Creationism in Crisis - How Human Skin Colour Evolved in Africa Long Before 'Creation Week'

PIK Professor Sarah Tishkoff led a collaborative team of researchers who have discovered key insights into the molecular basis of skin color differences among Africans

Image: Courtesy of Sarah Tishkoff
and Alessia Ranciaro

1996 map of the major ethnolinguistic groups of Africa, by the Library of Congress Geography and Map Division (substantially based on G.P. Murdock, Africa, its peoples and their cultural history, 1959).

Source: Wikipedia

A molecular look at the mechanisms behind pigmentation variation | Penn Today

While creationism's god was creating a small flat Earth with a dome over it to keep the water above the sky out, the people of Africa were evolving and diversifying according to local conditions and gene flow between populations that has resulted in a whole range of skin tones and a genetic variance that is greater in a small population of Africans than in the whole of the extra-African population of the world, reflecting the genetic bottleneck of a small band of migrants moving out of Africa into Eurasia.

Africans had of course had several hundred thousand years to diversify prior to the mythical 'Creation Week' when creationists believe a magic man made of nothing came from nowhere and magicked a universe out of nothing with some magic words, spoken in a language that no-one understood because there was no-one to understand it.

What are the main population groups in Sub-Saharan Africa? Sub-Saharan Africa is a diverse region with a multitude of ethnic, linguistic, and cultural groups. It is challenging to provide an exhaustive list due to the vast diversity, but here are some major population groups in Sub-Saharan Africa:

1. Bantu Peoples: Bantu ethnic groups are spread across a large part of Sub-Saharan Africa, including countries like Nigeria, South Africa, Kenya, Tanzania, and the Democratic Republic of Congo.
2. Hausa-Fulani: Found predominantly in West Africa, the Hausa-Fulani ethnic group is prominent in countries like Nigeria, Niger, and Cameroon.
3. Yoruba: The Yoruba people are concentrated in Nigeria, Benin, and Togo, and they have a rich cultural heritage.
4. Igbo: Another significant ethnic group in Nigeria, the Igbo people are primarily found in the southeastern part of the country.
5. Zulu: The Zulu people are the largest ethnic group in South Africa and are known for their history, traditions, and language.
6. Maasai: The Maasai are a pastoralist ethnic group located in Kenya and Tanzania, known for their distinctive customs, clothing, and lifestyle.
7. Amhara and Oromo: In Ethiopia, the Amhara and Oromo are two major ethnic groups, each with its own language and cultural identity.
8. Hutu and Tutsi: In countries like Rwanda and Burundi, the Hutu and Tutsi ethnic groups have historically played significant roles, and their interactions have been complex.
9. Igala and Yoruba: In Nigeria, the Igala people are found in the central part of the country, while the Yoruba are concentrated in the southwest.
10. San (Bushmen) and Khoikhoi (Hottentots): Indigenous peoples like the San and Khoikhoi are found in Southern Africa, particularly in countries like Botswana, Namibia, and South Africa.

It's important to note that these are just a few examples, and there are many more ethnic groups in Sub-Saharan Africa, each contributing to the rich cultural tapestry of the region. Additionally, the composition and distribution of these groups can vary within and between countries.

Tell me more about the San.

The San people, also commonly referred to as Bushmen, are indigenous hunter-gatherer peoples of Southern Africa. They are believed to be one of the oldest human populations with a history dating back tens of thousands of years. The San are known for their unique languages, distinctive click consonants, and a traditional way of life that revolves around hunting and gathering. Here are some key aspects of the San people:

1. Geographic Distribution: The San traditionally inhabit the Kalahari Desert, which spans across parts of Botswana, Namibia, Angola, Zambia, Zimbabwe, and South Africa. Their nomadic lifestyle has historically involved moving across this arid region in search of food and water sources.
2. Hunter-Gatherer Lifestyle: The San are renowned for their skills in hunting and gathering. They rely on a deep knowledge of their environment, using traditional tools and techniques for hunting game, gathering edible plants, and finding water sources. Their diet typically includes a variety of plants, fruits, nuts, and the meat of wild animals.
3. Languages and Click Consonants: The San people speak various languages that are characterized by the use of click consonants. These clicks are unique to the Khoisan language family, and different San groups may have distinct click patterns in their languages. The most well-known of these languages is probably !Xóõ.
4. Rock Art: The San have a rich tradition of rock art, creating intricate paintings on rocks and in caves. These paintings often depict scenes of daily life, animals, and spiritual or ritualistic themes. The rock art serves as a historical and cultural record of the San people and their beliefs.
5. Social Structure: San society traditionally has been organized in small, mobile groups known as bands. These bands are often composed of extended family members and cooperate in hunting and gathering activities. Social cohesion is important, and decision-making tends to be based on consensus.
6. Challenges and Cultural Preservation: The San have faced numerous challenges over the years, including displacement, marginalization, and encroachment on their traditional lands. Efforts have been made to preserve their cultural heritage and traditional knowledge, but many San communities continue to grapple with issues related to land rights, education, and cultural preservation.

Efforts are ongoing to raise awareness about the unique cultural heritage of the San people and to address the challenges they face in the modern world while respecting their traditional way of life.

Now an international team lead by David and Lyn Silfen Professor Sarah Tishkoff, of the Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA, has discovered key insights into the molecular basis of skin color variations among African populations. Their findings are published in Nature Genetics and described in a University of Pennsylvania press release.

“Despite the abundant genetic diversity within African populations, they have been historically underrepresented in genetic studies,” says senior author Sarah Tishkoff, a Penn Integrates Knowledge University Professor with appointments in the Perelman School of Medicine and School of Arts & Sciences. “Our findings offer novel information about the genetic basis and evolutionary history of skin color diversity, contributing to a clearer depiction of human evolution.”

The story of human evolution is as rich and diverse as the adaptations found across the world’s populations, Tishkoff says. She notes that, among many adaptive traits, skin color stands out as one of the most well-known. Darker skin tones, prevalent in equatorial regions, serve as nature’s very own sunblock, evolving over millennia to shield these populations from the sun’s intense ultraviolet radiation. Conversely, lighter pigmentation, as seen in populations closer to the poles, is an adaptation to mitigate the risks of insufficient sun exposure by maximizing vitamin D production, which is triggered by UV exposure.

“Our approach involved genome-wide association studies of skin color from more than 1,500 eastern and southern African individuals as well as scanning the genome to identify genetic variants that are highly differentiated between the lightly-pigmented Khoesan-speaking San population and other darkly pigmented Africans and may play a role in local adaptation in that population,” says Yuanqing Feng, first author of the paper and a postdoctoral researcher in the Tishkoff Lab.

The researchers note that pigmentation is a complex trait influenced by hundreds of variants scattered across the genome, with the majority situated in noncoding regions. These noncoding variants may affect the expression of genes located up to one million bases away. The vast number of mutations associated with skin color and the uncertainty surrounding the target genes regulated by these mutations make it particularly arduous for researchers to find the precise genetic mechanisms governing this trait.

Feng and collaborators used massively parallel reporter assays to discern the regulatory activities of thousands of variants. This high-throughput technique narrowed down the thousands of candidates to 165 functional variants. To identify the target genes of these functional variants, Feng further constructed high-resolution chromatin interaction maps in melanocytic cells using chromatin conformation capture assays. “This is a high-resolution 3D genome map in melanoma cells that will be valuable for gene regulation studies in pigmentation and melanoma biology,” Feng says.

Using CRISPR/Cas9-based genome editing, the researchers discovered that mutations in an enhancer of OCA2, a gene associated with albinism, could lead to a 75% reduction in melanin levels when compared to control cells. Within the same OCA2 enhancer, the researchers identified two closely located regulatory variants, estimated to be 1.2 million years old and 57 thousand years old, with the latter coinciding with the period of human migration from Africa.

“This case illustrates the continuous evolution of human skin color, and it’s remarkable to observe the significant effects on skin pigmentation attributed to a single enhancer,” Feng says.

San people have relatively lighter pigmentation compared to other African populations and possess the oldest genetic lineages in humans. While it is hypothesized that the light skin color of the San may result from adaptation to a southern African environment, the genetic underpinnings of this adaptation remain elusive. The researchers pinpointed several crucial regulatory variants near MITF, LEF1, and TRPS1 that contribute to the skin color adaptation observed in the San. “MITF, LEF1, and TRPS1 are involved in signaling pathways regulating both melanocyte differentiation and hair development,” Tishkoff says. “This suggests that the variants influencing the lighter skin pigmentation observed in the San people may also contribute to their distinctive hair morphology.” Notably, the variant near TRPS1 associated with lighter skin color is at nearly 100% frequency in the San and in most non-Africans, whereas the variant associated with darker skin color is common in most other African populations and in the darkly pigmented Melanesian population, a striking example of global adaptations to UV exposure.” Additionally, the researchers found a novel gene impacting human skin pigmentation, CYB561A3, which regulates iron homeostasis and influences melanin levels in melanocytic cells. “To our knowledge, the role of CYB561A3 in skin pigmentation has not been reported before. Intriguingly, there have been reports linking intravenous iron infusion to skin hyperpigmentation. Given that CYB561A3 encodes an iron reductase, I am curious about the role of this protein in this process,” Tishkoff says. “Our findings underscore the complexity of genetic factors influencing skin color and the benefits of including ethnically diverse and underrepresented populations in genetic studies,” she says. “Conducting functional studies on the impact of noncoding variants will enhance our comprehension of the genetics underlying complex human traits and disease risk.” “The populations included in this study are from remote regions of Africa and required the use of a mobile lab set up in the field sites,” Tishkoff says. “The collaboration with our partners in Africa was key to the success of this research project.” In future research, the Tishkoff lab would like to use its innovative functional genomics approach to identify more genetic variants contributing to human pigmentation and other adaptive traits in a larger sample of ethnically diverse Africans.

It's worth pointing out a couple of things here: one of the variants withing the OCA2 enhancer region evolved 1.2 million years ago, i.e., before Homo sapiens had evolved as a distinct species. Creationists sometime seem to find it hard to understand how most genes and their variants evolved in evolutionary ancestors and are inherited from them; they don't all arise afresh in each species.

The other thing to note is that one variant associated with lighter skin colour is present at nearly 100% in the San people and in most non-Africans. This suggests that the Homo sapiens who migrated out of Africa into Eurasia and then the rest of the world were closer to the San people than to the other African peoples. It also suggests that the darker skin of other African groups is a later adaptation to local conditions, as an adaptation to UV light intensity, probably closer to the Equator.

In other words, the original skin colour of early Homo sapiens was closer to the pale brown of the San people and both the pale skin of non-African people and the black skin of other African people are both evolutionary adaptations to local conditions, balancing the need for vitamin D and protection from damaging UV light.

What is the relationship between human skin colour and UV light intensity? The relationship between human skin color and UV (ultraviolet) light intensity is influenced by evolutionary factors and adaptation to the environment. The primary role of melanin, the pigment responsible for skin, hair, and eye color, is to provide protection against the harmful effects of ultraviolet radiation from the sun. Here are the key points to understand the relationship:

1. Evolutionary Adaptation: Human populations have evolved over time in response to their environments. In regions with high UV intensity, there is a selective pressure for individuals to develop darker skin to provide better protection against the increased levels of UV radiation. In contrast, in regions with lower UV intensity, lighter skin may be advantageous as it allows for better synthesis of vitamin D, a crucial nutrient that is produced in the skin in response to UVB radiation.
2. Melanin and UV Protection: Melanin comes in different forms (eumelanin and pheomelanin) and varying concentrations, resulting in a range of skin colors. Darker skin contains more eumelanin, which absorbs and disperses UV radiation, protecting the underlying layers of the skin from damage. In areas with high UV intensity, such as near the equator, populations tend to have darker skin to provide effective UV protection.
3. Latitude Gradient: There is a general pattern known as the "latitude gradient" in which skin color tends to vary with latitude. People living closer to the equator, where UV intensity is higher, often have darker skin, while populations at higher latitudes, where UV intensity is lower, may have lighter skin.
4. Vitamin D Synthesis: UV radiation is essential for the synthesis of vitamin D in the skin. In regions with lower UV intensity, where there is less sunlight, individuals with lighter skin can produce vitamin D more efficiently. This adaptation is thought to be advantageous in environments where dietary sources of vitamin D are limited.
5. Migration and Skin Color Diversity: Human migration patterns have further contributed to the diversity of skin colors. As populations migrated and settled in different regions with varying UV intensities, natural selection favored traits that provided the best balance between UV protection and vitamin D synthesis.

It's important to note that while these general patterns exist, there is considerable variation within populations, and skin color is influenced by a complex interplay of genetic, environmental, and cultural factors. Additionally, human mobility and intermingling of populations have led to a blending of genetic traits, contributing to the diversity of skin colors observed today.

From the team's paper in Nature Genetics, which is regrettably behind an expensive paywall:

Abstract

Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.

Feng, Y., Xie, N., Inoue, F. et al.
Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet (2024). https://doi.org/10.1038/s41588-023-01626-1

© 2024 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

As though this evidence of human evolution in Africa a million or more years before 'Creation Week' wasn't bad enough for creationists, there is the additional disappointment for those trying to convince themselves that they are winning the argument and scientists are converting to belief in magic creation and a supernatural creator, in place of the Theory of Evolution by Natural Selection, these scientists are firmly of the opinion that evolution by natural selection, exactly as the TOE describes, is responsible for variations in human skin color. No magic was required to explain the observations.

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