additional ancestry source to each group: Kongo / Cabinda; southern Mozambique (Tsonga and Chopi).
Kongo / Cabinda: western rainforest hunter-gatherer-related.
Southern Mozambique: Khoe/San-related.
Give two limitations that should make us cautious about generalizing the results to all Bantu-speaking populations.
Answers: limited or uneven sampling; geographic gaps; model assumptions; sequencing or phasing errors.
Does an estimate of Nₑ = 10,000 mean exactly 10,000 people lived in the population? Explain.
No. Effective population size is not census population size.
Which framework simulates demographic histories and compares their genetic summaries with observed data?
ABC: Approximate Bayesian Computation.
In 2014, Dr. Matute won an award named after what famous evolutionary geneticist?
Theodosius Dobzhansky
What shared movement happened BEFORE the major western/eastern branching in the late-split model?
An initial southward movement through the equatorial rainforest, followed by branching south of it.
Why remove 340 individuals from 1000G when adding 340 CAB/MOZ individuals to the reference panel?
To keep panel size comparable and test population representation rather than simply a larger panel.