Mixed Race Studies

Before Arguing About DNA Tests, Learn the Science Behind Them

The New York Times
2018-10-18

Carl Zimmer

Senator Elizabeth Warren’s DNA test results indicated that she had a Native American ancestor several generations ago. Bridget Bennett for The New York Times

Our genetic code cannot be treated as a matter of simple fractions.

People have always told stories about their ancestral origins. But now millions of people are looking at their DNA to see if those stories hold up. While genetic tests can indeed reveal some secrets about our family past, we can also jump to the wrong conclusions from their results.

The reception of Senator Elizabeth Warren’s DNA results is a textbook case in this confusion…

…Slavery, too, led to an obsession with increasingly tiny fractions of ancestral blood, reaching the absurd extreme of the “one drop” rule. A single black ancestor — no matter how far back in the family tree, no matter how tiny the mythical drop of blood he or she contributed — was enough to make a person black…

…But DNA is not a liquid that can be divided down into microscopic drops. It’s a string-like molecule, arranged into 23 pairs of chromosomes, that gets passed down through the generations in a counterintuitive way.

Eggs and sperm randomly end up with one copy of each chromosome, coming either from a person’s mother or father. In the process, some DNA can shuffle from one chromosome to its partner. That means we inherit about a quarter of our DNA from each grandparent — but only on average. Any one person may inherit more DNA from one grandparent and less from another.

Over generations, this randomness can lead to something remarkable. Look back far enough in your family tree, and you’ll encounter ancestors from whom you inherit no DNA at all…

Read the entire article here.

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.

Read or purchase the article here.

The Great Migration and African-American Genomic Diversity

PLOS Genetics
2016-05-27
27 pages
DOI: 10.1371/journal.pgen.1006059

Soheil Baharian
Department of Human Genetics
McGill University, Montreal, Quebec, Canada
Genome Quebec Innovation Centre, Montreal, Quebec, Canada

Maxime Barakatt
McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada

Christopher R. Gignoux
Department of Genetics
Stanford University School of Medicine, Stanford, California

Suyash Shringarpure
Department of Genetics
Stanford University School of Medicine, Stanford, California

Jacob Errington
Department of Human Genetics
McGill University, Montreal, Quebec, Canada
Genome Quebec Innovation Centre, Montreal, Quebec, Canada

William J. Blot
Division of Epidemiology
Vanderbilt University School of Medicine, Nashville, Tennessee
International Epidemiology Institute, Rockville, Maryland

Carlos D. Bustamante
Department of Genetics
Stanford University School of Medicine, Stanford, California

Eimear E. Kenny
Department of Genetics and Genomic Sciences
The Icahn School of Medicine at Mount Sinai, New York, New York

Scott M. Williams
Department of Genetics
Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, New Hampshire

Melinda C. Aldrich
Division of Epidemiology, Department of Thoracic Surgery
Vanderbilt University School of Medicine, Nashville, Tennessee

Simon Gravel
Department of Human Genetics
McGill University, Montreal, Quebec, Canada
Genome Quebec Innovation Centre, Montreal, Quebec, Canada

Fig 3. Pairwise genetic relatedness across US census regions among (A) African-Americans, (B) European-Americans, and (C) African-Americans and European-Americans. (D) Census-based prediction for African-Americans (see Materials and Methods). On each map, the line connecting two regions shows the average relatedness between individuals in those regions, and the thickness and opacity of the lines are on a linear scale between the minimum and maximum values shown above the map. Relatedness between regions with fewer than 10,000 possible pairs of individuals is not shown (see Materials and Methods for details). All numbers are in units of cM. (E) Decay of average IBD (shown in logarithmic scale) as a function of distance using IBD segments of length 18cM or longer from HRS (dots), compared to the analytical model (lines).

Abstract

We present a comprehensive assessment of genomic diversity in the African-American population by studying three genotyped cohorts comprising 3,726 African-Americans from across the United States that provide a representative description of the population across all US states and socioeconomic status. An estimated 82.1% of ancestors to African-Americans lived in Africa prior to the advent of transatlantic travel, 16.7% in Europe, and 1.2% in the Americas, with increased African ancestry in the southern United States compared to the North and West. Combining demographic models of ancestry and those of relatedness suggests that admixture occurred predominantly in the South prior to the Civil War and that ancestry-biased migration is responsible for regional differences in ancestry. We find that recent migrations also caused a strong increase in genetic relatedness among geographically distant African-Americans. Long-range relatedness among African-Americans and between African-Americans and European-Americans thus track north- and west-bound migration routes followed during the Great Migration of the twentieth century. By contrast, short-range relatedness patterns suggest comparable mobility of ∼15–16km per generation for African-Americans and European-Americans, as estimated using a novel analytical model of isolation-by-distance.

Author Summary

Genetic studies of African-Americans identify functional variants, elucidate historical and genealogical mysteries, and reveal basic biology. However, African-Americans have been under-represented in genetic studies, and relatively little is known about nation-wide patterns of genomic diversity in the population. Here, we study African-American genomic diversity using genotype data from nationally and regionally representative cohorts. Access to these unique cohorts allows us to clarify the role of population structure, admixture, and recent massive migrations in shaping African-American genomic diversity and sheds new light on the genetic history of this population.

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Mexico boasts a staggering genetic diversity, study shows

Los Angeles Times
2014-06-12

Geoffrey Mohan

SHARELINES

▼ DNA offers a nuanced answer to what it means to be Mexican
▼ Ancient genetic signal survived conquest in Mexico
▼ Latino and Hispanic labels don’t do justice to Mexico’s genome

Writers, artists and historians have long pondered what it means to be Mexican. Now science has offered its answer, and it could change how medicine uses racial and ethnic categories to assess disease risk, testing and treatment..

The broadest analysis of the Mexican genome ever undertaken reveals a nation of staggering genetic diversity, where European conquest only thinly masks the ancestral DNA of Native Americans, and where some populations remain as distinct from one another as Europeans are from Chinese, according to findings published Thursday in the journal Science.

Forty researchers, who share Latino heritage as well as professional qualms over the significance of ethnic and racial categories, teamed up across borders to analyze more than 1 million variations in the building blocks of DNA. They examined more than 500 samples collected in Mexico’s remote Indian villages and polyglot cities, and from Mexican Americans in California.

“Because these populations are so rich, so genetically differentiated, you can’t just lump them all in,” said lead investigator Carlos Bustamante, a population geneticist and co-director of Stanford University’s Center for Computational, Evolutionary and Human Genomics. “You really have to embrace that diversity and think about doing medical genetic studies on a very large scale.”

To illustrate their point, the researchers compared their new genetic data with the results of lung function tests for children in Mexico City and Latinos in the San Francisco Bay Area. They discovered that pulmonary function varied in ways that were mirrored in DNA. It was as if someone with a fraction of Maya ancestry had lungs that were 10 years older than someone with a bit of northern indigenous heritage…

…Researchers not involved in the study, however, caution that correlations between disease risk and ancestry may not have much of a genetic basis at all. In many cases, they might mask socioeconomic or environmental factors — where and how you live.

The suggestion that differences in DNA are responsible for observed differences in lung capacity “is an enormous leap,” said UC Berkeley sociologist Troy Duster, who has written extensively on the intersection of race, biology and public policy.

Lundy Braun, an Africana studies professor at Brown University who studies the intersection of race and medicine, said medicine’s focus on genetics may be overshadowing other avenues of research.

“The effects of social class on lung function have been largely ignored in favor of the focus on race and ethnic difference,” she said.

Braun and Duster worry that such genomic studies may unwittingly lend legitimacy to widely discredited ideas about racial disparities.

“There is always lurking danger that this kind of research, which emphasizes the genetic structure of ethnic and racial groups, fuels the notion that the biology or genetics of those groups explains their condition,” Duster said…

Read the entire article here.