Ancient DNA sheds light on what happened to the Taino, the native Caribbeans

Posted in Anthropology, Articles, Caribbean/Latin America, Health/Medicine/Genetics, Media Archive on 2018-02-20 04:22Z by Steven

Ancient DNA sheds light on what happened to the Taino, the native Caribbeans

Ars Technica
2018-02-19

Kiona N. Smith


Reconstruction of a Taino village in Cuba. Michal Zalewski

A new DNA study explores where the Taino came from and where they went.

The Caribbean was one of the last parts of the Americas to be settled by humans, although scientists don’t agree on when the first settlers arrived or where they came from. Some argue that people probably arrived from the Amazon Basin, where today’s Arawakan languages developed, while others suggest that the first people to settle the islands came from even farther west, in the Colombian Andes.

“The differences in opinion illustrate the difficulty of tracing population movements based on a patchy archaeological record,” wrote archaeologist Hannes Schroeder of the University of Copenhagen, Denmark, and his colleagues. Schroeder’s research team has a new study on the genetics of the long-lost Taino people, which gives some clear indications of their origin and where they went after European colonization…

Not vanished after all

The recent work also shows that the vanished people of the Caribbean didn’t actually disappear without a trace. Modern inhabitants of the Caribbean islands mostly have a mixture of African and European ancestry, but some have a little indigenous DNA as well. That’s not entirely surprising; Spanish colonists reportedly married Taino wives, and other records say that Taino and escaped African slaves also intermarried and formed communities. Some people have made an effort to revive Taino culture and identity in the last century and a half or so, but it has never been clear how genetically related modern Caribbean residents are to the presumably vanished tribes…

Read the entire article here.

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New gene variants reveal the evolution of human skin color

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2018-02-20 00:53Z by Steven

New gene variants reveal the evolution of human skin color

Science
2017-11-12

Ann Gibbons, Contributing Correspondent


Researchers have identified genes that help create diverse skin tones, such as those seen in the Agaw (left) and Surma (right) peoples of Africa.
ALESSIA RANCIARO & DR. SIMON R. THOMPSON

Most people associate Africans with dark skin. But different groups of people in Africa have almost every skin color on the planet, from deepest black in the Dinka of South Sudan to beige in the San of South Africa. Now, researchers have discovered a handful of new gene variants responsible for this palette of tones.

The study, published online this week in Science, traces the evolution of these genes and how they traveled around the world. While the dark skin of some Pacific Islanders can be traced to Africa, gene variants from Eurasia also seem to have made their way back to Africa. And surprisingly, some of the mutations responsible for lighter skin in Europeans turn out to have an ancient African origin.

“This is really a landmark study of skin color diversity,” says geneticist Greg Barsh of the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama.

Researchers agree that our early australopithecine ancestors in Africa probably had light skin beneath hairy pelts. “If you shave a chimpanzee, its skin is light,” says evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania, the lead author of the new study. “If you have body hair, you don’t need dark skin to protect you from ultraviolet [UV] radiation.”

Until recently, researchers assumed that after human ancestors shed most body hair, sometime before 2 million years ago, they quickly evolved dark skin for protection from skin cancer and other harmful effects of UV radiation. Then, when humans migrated out of Africa and headed to the far north, they evolved lighter skin as an adaptation to limited sunlight. (Pale skin synthesizes more vitamin D when light is scarce.)…

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They considered themselves white, but DNA tests told a more complex story

Posted in Articles, Health/Medicine/Genetics, Media Archive, Passing, United States on 2018-02-14 23:26Z by Steven

They considered themselves white, but DNA tests told a more complex story

The Washington Post
2018-02-06

Tara Bahrampour

As more Americans take advantage of genetic testing to pinpoint the makeup of their DNA, the technology is coming head to head with the country’s deep-rooted obsession with race and racial myths. This is perhaps no more true than for the growing number of self-identified European Americans who learn they are actually part African.

For those who are surprised by their genetic heritage, the new information can often set into motion a complicated recalibration of how they view their identity.

Nicole Persley, who grew up in Nokesville, Va., was stunned to learn that she is part African. Her youth could not have been whiter. In the 1970s and ’80s in her rural home town, she went to school with farmers’ kids who listened to country music and sometimes made racist jokes. She was, as she recalls, “basically raised a Southern white girl.”

But as a student at the University of Michigan: “My roommate was black. My friends were black. I was dating a black man.” And they saw something different in her facial features and hair.

“I was constantly being asked, ‘What are you? What’s your ethnic background?’ ”…

…The test results can present an intriguing puzzle. When a significant amount of African DNA shows up in a presumably white person, “there’s usually a story — either a parent moved away or a grandparent died young,” said Angela Trammel, an investigative genealogist in the Washington area. “Usually a story of mystery, disappearance — something.”

For Persley, 46, the link turned out to be her grandfather, who had moved away from his native Georgia and started a new life passing as white in Michigan. He married a white woman, who bore Persley’s father…

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What Doctors Should Ignore

Posted in Articles, Health/Medicine/Genetics, Media Archive, United States on 2018-02-14 04:27Z by Steven

What Doctors Should Ignore

The New York Times
2017-12-08

Moises Velasquez-Manoff


Joan Wong

Science has revealed how arbitrary racial categories are. Perhaps medicine will abandon them, too.

Sickle cell anemia was first described in 1910 and was quickly labeled a “black” disease. At a time when many people were preoccupied with an imagined racial hierarchy, with whites on top, the disease was cited as evidence that people of African descent were inferior. But what of white people who presented with sickle cell anemia?

Doctors twisted themselves into knots trying to explain those cases away. White sickle cell patients must have mixed backgrounds, they contended — a black forebear they didn’t know about perhaps, or one they didn’t want to mention. Or maybe white patients’ symptoms didn’t stem from sickle cell anemia at all, but some other affliction. The bottom line was, the disease was “black,” so by definition white people couldn’t get it.

Today, scientists understand the sickle cell trait as an adaptation to malaria, not evidence of inferiority. One copy of the sickle cell trait protects against malaria. Having two can cause severe anemia and even death. Scientists also know that the trait is common outside Africa across the “malaria belt” — the Arabian Peninsula, India and parts of the Mediterranean Basin. And people historically considered white can, in fact, carry it. In the Greek town of Orchomenos, for example, the gene is more prevalent than it is among African-Americans.

We know all this, and yet the racialization of the disease, the idea that it occurs only in people of sub-Saharan African descent, persists. “When I talk to medical students, I get this all the time — ‘Sickle cell is a black trait,’ ” Michael Yudell, chairman of the department of community health and prevention at the Dornsife School of Public Health at Drexel University, told me.

That’s worrisome for many reasons, he says, chief among them that it may result in subpar medical care for some patients. Case in point: California’s universal blood disorder screening program has identified thousands of nonblack children with the sickle cell trait and scores with the disease — patients who, had doctors stuck to received “wisdom,” might have been missed.

Professor Yudell belongs to a growing chorus of scholars and researchers who argue that in science at least, we need to push past the race concept and, where possible, scrap it entirely. Professor Yudell and others contend that instead of talking about race, we should talk about ancestry (which, unlike “race,” refers to one’s genetic heritage, not innate qualities); or the specific gene variants that, like the sickle cell trait, affect disease risk; or environmental factors like poverty or diet that affect some groups more than others…

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Tests of fit of historically-informed models of African American Admixture

Posted in Anthropology, Articles, Health/Medicine/Genetics, Media Archive, United States on 2018-02-13 01:49Z by Steven

Tests of fit of historically-informed models of African American Admixture

American Journal of Physical Anthropology
Volume 165, Issue 2, February 2018
Pages 211–222
DOI: 10.1002/ajpa.23343

Jessica M. Gross
Department of Anthropology
University of New Mexico

African American populations in the U.S. formed primarily by mating between Africans and Europeans over the last 500 years. To date, studies of admixture have focused on either a one-time admixture event or continuous input into the African American population from Europeans only. Our goal is to gain a better understanding of the admixture process by examining models that take into account (a) assortative mating by ancestry in the African American population, (b) continuous input from both Europeans and Africans, and (c) historically informed variation in the rate of African migration over time.

Materials and methods

We used a model-based clustering method to generate distributions of African ancestry in three samples comprised of 147 African Americans from two published sources. We used a log-likelihood method to examine the fit of four models to these distributions and used a log-likelihood ratio test to compare the relative fit of each model.

Results

The mean ancestry estimates for our datasets of 77% African/23% European to 83% African/17% European ancestry are consistent with previous studies. We find admixture models that incorporate continuous gene flow from Europeans fit significantly better than one-time event models, and that a model involving continuous gene flow from Africans and Europeans fits better than one with continuous gene flow from Europeans only for two samples. Importantly, models that involve continuous input from Africans necessitate a higher level of gene flow from Europeans than previously reported.

Discussion

We demonstrate that models that take into account information about the rate of African migration over the past 500 years fit observed patterns of African ancestry better than alternative models. Our approach will enrich our understanding of the admixture process in extant and past populations.

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Southerner For Miscegenation

Posted in Articles, Autobiography, Health/Medicine/Genetics, Media Archive, United States on 2017-12-27 01:53Z by Steven

Southerner For Miscegenation

The Denver Star (Source: Chronicling America: Historic American Newspapers)
Denver, Colorado
Saturday, 1913-07-05
page 1, columns 1-2

(New York Age.)

Prof. H. E. Jordan, a Southern white man, of the University of Virginia, advances an opinion which means that miscegenation will be the ultimate solution of the Negro problem. He makes the assertion in an article in The Popular Science Monthly for June in which occurs the remarkable statement that the mulatto is the leaven with which to lift the Negro race.

Prof. Jordan does not hold to the commonly accepted accepted opinion that half-breeds are inferior to the race of either parent. On the contrary he thinks that the half-breed is usually a better and more useful citizen than the man of pure race.

He believes that the solution of the Negro problem is facilitated instead of complicated by the presence of the mulatto, and claims that the breed has been proved most effective in some other lands notably in the English island colony of Jamaica. In Jamaica there are about 50,000 mulattoes in a population of 700,000, and it is noted he says, that the mulattoes contribute the artisans, the teachers, the business and professional men. “They are the very backbone of wonderful Jamaica.”

There Will Be More Mulattoes.

There are now two million mulattoes in-the United States and there will be more, says Prof. Jordan, if statements are worth anything, He claims that the prevalence of defective half-breeds is due to mating of inferior types of the black and white races but that a Negro-white cross does not inherently mean degeneracy.

Discussing this phase of the question, he says:

“I admit the general inferiority of the black-white offspring. Defective half-breeds are too prevalent and obtruding to permit denying the apparently predetermined result of such crosses. But I emphatically deny that the result is inherent in the simple fact of cross breeding. There are not a few very striking exceptions among my own acquaintances. Absolutely the best mulatto family I have ever known traces its ancestry back on both the maternal and paternal side to high grade white grandfathers and pure type Negro grandmothers. The reason for the frequently inferior product of such crosses is that the better elements of both races under ordinal conditions of easy mating with their own type feel an instinctive repugnance to intermarriage. Under these usual circumstances a white man who stoops  to mating with a colored woman or a colored woman who will accept a white man, are already of quite inferior type. One would not expect inferior offspring from such parents if it concerned horses or dogs.

Why should we expect the biologically impossible in the case of man? If the parents are of good type, so will be the offspring. And even with the handicap of frequently degraded white ancestry, the mulatto of our country forms the most intelligent and potentially useful element of our colored population.

Negro-White Cross Does Note Mean Degeneracy.

The fact, then, is established beyond all possibility of disproof, it seems to me that a Negro-white cross does not inherently mean degeneracy; and that the mulatto, measured by present day standards of Caucasian civilization, from economic and civic standpoints, is an advantage upon a pure Negro. In further support of the potency of even a relative remote white ancestor may be cited the almost unique instance of the Moses of the colored race, Booker T. Washington. As one mingles day by day with colored people of all grades and shades one is impressed with the significance of even small admixtures of Caucasian blood. What elements of hope or menace lie hidden in these mulatto millions? How can they help to solve or confuse the ‘problem’?”

Prof. Jordan asserts that the Negro cannot undergo mental development beyond a certain maximum, and that it is possible to approximate a “pure” mulatto race combining the best elements of black and white. We can approach it, he holds, by education and the fostering of Negro racial pride. He says further:

“The point seems clear that in the presence of 2,000,000 mulattoes, steadily increasing in number, we have a key to the solution of our problem, The mulatto is the leaven with which to lift the Negro race. He serves as our best lever for Negro elevation.”

The mulatto does not feel the instinctive mental nausea to Negro mating. He might even be made to feel a sacred mission in this respect. Possibility of marriage with mulatto would be a very real incentive to serious efforts for development on the part of the Negro. The logical conclusion may follow in the course of the ages. At any rate, from present indications our hope lies in the mulatto.

A wise statesmanship and rational patriotism will make every effort to conserve him, and imbue him with his mission in the interests of brotherhood of a better man. The problem seems possible of solution only as the mulatto will undertake it, with the earnest help of the white.

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Why Is Skin Color Different? Huge Genetic Study Reveals Prevailing Theory of Pigmentation is Wrong

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2017-12-04 04:20Z by Steven

Why Is Skin Color Different? Huge Genetic Study Reveals Prevailing Theory of Pigmentation is Wrong

Newsweek
2017-11-30

Kastalia Medrano, Staff Writer


These are South African individuals in a household that exemplify the substantial skin pigmentation variability in the Khomani and Nama populations.
Brenna Henn

Scientists used to think that the same small handful of genes accounted for about half of all pigment variation in human skin. A new study shows the genetic picture behind skin color is far more complex.

Research supporting the prior, simpler conclusion was skewed by Eurocentrism. Because it focused almost exclusively on Northern Eurasian populations from higher latitudes, the data missed a huge swath of the globe. Now, scientists have factored in people of color living in lower latitudes—and found that the prevailing theory is wrong.

Scientists from the Broad Institute of MIT and Harvard, Stanford University, and Stony Brook University worked with groups of indigenous southern African peoples called the KhoeSan, notable to some for their use of “click” language. They interviewed them, measured their respective heights and weights, and used a tool called a reflectometer to measure their skin pigmentation.

After seven years of research, and data gathered from about 400 individuals, the researchers realized that the closer a population lives to the equator, the greater the number of genes play a part in determining skin pigmentation. A paper describing the research was published November 30 in the scientific journal Cell.

“Previous work has shown the biomedical consequences of ethnically biased studies. Over the past 10 years, approximately 80 percent of genetic association studies were performed in European-descent groups,” Alicia Martin, a postdoctoral scientist in the lab of Broad Institute member Mark Daly, told Newsweek by email. “What we find here is that the biology of pigmentation or ‘architecture’ can be very different in Africans.” Martin says the findings emphasize the need to fund more genetic work in diverse populations…

Read the entire article here.

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Loci associated with skin pigmentation identified in African populations

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2017-12-04 01:50Z by Steven

Loci associated with skin pigmentation identified in African populations

Science
2017-10-12
eaan8433
DOI: 10.1126/science.aan8433

Nicholas G. Crawford, Derek E. Kelly, Matthew E. B. Hansen, Marcia H. Beltrame, Shaohua Fan, Shanna L. Bowman, Ethan Jewett, Alessia Ranciaro, Simon Thompson, Yancy Lo, Susanne P. Pfeifer, Jeffrey D. Jensen, Michael C. Campbell, William Beggs, Farhad Hormozdiari, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Thomas Nyambo, Dawit Wolde Meskel, Gurja Belay, Jake Haut, NISC Comparative Sequencing Program, Harriet Rothschild, Leonard Zon, Yi Zhou, Michael A. Kovacs, Mai Xu, Tongwu Zhang, Kevin Bishop, Jason Sinclair, Cecilia Rivas, Eugene Elliot, Jiyeon Choi, Shengchao A. Li, Belynda Hicks, Shawn Burgess, Christian Abnet, Dawn E. Watkins-Chow, Elena Oceana, Yun S. Song, Eleazar Eskin, Kevin M. Brown, Michael S. Marks, Stacie K. Loftus, William J. Pavan, Meredith Yeager, Stephen Chanock, Sarah Tishkoff

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

Variation in epidermal pigmentation is a striking feature of modern humans. Human pigmentation is correlated with geographic and environmental variation (Fig. 1). Populations at lower latitudes have darker pigmentation than populations at higher latitudes, suggesting that skin pigmentation is an adaptation to differing levels of ultraviolet radiation (UVR) (1). Because equatorial regions receive more UVR than temperate regions, populations from these regions (including sub-Saharan Africans, South Asians, and Australo-Melanesians) have darker pigmentation (Fig. 1), which likely mitigates the negative impact of high UVR exposure such as skin cancer and folate degradation (1). In contrast, the synthesis of vitamin D3 in response to UVR, needed to prevent rickets, may drive selection for light pigmentation at high latitudes (1).

The basal layer of human skin contains melanocytes, specialized pigment cells that harbor subcellular organelles called melanosomes in which melanin pigments are synthesized and stored and then transferred to keratinocytes (2). Melanosome morphology and content differs between melanocytes that synthesize mainly eumelanins (black-brown pigments) or pheomelanins (pigments which range from yellow to reddish-brown) (3). Variation in skin pigmentation is due to the type and quantity of melanins generated, melanosome size, and the manner in which keratinocytes sequester and degrade melanins (4).

While over 350 pigmentation genes have been identified in animal models, only a subset of these genes have been linked to normal variation in humans (5). Of these, there is limited knowledge about loci that affect pigmentation in populations with African ancestry (6, 7).

Skin pigmentation is highly variable within Africa

To identify genes affecting skin pigmentation in Africa, we used a DSM II ColorMeter to quantify light reflectance from the inner arm as a proxy for melanin levels in 2,092 ethnically and genetically diverse Africans living in Ethiopia, Tanzania, and Botswana (table S1 and figs. S1 and S2) (8). Skin pigmentation levels vary extensively among Africans, with darkest pigmentation observed in Nilo-Saharan speaking pastoralist populations in Eastern Africa and lightest pigmentation observed in San hunter-gatherer populations from southern Africa (Fig. 2 and table S1)…

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Skin pigmentation is far more genetically complex than previously thought

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2017-12-03 22:33Z by Steven

Skin pigmentation is far more genetically complex than previously thought

Broad Institute
Massachusetts Institute of Technology, Cambridge, Massachusetts
2017-11-30

David Cameron, Director of Communications/Media Relations


Credit : Brenna Henn
South African individuals in a household that exemplify the substantial skin pigmentation variability in the Khomani and Nama populations. Picture taken with consent for publication.

By studying an African population underrepresented in most datasets, researchers find genetic complexity of pigmentation varies by latitude

Many studies have suggested that the genetics of skin pigmentation are simple. A small number of known genes, it is thought, account for nearly 50 percent of pigment variation. However, these studies rely on datasets that heavily favor northern Eurasian populations—those that reside mostly in higher latitude regions.

Reporting in the November 30 issue of Cell, researchers from the Broad Institute of MIT and Harvard, Stanford University, and Stony Brook University report that while skin pigmentation is nearly 100 percent heritable, it is hardly a straightforward, Mendelian trait. By working closely with the KhoeSan, a group of populations indigenous to southern Africa, the researchers have found that the genetics of skin pigmentation become progressively complex as populations reside closer to the equator, with an increasing number of genes—known and unknown—involved, each making a smaller overall contribution.

“Africa has the greatest amount of phenotypic variability in skin color, and yet it’s been underrepresented in large scale endeavors,” said Alicia Martin, a postdoctoral scientist in the lab of Broad Institute member Mark Daly. “There are some genes that are known to contribute to skin pigmentation, but by and large there are many more new genes that have not been discovered.”

“We need to spend more time focusing on these understudied populations in order to gain deeper genetic insights,” said Brenna Henn, assistant professor in the Department of Ecology and Evolution at Stony Brook University who, along with Martin, is a co-corresponding author…

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An Unexpectedly Complex Architecture for Skin Pigmentation in Africans

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2017-12-03 03:40Z by Steven

An Unexpectedly Complex Architecture for Skin Pigmentation in Africans

Cell
Volume 171, Issue 6, 2017-11-30
pages 1340–1353.e14
DOI: 10.1016/j.cell.2017.11.015

Alicia R. Martin, Meng Lin, Julie M. Granka, Justin W. Myrick, Xiaomin Liu, Alexandra Sockell, Elizabeth G. Atkinson, Cedric J. Werely, Marlo Möller, Manjinder S. Sandhu, David M. Kingsley, Eileen G. Hoal, Xiao Liu, Mark J. Daly, Marcus W. Feldman, Christopher R. Gignoux, Carlos D. Bustamante, Brenna M. Henn

Highlights

  • Skin pigmentation in Africans is far more polygenic than light skin in Eurasians
  • Southern African KhoeSan populations have lighter skin compared to equatorial Africans
  • Highly heritable KhoeSan skin color variation is poorly explained by known genes
  • The study of African skin color identifies novel and canonical pigmentation genes

Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

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