From Africa to Aotearoa Part 1: Out of Africa
The spread of modern humans out of Africa started around 65,000 years
ago, and ended with the settlement of New Zealand 750 years ago.
These PowerPoint presentations trace that journey in two parts:
Part 1 (this presentation): The migration of the first modern humans out of
Africa into Europe and Asia – how many migration events were there, and
who did Homo sapiens meet along the way? What does genetic evidence
tell us about the relatedness of human “races”?
Part 2 (coming in June 2012): When did humans first venture into the
Pacific, and what route did they take to reach New Zealand?
The story of modern humans began less than 200,000 years ago in
Africa. This is where Homo sapiens - anatomically modern humans who
looked much like you or I - first arose (click 1). However, at this time
there were older hominid lineages living across much of Europe and Asia
(click 2), as well as in other parts of Africa. These lineages were the
descendants of Homo erectus, who began to migrate out of Africa
hundreds of thousands of years earlier. Eventually these other lineages
were replaced by Homo sapiens, as we shall see later in the presentation.
Evidence for our recent African origins comes from both fossils and
genetics.
The earliest fossils of anatomically modern human are from Ethiopia.
This skull is one of the earliest and dates back to 160,000 years ago. A
partial Homo sapiens skeleton dating back to 195,000 years has also
been found in Ethiopia.
Genetic studies also show that Homo sapiens originated less than
200,000 years ago in Africa: In 1987, New Zealander Allan Wilson
showed that all humans alive today can trace their mitochondrial DNA
back to a single female who lived in Africa 150,000 to 200,000 years ago.
She is dubbed “Mitochondrial Eve”.
Modern humans, descended from Mitochondrial Eve, spread out of Africa
within the last 100,000 years, spreading to all corners of the globe and
replacing all the existing older hominid species. This hypothesis is
referred to as “Out of Africa” or “Recent African Origin”
The first evidence of Homo sapiens outside of Africa comes from fossils
discovered in Israel dated to 90,000 - 100,000 years ago. We can’t tell
from these fossils alone whether they are the direct ancestors of humans
that spread across the rest of the globe – they may represent an early
migration which did not spread outside the middle east.
In the last 25 years, researchers have relied more and more on DNA to fill
in the gaps in the fossil record. Although fossils are important, in many
ways DNA is more informative - a fossil will only tell you what was there at
a particular time, whereas DNA can trace where someone came from.
We will see later how researchers are now using DNA from fossils to gain
even more information about human origins.
How can we trace our ancestry with DNA?
DNA changes (or “mutates”) over time, and these changes are passed
from parent to child. As these changes build up over time, and
populations migrate around the globe, each population will have some
changes (which we refer to as “markers”) that are specific to their area
and others that reflect where that population came from [click 4 times to
show changes building up over time and placement of populations on
tree]. The more DNA markers two populations have in common, the more
closely related those populations are likely to be. In this example,
populations 3 and 4 are more closely related (i.e. share a more recent
common ancestor), than populations 1 and 4.
By comparing the number of DNA changes over time, and calibrating this
with the fossil record, researchers can estimate how many years have
passed since two populations split.
Allan Wilson used mitochondrial DNA to show we have a recent African
origin.
Mitochondrial DNA is found in the body of the cell, not in the nucleus. It is
present in the egg but not in the head of sperm, so it is always inherited
from the mother. Because it doesn’t get mixed with DNA from the father,
changes in mitochondrial DNA over time can easily be traced back, and
can be used to track the female line of inheritance.
By studying mitochondrial DNA (mtDNA) sequences from people all over
the world today, researchers have been able to build up a picture of how
populations are related, and where they are likely to have come from.
Mitochondrial markers show that around 65,000 years ago, women
carrying one of the major African mtDNA lineages moved out of Africa
(click 1). This lineage split into two branches– one moved east, into
South East Asia (click 2), and the other moved north into Europe and the
near East (click 3), eventually reaching the far east and crossing the
Bering Strait into the Americas.
We know modern humans reached South East Asia and Australia around
50,000 years ago (click 4), and Europe around 40,000 years ago (click 5).
But mitochondrial DNA only tells us part of the story.
By studying the Y chromosome researchers can trace the male lineage,
providing more detail on migration routes and timing. The Y chromosome
is the sex-determining chromosome in humans, and is passed down only
from father to son. Most of the Y chromosome is extremely different to
the X chromosome, so does not recombine (“cross-over”) with the X
during meiosis. This means it is inherited unshuffled, much like
mitochondrial DNA.
All modern-day Y chromosome lineages are descended from a single
African lineage, and began to diverge around 60,000 years ago, which fits
with mtDNA evidence suggesting migrations out of Africa beginning
around this time.
As researchers have gathered more and more Y chromosome and
mtDNA data, a complex picture of human migrations has emerged, as this
map showing the spread of Y chromosome (blue) and mtDNA types (red)
shows. This genetic evidence suggests there were multiple migrations
events, and multiple routes taken to reach different areas of the globe.
A long-term, large scale international research project, called the
Genographic project, is currently underway to disentangle these routes.
This project is gathering mitochondrial DNA and Y chromosome markers
from tens of thousands of people from all around the world, in order to fill
in the details on how and when humans spread across the globe. The
Genographic project includes researchers from the Allan Wilson Centre,
who are focussing on the spread of people through the pacific.
An in-depth timeline of the routes shown on this map is available at
https://genographic.nationalgeographic.com/genographic/lan/en/atlas.html
But Y chromosome and mtDNA still only trace part of our ancestry. The Y
chromosome is traced back to a single male ancestor (click 1), and
mtDNA to a single female (click 2). Our many other ancestors are
invisible with these markers (click 3).
We need to study the autosomes (chromosomes other than the X and Y)
in order to see the genetic signature of all our ancestors. These
chromosomes get shuffled at each generation, meaning we are a mosaic
of all our ancestors.
In order to see all these previously “invisible” ancestors, we need DNA
sequences from all parts of the human genome.
Advances in DNA sequencing technology mean that it is now possible to
sequence whole human genomes far more quickly, and far more cheaply,
than in the past. This has given researchers more power than ever
before to trace who our ancestors were. Genomics is having a huge
impact on the study of human evolution – many of the major recent
discoveries about our origins have come from analysing genomes, rather
than archaeology.
A study of the Aboriginal genome, published in 2011, shows how whole
human genome sequences are refining our ideas about human migration.
The Aboriginal genome was sequenced by a group of researchers from
Denmark, China, US and Australia, and compared with genomes from
European, Chinese, Melanesian and African individuals. Aborigines are
known to be one of the oldest continuous populations outside Africa, with
fossil evidence placing them in Australia as long ago as 50,000 years.
The genome sequence enabled the researchers to more accurately date
when Aboriginals diverged from other human lineages, and who their
closest relatives are. The findings shed light not only on the history of
Aborigines, but on the history of human migration into Asia.
Their study suggests that the ancestors of Melanesians and Aboriginals
split off from other non-African lineages quite early, around 60-75,000
years ago, moving down into South-East Asia (click 1). However, this
migration event did not give rise to other Asian lineages, such as the
Chinese. Instead, China was populated by a second wave of migration
into Asia (click 2). The Chinese and European lineages diverged around
25-40,000 years ago (click 3).
As the second wave of migrants entered Asia, they probably interbred
with the descendants of the first migration (click 4).
This phylogenetic tree demonstrates how these groups are related. The
ancestors of Melanesian and Aboriginal populations diverged from other
non-African lineages early on (click 1), while the ancestors of Chinese
and European populations diverged much later (click 2). This means that
Chinese and European populations are more closely related to each other
than they are to Melanesian and Aboriginal populations, although there
has been some exchange of genetic material (black arrow) since the
initial divergence.
Genome sequences are also shedding light on our interactions with other
ancient hominid lineages, such as the Neanderthals.
As modern humans spread across Europe and Asia they would have
come into contact with the older hominid lineages already living there descendants of Homo erectus who first migrated out of Africa hundreds of
thousands of years earlier.
In Europe, these populations became the Neanderthals – they were living
in Europe at least 150,000 to 30,000 years ago.
Neanderthals were stockier than modern humans, with large brow ridges,
a heavier frame and barrel chest. They were similar to modern humans in
some cultural aspects, such as burying their dead and use of clothing and
jewellery.
The youngest Neanderthal fossils are from about 28,000 years ago – after
that there are no traces of Neanderthal in the fossil record, suggesting
that they were completely replaced by Homo sapiens. But Neanderthals
and modern humans would have overlapped in parts of Europe over
several thousand years.
It had long been assumed, under the Out of Africa hypothesis, that
modern humans completely replaced Neanderthals. The mitochondrial
DNA data shows no evidence of interbreeding.
However, comparing the whole Neanderthal genome with our own is the
only way to answer this question for sure.
Researchers from the Max Planck Institute for Evolutionary Anthropology
in Germany recently did just that. They were able to extract Neanderthal
DNA from fossilised bones retrieved from four sites (shown on the map,
with approximate ages of the bones). Three bones from Vindija yielded
good enough DNA to determine the entire genome sequence.
To extract DNA from fossilised bones, researchers use a drill to reduce
the bone tissue to a powder, then use a series of chemical treatments to
extract the DNA (click 1).
Extreme care needs to be taken to avoid contaminating the Neanderthal
DNA with modern human DNA. Researchers work in specially built
“ancient DNA” labs (where no modern DNA work is carried out), and wear
safety suits to avoid contamination.
The DNA extracted is extremely fragmented, but modern DNA
sequencers can produce millions of short DNA sequences from these
fragments, which researchers then piece back together using highperformance computers (click 2).
When the Neanderthal genome sequence was compared with modern
human genome sequences something unexpected was found.
Although overall the Neanderthal genome is significantly different from all
modern humans, individuals from Europe and Asia (but not Africa) share
around 2% of their DNA with Neanderthals. This suggests that they
interbred with Neanderthals at some point in their history.
The Neanderthals may not have been the only ancient relative Homo
sapiens encountered.
In 2008 a fingerbone and a tooth were found in this cave in southern
Siberia.
They were initially thought to be Neanderthal, but DNA sequencing
showed that they were from a previously unknown lineage of early human
that probably diverged from the Neanderthal lineage several hundred
thousand years ago. They were neither Neanderthal, nor modern human,
so they were dubbed the “Denisovans”, after the region in which they
were found. The ancestors of Denisovans and Neanderthals probably left
Africa around 300,000 years ago then diverged into two groups –
Neanderthals in Europe, and Denisovans in Asia.
The Denisovan genome was sequenced in 2010, and once again there
was some overlap with modern humans. Denisovan DNA shows up in
the genes of modern Melanesians, Aboriginals and some indigenous
South East Asian populations, suggesting interbreeding between these
groups.
This genetic evidence also suggests that Denisovans lived from Siberia
down to South East Asia.
So from the genetic evidence it appears that modern humans interbred
with Neanderthals early on, probably in North Africa or the Middle East
when they first moved out of Africa (click 1). An early migration then
headed towards South-East Asia and Australia, and interbred with
Denisovans along the way (click 2). The second, later migration which
produced the Chinese lineage didn’t interbreed with Denisovans.
Eventually Homo sapiens replaced, or assimilated, the older populations
entirely.
So what do these new genomics studies mean for the Out of Africa
hypothesis? This hypothesis is still the best explanation for human
origins, but these recent discoveries show that the picture is not as simple
as was once thought. We are mostly of recent African origin, but with a
small contribution from Neanderthal and Denisovan interbreeding.
Interbreeding would have been very uncommon, however.
A recent study modelled how much interbreeding must have happened for
2% Neanderthal DNA to have ended up in our genome. The researchers
found that as few as 200 interbreeding events could leave us with about
one percent Neanderthal DNA; three percent would only require about
430 matings. If you assume that the two groups overlapped for about
10,000 years, that works out to once every 25-50 years.
The finding that we are all of recent African origin had profound
implications for the way we view race.
All the features we now regard as “racial” characteristics, such as skin
colour, eye colour and shape, and hair type, must have evolved within the
last 100,000 years after Homo sapiens began migrating out of Africa into
new environments.
Before the discovery of our recent African origins, the different races of
human were regarded as being extremely distinct, the result of
divergence of human lineages hundreds of thousands of years ago. This
diagram from the 1930s shows how the different races were virtually
regarded as different species.
Beginning in the 1940s, scientists began to argue that racial categories
based on physical differences alone were imprecise and arbitrary, and
began to use genetics to understand the variation in human populations.
As the discovery of our recent African origins became more widely
accepted, and genetic studies became more advanced, scientists began
to realise that the concept of “race” is meaningless at the genetic level.
We now know that “racial” characteristics, like size, skin colour and facial
features are the result of only superficial changes in small numbers of
genes and evolved after modern humans started to spread out of Africa,
within the last 100,000 years.
For example, blue eye colour is the result of a single mutation in one gene
that arose in Europe around 10,000 years ago. It is thought that blue
eyes were deemed attractive, so quickly rose to become common.
These days in some parts of Europe more than 80% of the population
have either blue or green eyes.
Differences in skin colour largely result from adaptation to differences in
the level of UV–radiation at the equator vs northern or southern regions.
Because UV-levels are lower in northern climates, light skin colour is
needed for the sun's ultra- violet light to penetrate into the body and
transform vitamin D into a usable form.
The underlying genetic basis in skin colour is not completely worked out,
but differences in skin colour appear to result from small changes in
multiple genes. In many cases different genetic changes have produced
the same end result – for instance different mutations appear to be
responsible for the lighter skin pigmentation in Europeans and East
Asians, an example of convergent evolution in response to similar
environmental pressures. Thus, populations with similar pigmentation
may be genetically no more similar than other widely separated groups.
So, the kinds of differences that people notice, such as skin pigmentation,
eye colour or height are basically surface features that have been
selected for in the environment. When you peer beneath the surface at
the underlying level of genetic variation, we are all much more similar
than we appear to be. In fact, overall humans are 99.9% identical at the
DNA level – this low level of variation reflects our recent origins.
Populations that are closer geographically do share more genetic variants
than those that are further away, which is how we are able to track the
history of populations. But this genetic variation is a continuum – there
are no definite boundaries between populations, and different “racial”
groups can’t be placed into discrete clusters.
For instance, if you consider Africa, Asia and Europe to represent 3 major
racial groups:
85-90% of human genetic variation occurs within each group, and only
10-15% between groups. So for example individuals within Asia (red
circle) may be more different from one another overall than an Asian and
African (blue circle) individual. 90% of the world’s variation could be
found by looking within a single continent, and only another 10% would be
added by adding individuals from another continent.
The genetic variation that we can use to classify human populations on
the basis of geographical ancestry is this 10-15% of the total variation that
varies between populations (so this is 10-15% of the 0.1% of our DNA
that varies).
Thus, most of the genetic variation among humans has nothing to do with
differences in populations. The genetic differences between 'races' are
minor compared to the differences between people in general.
It is more accurate to think about “ancestry”, rather than race. This
acknowledges the overlap between groups, and the continuous nature of
the way people and genes spread today, and allows us to understand our
history is intertwined with other humans across the globe.
References and Resources:
Genographic project: https://genographic.nationalgeographic.com/genographic/index.html
Using mitochondrial and Y chromosome DNA to trace human migration. Website includes interactive timelines
of human history, an overview of genetic techniques, and instructions on how to participate.
Aboriginal Genome:
Research paper:
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Rasmussen et al., 2011,
Science Vol. 334 pages 94-98. http://www.sciencemag.org/content/334/6052/94
Commentary:
First Aboriginal Genome Sequenced. http://www.nature.com/news/2011/110922/full/news.2011.551.html
Neanderthal Genome
Research paper:
A draft sequence of the Neandertal genome. Green et al. 2010, Science Vol. 328 pages 710-722
http://www.sciencemag.org/content/328/5979/710.full
Commentary:
Close encounters of the Prehistoric kind http://www.sciencemag.org/content/328/5979/680.summary
Neanderthals Live! http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/neandertals-livegenome-sequencing-2010.html
Denisovan Genome
Research paper:
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Reich et al., 2010. Nature Vol
468, pages 1053-1060. http://www.nature.com/nature/journal/v468/n7327/full/nature09710.html
Commentary:
Complete Denisovan genome offers glimpse of ancient variation.
http://blogs.nature.com/news/2012/02/complete-denisovan-genome-offers-glimpse-of-ancient-variation.html
Fossil genome reveals ancestral link. http://www.nature.com/news/2010/101222/full/4681012a.html
Human skin colour
Jablonski, N.G. & G. Chaplin. (2000). The evolution of human skin coloration, Journal of Human Evolution,
vol. 39, pages 57-106.
http://www.bgsu.edu/departments/chem/faculty/leontis/chem447/PDF_files/Jablonski_skin_color_2000.pdf
(Investigates the potential role of folic acid and Vitamin D in the evolution of human skin colour)
Quillen, E., M. Bauchet, et al. (2011) OPRM1 and EGFR contribute to skin pigmentation differences between
Indigenous Americans and Europeans. Human Genetics: 1-8.
http://www.springerlink.com/content/bq4mn02526q64640/
(Research paper showing 4 genes primarily affect skin colour in Europeans and Indigenous Americans)
Skin colour, Vitamin D and Folate: http://blogs.discovermagazine.com/gnxp/2007/07/skin-color-vitamin-dfolate/ (Commentary on theories about Vitamin D and human skin color)
Blue eye colour in humans
Research paper:
Eiberg, H., J. Troelsen, et al. (2008). Blue eye color in humans may be caused by a perfectly associated
founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. Human
Genetics Vol. 123, pages 177-187.
http://www.springerlink.com/content/2045q6234h66p744/fulltext.html
Commentary:
Blue-eyed humans have a single common ancestor.
http://www.sciencedaily.com/releases/2008/01/080130170343.htm