From Africa to Aotearoa Part 1: Out of Africa

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1 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 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.

2 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.

3 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 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.

4 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.

5 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.

6 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 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.

7 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.

8 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.

9 References and Resources: Genographic project: 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 Commentary: First Aboriginal Genome Sequenced. Neanderthal Genome Research paper: A draft sequence of the Neandertal genome. Green et al. 2010, Science Vol. 328 pages Commentary: Close encounters of the Prehistoric kind Neanderthals Live! Denisovan Genome Research paper: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Reich et al., Nature Vol 468, pages Commentary: Complete Denisovan genome offers glimpse of ancient variation. Fossil genome reveals ancestral link. Human skin colour Jablonski, N.G. & G. Chaplin. (2000). The evolution of human skin coloration, Journal of Human Evolution, vol. 39, pages (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: (Research paper showing 4 genes primarily affect skin colour in Europeans and Indigenous Americans) Skin colour, Vitamin D and Folate: (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 Commentary: Blue-eyed humans have a single common ancestor.

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