Genes for Skin Color Rebut Dated Notions of Race, Researchers Say

By Carl Zimmer
A gallery of busts from the 19th century showing human diversity on display in the Museum of Mankind in Paris. Scientists have found that the genetic variations that determine skin color are widely shared. CreditRomuald Meigneux/SIPA, via Associated Press

For centuries, skin color has held powerful social meaning — a defining characteristic of race, and a starting point for racism.

“If you ask somebody on the street, ‘What are the main differences between races?,’ they’re going to say skin color,” said Sarah A. Tishkoff, a geneticist at the University of Pennsylvania.

On Thursday, Dr. Tishkoff and her colleagues showed this to be a profound error. In the journal Science, the researchers published the first large-scale study of the genetics of skin color in Africans.

The researchers pinpointed eight genetic variants in four narrow regions of the human genome that strongly influence pigmentation — some making skin darker, and others making it lighter.

These genes are shared across the globe, it turns out; one of them, for example, lightens skin in both Europeans and hunter-gatherers in Botswana. The gene variants were present in humanity’s distant ancestors, even before our species evolved in Africa 300,000 years ago

The widespread distribution of these genes and their persistence over millenniums show that the old color lines are essentially meaningless, the scientists said. The research “dispels a biological concept of race,” Dr. Tishkoff said.

Humans develop color much as other mammals do. Special cells in the skin contain pouches, called melanosomes, packed with pigment molecules. The more pigment, the darker the skin.

Skin color also varies with the kind of pigments: Melanosomes may contain mixtures of a brown-black called eumelanin and a yellow-red called pheomelanin.

To find the genes that help produce pigments, scientists began by studying people of European ancestry and found that mutations to a gene called SLC24A5 caused cells to make less pigment, leading to paler skin. Unsurprisingly, almost all Europeans have this variant.

We knew quite a lot about why people have pale skin if they had European ancestry,” said Nicholas G. Crawford, a postdoctoral researcher at the University of Pennsylvania and a co-author of the new study. “But there was very little known about why people have dark skin.”

Since the early 2000s, Dr. Tishkoff has studied genes in Africa, discovering variants important to everything from resistance to malaria to height.

African populations vary tremendously in skin color, and Dr. Tishkoff reasoned that powerful genetic variants must be responsible.

Studying 1,570 people in Ethiopia, Tanzania and Botswana, she and her colleagues discovered a set of genetic variants that account for 29 percent of the variation in skin color. (The remaining variation seems tied to genes yet to be discovered.)

One variant, MFSD12, was particularly mysterious: No one knew what it did anywhere in the body. To investigate its function, the researchers altered the gene in reddish lab mice. Giving them the variant found in darker-skinned Africans turned the mice gray.

As it turned out, MFSD12 can affect the production of brown-black eumelanin, producing a darker skin color.

The eight gene variants that Dr. Tishkoff and her colleagues discovered in Africans turned out to be present in many populations outside the continent. By comparing the DNA of these people, the researchers were able to estimate how long ago the genes appeared.

They turned out to be immensely old. A variant for light skin — found in both Europeans and the San hunter-gatherers of Botswana — arose roughly 900,000 years ago, for example.

Even before there were Homo sapiens, then, our distant forebears had a mix of genes for light and dark skin. Some populations may have been dark-skinned and others light-skinned; or maybe they were all the same color, produced by a blend of variants.

Neanderthals split off from our own ancestors an estimated 600,000 years ago, spreading across Europe and eastern Asia. While they became extinct about 40,000 years ago, some of their DNA has survived.

These hominins inherited the same combination of variants determining skin color, Dr. Tishkoff and her colleagues also discovered. It’s possible that some populations of Neanderthals, too, were light-skinned, and others dark-skinned.

Living humans come packaged in a wide range of hues — from pale and freckly in Ireland to dark brown in southern India, Australia and New Guinea. Researchers have argued that these varying colors evolved partly in response to sunlight.

The idea is that people who live with intense ultraviolet light benefited from dark color, pigments that shielded important molecules in their skin. In places with less sunlight, people needed lighter skin, because they were able to absorb more sunlight to make vitamin D.

The new genetic evidence supports this explanation, but adds unexpected complexity. The dark-skinned people of southern India, Australia and New Guinea, for example, did not independently evolve their color simply because evolution favored it.

They inherited the ancestral dark variants Dr. Tishkoff’s team found in Africans. “They had to be introduced from an African population,” said Dr. Tishkoff.

Yet the same is true for some genes that produce light skin in Asia and Europe. They also originated in Africa and were carried from the continent by migrants.

As Africans moved into Europe and Asia, they interbred with Neanderthals on several occasions. Last week, Michael Dannemann and Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Germany reported that people in Britain still carry a number of Neanderthal variants that color skin.

Some of the newly discovered genes appeared relatively recently in our evolution.

The pale-skin variant of SLC24A5 that’s overwhelmingly common in Europe, for example, is a recent addition to the genome, arising just 29,000 years ago, according to the new study. It became widespread only in the past few thousand years.

Dr. Tishkoff and her colleagues found it frequently not just in Europe, but also in some populations of lighter-skinned Africans in East Africa and Tanzania. Studies of ancient DNA recently discovered in Africa point to an explanation.

Several thousand years ago, it seems, a migration of early Near Eastern farmers swept into East Africa. Over many generations of interbreeding, the pale variant of SLC24A5 became common in some African populations.

In all, the new study provides “a deeper appreciation of the genetic palette that has been mixed and matched through evolution,” said Nina Jablonski, an expert on skin color at Pennsylvania State University.

DNA From Old Skeleton Suggests Humanity’s Been Here Longer Than We Thought

Original Article

By John Timmer

Enlarge / Our family tree, with the dates inferred from this new data. Note how many major branches there are within Africa, and the recent exchange of DNA at the bottom.
Schlebusch et al., Science

When did humanity start? It’s proven to be a difficult question to answer. Anatomically modern humans have a distinct set of features that are easy to identify on a complete skeleton. But most old skeletons are partial, making identification a challenge. Plus, other skeletons were being left by pre-modern (or archaic) human relatives like Neanderthals who were present in Africa and Eurasia at the same time. While Neanderthals et al. have distinct features as well, we don’t always have a good idea how variable those features were in these populations.

So, when a recent paper argued that a semi-modern skull meant that humanity was older than we thought, some people dismissed it as an overhyped finding.

All around Africa

Genetics and paleontology have both agreed that Africa gave rise to modern humans. The earliest clearly modern skeletons are found there, and genetics have suggested a group of African hunter-gatherers represent the earliest ethnic group on Earth. This group, the Khoe-San, have the most genetic diversity of any human population we’ve sampled. Since diversity accumulates with time, this implies they’re the oldest. Thus, it appears that the Khoe-San were the earliest group to branch off the modern human family tree and survive to the present.

Given some measures—like the frequency of mutations and the typical time for each generation of humans to reproduce—it’s possible to use that diversity to estimate the age of the Khoe-San split at between 100,000 and 150,000 years ago. Humanity as a whole, therefore, has to be at least that old. When first estimated, it was consistent with the appearance of modern human skeletal features in the paleontological record. So nearly everyone was happy.

But more recently, there have been finds like the skeleton mentioned above. And others have questioned whether the Khoe-San had such a neat genetic split from the rest of us. The region of southwest Africa they inhabit was swept through by the immense Bantu expansion, which spread agriculture and Iron Age technology throughout sub-Saharan Africa. If some Bantu DNA ended up spreading into the Khoe-San population, then our estimates would be off.

 

(The team also sequenced DNA from four Iron Age African skeletons at the same time and showed that the Bantu didn’t just bring technology; they carried genetic variants that provided some resistance to malaria and sleeping sickness. These were absent from the Stone Age skeletons.)

You look old

The authors only got one decent-quality genome out of the three Stone Age bones from which they obtained DNA. But that skeleton clearly groups with the Khoe-San genetically, indicating that the researchers’ expectation about its affinities were correct. A comparison with modern Khoe-San genomes, however, indicated that the modern ones have gotten contributions from an additional human lineage. All indications are that this DNA originated in East Africa and came from a population that had already been interbreeding with Eurasians.

This doesn’t mean that the Khoe-San aren’t the oldest lineage of humanity, but it does mean that they haven’t been genetically isolated from the rest of us. Which would throw off the date of their split from all of humanity’s other lineages.

So, how old are they? Comparing the Stone Age genome with other modern human genomes produces values of 285,000 to 365,000 years. The most extreme split is with the Mandinka, a population that currently occupies much of West Africa; the date of that appears to be 356,000 years.

Again, the Khoe-San are modern humans. And if they split off that long ago, then modern humans have existed for at least that long. And that’s substantially older than earlier genetic estimates.

But there are caveats. These estimates are very sensitive to the frequency at which new mutations arise in human lineages, as well as the typical human generation time. Both of those values have been in dispute in recent years. If the field arrives at a different consensus value, then these estimates will change. The authors also point out it’s possible that the split looks older because the ancestors of the Khoe-San had interbred with a population of archaic humans, much as the ancestor of non-Africans interbred with Neanderthals. That possibility’s going to be hard to exclude.

In the big picture of human evolution, a date of roughly 300,000 years ago would place the origin of modern humans almost half way between the present and when Neanderthals and Denisovans split off from our lineage. It also happens to be about the same time as the technology of the Middle Stone Age. It’s appealing to think that whatever breakthrough made us “modern” led to some sort of mental leap that enabled new technology. But, as the Bantu themselves demonstrated, the connection between a skeleton’s appearance and the technology its owner used can be extremely tenuous.

 

Earth Had Life From Its Infancy

Original Article

By Ed Yong

The Torngat Mountains in northeastern Canada are full of life. Reindeer graze on lichen, polar bears prowl the coastlines, and great whales swim in the offshore waters. Scientists patrol the land, too, looking for the oldest rocks on the planet, which were formed almost 4 billion years ago, when the Earth was just an infant world.

Back then, the landscape would have been very different. The Earth was a hellish place that had only just acquired a firm crust. Its atmosphere was devoid of oxygen, and it was regularly pelted with asteroids. There were no reindeer, whales, polar bears, or lichen. But according to new research, there was life.

In a rock formation called the Saglek Block, Yuji Sano and Tsuyoshi Komiya from the University of Tokyo found crystals of the mineral graphite that contain a distinctive blend of carbon isotopes. That blend suggests that microbes were already around, living, surviving, and using carbon dioxide from the air to build their cells. If the two researchers are right—and claims about such ancient events are always controversial—then this Canadian graphite represents one of the earliest traces of life on Earth.

The Earth was formed around 4.54 billion years ago. If you condense that huge swath of prehistory into a single calendar year, then the 3.95-billion-year-old graphite that the Tokyo team analyzed was created in the third week of February. By contrast, the earliest fossils ever found are 3.7 billion years old; they were created in the second week of March.

Those fossils, from the Isua Belt in southwest Greenland, are stromatolites—layered structures created by communities of bacteria. And as I reported last year, their presence suggests that life already existed in a sophisticated form at the 3.7-billion-year mark, and so must have arisen much earlier. And indeed, scientists have found traces of biologically produced graphite throughout the region, in other Isua Belt rocks that are 3.8 billion years old, and in hydrothermal vents off the coast of Quebec that are at least a similar age, and possibly even older.

“The emerging picture from the ancient-rock record is that life was everywhere,” says Vickie Bennett from Australian National University, who was not involved in the latest study. “As far back as the rock record extends—that is, as far back as we can look for direct evidence of early life, we are finding it. Earth has been a biotic, life-sustaining planet since close to its beginning.”

This evidence hinges on a quirk of chemistry. Carbon comes in two stable isotopes—carbon-12, which is extremely common, and carbon-13, which is rarer and slightly heavier. When it comes to making life, carbon-12 is the more pliable building block. It’s more reactive than its heavier cousin, and so easier to transform into molecules like carbohydrates and proteins.

So living organisms concentrate carbon-12 in their cells—and when they die, that signature persists. When scientists find graphite that’s especially enriched in carbon-12, relative to carbon-13, they can deduce that living things were around when that graphite was first formed. And that’s exactly what the Tokyo team found in the Saglek Block—grains of graphite, enriched in carbon-12, encased within 3.95-billion-year-old rock.

But are those graphite grains the same age? The rocks around them are metamorphic—they’ve been warped and transformed at extreme temperatures and pressures. During that process, and all the subsequent geological tumult that this region has experienced, it’s possible that much younger graphite somehow infiltrated the older rock, creating a false signal of early life.

To rule out that possibility, the Tokyo team looked at the structure of the graphite grains. The more orderly and crystalline those structures, the hotter the grains were when they formed. Based on that relationship, the team calculated the graphite was created at temperatures between 536 and 622 Celsius—a range that’s consistent with the temperatures at which the surrounding metamorphic rocks were transformed. This suggests that the graphite was already there when the rocks were heated and warped, and didn’t sneak in later. It was truly OG—original graphite.

There’s still room for doubt, though. Given how ancient these rocks are, and how much geological tumult they have experienced, it’s hard to fully exclude the possibility that the graphite got there later. Also, other processes that have nothing to do with living things could potentially change the ratio of carbon-12 and carbon-13. It’s concerning that the ratio varies a lot in the samples that the Tokyo team analyzed, says Andrew Knoll from Harvard University. But he also says that the team has been careful, and their combined evidence “makes a strong case that life existed on earth nearly 4 billion years ago.”

“The authors have done as many checks as they could for whether they are indeed analyzing 3.95-billion-year-old graphite rather than later contamination,” adds Elizabeth Bell, a geochemist from the University of California, Los Angeles. “They make a plausible case that the graphite is original.”

Bell herself found the oldest graphite that’s been measured to date. It lurked within a 4.1-billion-year-old zircon gemstone from Western Australia, and also contained a blend of isotopes that hinted at a biological origin. That discovery is also controversial, especially since the graphite was completely cut off from its source environment, making it hard to know the conditions in which it was formed.

Still, all of this evidence suggests Earth was home to life during its hellish infancy, and that such life abounded in a variety of habitats. Those pioneering organisms—bacteria, probably—haven’t left any fossils behind. But Sano and Komiya hope to find some clues about them by analyzing the Saglek Block rocks. The levels of nitrogen, iron, and sulfur in the rocks could reveal which energy sources those organisms exploited, and which environments they inhabited. They could tell us how life first lived.