Download Honours Genetics Research Tutorial

Molecular Anthropology
Genetics Research Tutorial 1
www.abdn.ac.uk/~gen155/lectures/restut.ppt
Human Origins
Mya
5
0.1
4
3
Australopithecus
2
1
Early Homo sp
0
H sapiens
Neanderthals
Mya = million years ago
Birth of Jesus was 0.002 Mya
European Human Prehistory
• Most of European history is prehistory
• We (modern-type humans) got here about
40000 years ago: the Palaeolithic (old stone
age) - primarily hunter-gatherer economy displacing the indigenous Neanderthal type
humans
• Farming spread across Europe from the
Middle East (“Fertile Crescent”) from
around 7000 Ya - Neolithic (new stone age)
European
time chart
Neanderthal, Cro-Magnon and modern
Low forehead,
prominent eyebrow ridges
Very similar to us
Paleolithic Cave Art from Lascaux
(Dordogne, France)
(About 17000 Ya)
The mitochondrial chromosome
• About 15kb of mtDNA
• Mutates quite rapidly
• In eggs but not sperm, so
shows maternal inheritance
The human Y chromosome
• The mammalian X and Y chromosomes
evolved from a pair of autosomes
• The human Y has a block of material that
transposed (moved) from the X since the
divergence of chimps and humans
Phylogeny based on haplotypes
• If there has been no recombination, we can deduce
the phylogeny of the haplotypes by parsimony
Mutation (SNP)
acgt
Outgroup
e.g. chimp
acgt
acga acca agca tgca
Modern humans
Dating the mutational events
• The Y chromosome also has rapidly-mutating
microsatellites (short tandemly repeated
sequences such as CACACA….)
• The older a mutation, the more diverse
microsatellite alleles associated with it
Haplogroup
Ovchinnikov et al (2000)
• Neanderthal mtDNA from Asia
• Phylogenetic analysis of Neanderthal and modern
human DNAs
• Evidence for the Out-of-Africa model of modern
human origins
• Estimation of the age of the MRCA for modern
humans and Neanderthals
• Used phylogenies based on distance and
parsimony
Capelli et al (2003)
• A Y-chromosome census of the British Isles
• Compares Y chromosomes from regions of UK,
with those in Denmark, Germany, Ireland, Norway
• Different parts of UK have differing proportions
of “indigenous” and “invading” Y chromosomes
• Uses Y chromosome SNPs (which they call UEPs)
and microsatellites
•
Capelli C, Redhead N, Abernethy JK, Gratrix F, Wilson JF, Moen T, Hervig T, Richards M, Stumpf MP, Underhill PA,
Bradshaw P, Shaha A, Thomas MG, Bradman N, Goldstein DB. (2003) A Y chromosome census of the British Isles.
Curr Biol. 13:979-84.
Caramelli et al (2003)
• Analysis of mtDNA from 24,000 year old
anatomically modern (Cro-Magnon) humans
• Evidence that Cro-Magnon types, not
Neanderthals, are the ancestors of modern humans
• Used multidimensional scaling to represent
sequences as points in space, distance between
them is a measure of genetic distance
• Also used a simple measure of genetic distance
Thomas et al (2000)
• Lemba (“Black Jews”) are Bantu-speakers living in
southern Africa
• Claim Jewish origin based on stories and customs
• Study compares their Y-chromosomes with other
African and Jewish populations
• Looked at distribution of haplotypes across
populations, and proportions of haplotype sharing
between populations
• Also constructed genealogical tree of haplotypes
The Exercise
• Look at the 4 set papers
• Highlight the questions we want you to investigate
• You can decide what the other interesting questions are,
and how they were answered
• Organise yourself into group(s) to do this - each group
should have at least one person who did the population
genetics module
• For each paper you should be able to understand how the
main conclusions were reached and what were the
important experimental results
• Be ready to present your paper to the class at next meeting
Additional papers
(Not set this year)
Brown et al (1998)
• Studied the mtDNA of modern Native Americans 4 main types (A-D)
• Minor 5th type (X) in Native Americans found
also in Europeans but not Asians
• So how did it get there? By crossing the Atlantic?
• Used a network based on maximum parsimony to
illustrate relationships of haplotypes, and
coalescent analysis to estimate ages
Helgason et al (2001)
• mtDNA analysis to deduce the orgins of people in islands
of North Atlantic (Iceland, Orkney, Scottish Western Isles,
Skye, etc)
• Relative contributions of Vikings from Scandinavia (about
1000 years ago) and Picts/Gaels from Britain/Ireland
(more ancient)
• Used r (rho) distance between samples as measure of the
average number of base changes between a member of one
population and a member of the other population
Kayser et al (2000)
• Study of the mutation rate and mechanism of Ychromosome microsatellites using father + son
DNA
• Important both for anthropological studies (dating
the age of lineages) and in forensics
• Used father-son DNA samples, a set of
microsatellite polymorphisms, to calculate
frequency and type of mutation
• Also estimated the probability of true paternity