Lecture 22 - Human Migration

Question 1

Why is mitochondrial DNA used to study human evolution?

Answer 1

As it is the most rapidly evolving part of the human genome which is needly in order to distinguish closely related populations

Mitochondria do not recombine so analysis is easier

Question 2

What is the problem with studying mitochondrial DNA?

Answer 2

It is just a single locus, equivalent to a single gene in the nuclear genome

It describes only female prehistory

It does not evolve in an entirely neutral fashion. It is subject to some natural selective pressures, possible adaptation to cold environments, or just purifying selection (the gradual removal of deleterious mutations from the genome)

Question 3

What is the most variable part of the genome?

Answer 3

The D-loop on mtDNA

Question 4

What are the two segments of the D-loop?

Answer 4

Hypervariable region1 (positions 16001-16568)

Hypervariable region2(001-574)

Question 5

Haplogroups

Answer 5

Groups based on the sequences of hypervariable regions, the various mitochondrial genomes exist in the human population can be divided into around 100 groups

Question 6

What are haplogroups made up of?

Answer 6

Haplotypes

Haplotypes share substitutions that define the haplogroup

Question 7

How can evolutionary relationships be worked out in mtDNA studies?

Answer 7

Defining substitutions between haplogroups

Question 8

What is an empty node?

Answer 8

A haplogroup that is unknown in the modern human population

It might exist in very few individuals whose DNA has not yet been sequenced

Or might have existed in the past but become extinct

Question 9

Coalescence

Answer 9

Simulate past population sizes and test models of gene flow

Estimate divergences and changes to population size measured in number of generations

Usually within populations or between two populations with recent migration

Infer rate of coalescence of alleles

Requires representative sample of alleles

Question 10

Coalescence time

Answer 10

The age of the haplogroup

Estimated from simulations using diversity of the haplotypes that make up the haplogroup

The greater the diversity among haplotypes, the more ancient the coalescence time

Coalescence times are estimated in generations because each generation is an opportunity for two allelic copies to coalesce (merge)

Question 11

Founder analysis

Answer 11

Bottleneck events can reduce diversity and dramatically change the proportions of some alleles

This uses haplogroup diversities to estimate the time of a population split, such as occurs when a group of people leave their parent population and migrate to another location

If bottleneck persists, this can lead to further loss of diversity through genetic drift

Question 12

When and where were the first modern humans found outside of Africa?

Answer 12

Skhul and Qafzeh caves in Levant around 90,000 years ago

Question 13

Why were the fossils found in Skhul and Qafzeh caves in Levant probably not the first real migrants out of Africa?

Answer 13

The caves were reoccupied by Neanderthals at a later date

Modern humans were not seen there again for some time

Question 14

What is the likely explanation for the Skhul and Qafzeh fossils?

Answer 14

Part of a failed attempt at colonization

An extension of the African population into Asia during the warm period

Question 15

What is the likely initial migration out of Africa?

Answer 15

Humans migrated out of Africa from Ethiopia directly to Asia across the entrance to the red sea enabled by the sea level being 70 metres lower than it is today

This was around 50,000-70,000 years ago. Around 74,000 years ago there was a massive eruption of a super volcano on Lake Toba in Sumatra around 74,000 years ago. This caused climactic changes that might have led to the movement of humans out of Africa in search of more productive hunting and plant getehring areas

Only a subsample of the African population (1000 -2500 people)

Question 16

What is the pattern of haplotype groups found in Africa today?

Answer 16

All haplotype groups are clustered together in the mtDNA network

Question 17

What African haplotype group are all haplotype groups found outside of Africa linked to?

Answer 17

Haplogroup L3

Question 18

What are and where were the immediate non-African descendants of haplogroup L3? What does this suggest?

Answer 18

M and N both found mainly in Asia suggesting that the initial migration was into Asia

Question 19

Where are the modern Africans whose L3 haplotypes are most similar to M and N located?

Answer 19

Ethiopia suggests that is where the migration started

Question 20

When did haplogroup M and N originate and what does this suggest?

Answer 20

50000-700000 years ago suggesting that the migration outside of Africa started around that time

Question 21

Where did the first migrants outside of Africa go?

Answer 21

They went along the coast to SE Asia

They kept going until they reached Australia

Question 22

When did humans reach Australia?

Answer 22

Archaeologists believe 50,000-60,000 years ago

Question 23

What haplotypes are found on the Andaman Islands?

Answer 23

M haplotype that coalesce at about 60,000 years ago

Suggesting they arrived there around that time

Question 24

What was the rate of migration along the southern Asia coast?

Answer 24

0.7-4km per year with side migration into the interior of the continent

Question 25

How many haplotype groups predominate in modern european human populations?

Answer 25

11 and all originate in the near east

Question 26

When did the haplotype groups enter Europe?

Answer 26

At different times

The oldest is U which appeared 50,000 years ago

Coincides with the period when the first modern humans moved into the continent as the ice withdrew to the north at the end of the last major glaciatoin

Question 27

What haplotypes led the later migrations into Europe?

Answer 27

The haplotype groups J and T1 that arrived about the same time as agriculture spread from the near east 8500-7000 years ago

Went by two routes

Question 28

Bering Strait

Answer 28

Seperates Siberia from Alaska

The obvious point of entry for humans into the new world

Quite shallow and if the sea level dropped by 50m it would be possible to walk from one continent to the other

The sea was shallow enough 60,000 and 11,000 years ago

But for a large part of this time it would have been impassable because of the build up of ice in the areas that are Alaska and northwest Canada

The glacier-free parts of Beringia would have been near-arctic but may have served as refugia

Question 29

What happened 14,000-12,000 years ago regarding the new world?

Answer 29

Beringian land bridge was open at a time when the climate was warming and the glaciers were receding

During this time there was an ice free corridor leading from Beringia to central North America

The implication is that the first modern humans might have reached the Americas about 13,000 years ago

Question 30

Haplogroups in the new world?

Answer 30

97% of Native Americans have one of four mitochondrial DNA haplogroups- A, B, C and D

These are common in East Asia suggesting that this is the source of colonizing populations indicating people went through the Bering Strait

The remaining 3% of native American mtDNAs belong to haplogroup X2.

It is very rare in Asia but found at low frequencies in some European populations. Implies some people from Europe colonized America. However Sub-groupX2a only in North America and dates to 15-17kya

Question 31

When was the coalescence of the haplogroups A, B, C, D and X? What does this suggest?

Answer 31

15,000 to 17,000 years ago

Possible evidence that the haplogroups entered the new world together

But this was earlier than when the route through the ice was open

Question 32

What is the Clovis-first hypothesis?

Answer 32

The first paloeindians were the clovis people

They made large spearheads called clovis points

First clovis points date to about 13,000 years ago so if they were the first Americans humans did not cross the Bering Strait until about that time

Question 33

Why do people question the Clovis-first hypothesis?

Answer 33

There may be evidence of human occupation at sites that date to earlier than 13,000 years ago

But skeletons are rarely found, so evidence that humans were present is indirect

Such things as the possible remains of hearth where a fire was tended and food was cooked

Question 34

When was there a megafauna extinction in North America?

Answer 34

12kya

The disappearance of 30+ genera of large mammals from the Americas

Humans may have been hunting in North America as much as 15kya

Question 35

Coprolites in America?

Answer 35

Coprolites dating over 14,000 years ago in Paisley Cave in Orgeon contained human mitochondrial DNA

Pushing back first migration into the Americas 15,000 years ago or earlier when the ice corridor was closed

Question 36

What is the updated view of how the first humans reached north America?

Answer 36

They followed the Pacific Coastal routh along the south of Beringia and then down the east of North and South America

Journey is thought to be possible anytime after 15,000 years ago