Molecular Anthropology Genetics Research Tutorial 1 gen155/lectures/restut.ppt.

Molecular Anthropology

Genetics Research Tutorial 1www.abdn.ac.uk/~gen155/lectures/restut.ppt

Human Origins

Australopithecus Early Homo sp H sapiens

Neanderthals

Mya

5 4 3 2 1

0.1

0

Mya = million years agoBirth 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

acgt tgcaagcaaccaacgt acgaOutgroupe.g. chimp Modern humans

Mutation (SNP)

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 (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 Y-chromosome 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