mtDNA evidence of the Aymara expansion

Batai K, Williams SR. Genetic evidence of the Aymara expansion and mitochondrial variation in the central Andes. American Journal of Human Biology 26(3):321-30.

I was interested in Andean prehistory for a long time.  Actually, that is how I got interested in anthropology.  Before I started working on anthropological genetics projects, I learned a lot about Andean archaeology (monumental architecture, mortuary practices, etc.).  There are very large pyramids in costal Peru which is as old as Egypt’s pyramids.  The dry climate in costal Peru is perfect to preserve human remains.  I had an opportunity to study human remains from ancient Peru stored in the Field Museum.

My first project that I worked was ancient DNA study to understand prehistoric migration in Peru using skeletal remains from Paloma, Kilometer 4, Nazca, Chiribaya Alta, and Moche.  Unfortunately, I could not amplify enough DNA to produce good data for my population genetics analysis.  Then, I decided to use samples from modern populations.

When I started my project to address Aymara prehistory, there was no previous population genetics study on the Aymara from Bolivia using large samples and mtDNA sequence.  In my study, I explored if demographic expansion or female migration was more important factor influencing mtDNA sequence variation.  The results of my analyses support archaeological and ethnohistorical data and suggest that both demographic expansion as well as female gene flow were important factors.  The Aymara experienced demographic expansion after the introduction of domesticated plants and animals and intensification of food production.  The Aymara probably had a constant female gene flow throughout their prehistory and history through the Aymara expansion incorporating surrounding populations, vertical use of Andean ecosystem, and modernization/urbanization.



Book Review: Medical Apartheid by Harriet A. Washington

On the Father’s day Sunday this year, I was at the Salem Baptist Church, south side mega church, for prostate specific antigen (PSA) screening and PSA study recruitment event.  We offered PSA screening for prostate cancer several occasions at this church and this church has an annual health event to encourage African American church members to have healthier lifestyle.  Five out of eight people who were working in the screening event that day were African Americans, including the PI of the project, who is African American male urologist at Northwestern medical school.  The first African American man who came in for PSA screening jokingly said, “Ok, I will be the first guinea pig.  What do I have to do?”

African American men have poorer health conditions compared to African American women or European American men and women, but African American men are usually underrepresented in many medical research projects, most likely due to difficulty recruiting them for medical research projects or clinical trials.  Why is it so difficult to recruit African American men?  Why do they refuse to participate in medical research?

This book, “Medical Apartheid,” illustrates the reasons why it is difficult to recruit African Americans for medical research and why they mistrust physicians or medical institutions rooted in the American history beginning the enslavement of Africans.  The author, Harriet A. Washington, illustrates history of injustice in health, not from the victors’ perspective.  The advance in medical science was achieved some way through exploitation of African Americans, but was hindered at the same time because of flaws in their research designs, scientific methods, and reasoning.

Considering the history of slavery and racial segregation, it was not surprising to read that White doctors did not treat the slaves like they would for white patients.  Slave owners, physicians’ real clients, did not want to spend much money to treat their slave, if treatment cost more than they could make a profit from their slaves.  African Americans knew that white doctors’ treatments did not work well or worsened the problems, and preferred their traditional healing methods (p.48).  Even after the slavery ended, African Americans suffered with poor health conditions because they did not have access to good health care due to low income, no health insurance, and poor living environments (p. 152).  Medical racism continued until recently, and medical procedures, such as hysterectomy, were done to African Americans and they were recruited to medical research without them fully understanding medical procedures, experiments, or research.

It was very surprising to read that a various painful and dangerous medical experiments were done to African Americans either poorly informed or without consent, without anesthesia during the slavery.  Tuskegee Syphilis Study that followed untreated African American men with syphilis over 40 years and performed autopsy for hundred subjects is well known, but there are many more.  For example, James Marion Sims, father of American gynecology, developed a surgical treatment for vesicovaginal fistula using slave women as experimental subjects (p.61-68).

Even after 1950s, medical experimentation targeted vulnerable segments of American society, low-income African Americans, prisoners, and children.  Between 1944 and 1994, nontherapeutic radiation was injected to study subjects, and African American had higher risk of being the subject of the experiments.  African Americans were targeted to experiment of biological weapon as well (p. 361-363).  Washington states that many African American subjects who went through medical experiments and African American patients who received medical procedures involuntary thought that physicians were really caring them (p. 219).  Washington further states that medical abuse is far from over and medical experimentations are still performed on people of African descent in this country as well as in Africa (p. 386-396).

Scientific racism was a major paradigm in the 19th century in the U.S. and Europe to show that African Americans and African as inferior subspecies of human.  Scientists and physicians tried to show scientifically that there are anatomical and physiological differences, such brain size, immune system, and skin color, and the body of African Americans were displayed in St. Louis World’s Fair in 1906, a zoo in New York City, and a saloon in New York City transformed into an operation room, to prove that African Americans and Africans were inferior.

Washington sees the contradictions.  Even though White physicians believed that African Americans were physically different from European Americans, African Americans were treated as a ‘clinical material’ in medical schools for instruction and experiment (p.106-108).  Unnecessary surgeries were performed to demonstrate clinical procedure to the medical students.  After death, their bodies were used for dissection, even in Georgia where anatomical dissection was illegal until 1887 and in northern states, using stolen bodies from graves (p.120).  Northern states imported African American bodies for dissection from southern states (p.123).

Today, clinical trial is one way to receive the best treatment available, especial for the people with an advanced disease condition and traditional established treatment methods failed to cure or improve their health.  However, African Africans are more likely to be recruited for high risk clinical trials for a newly developed HIV drag or an implantation of artificial heart than European Americans, but poor minority populations are less likely to be able to receive the expensive treatments after they are developed.  African Americans who have been subjected to experiments as a ‘clinical material’ may see clinical trial differently.  Washington quotes the Richmond Daily Dispatch published in 1854 saying that African Americans believed if they entered medical school hospital, they would not come out alive (p.108).

Having read this book, it is understandable if African Americans do not want to participate in clinical trial or medical research.  African American patients are feeling anxious about their medical conditions, when they come to a clinic in a hospital, an institutions that have similar social structure as in slavery.  Many physicians, high-rank nurses and administrative stuffs are European Americans, while lower-rank hospital stuffs are minorities.  Some hospital and medical school buildings have architectural styles and motives that symbolize the power of European civilization.

Embodiment of social inequality causes health disparities

Krieger, N. 2012 Methods for scientific study of discrimination and health: An ecosocial approach. American Journal of Public Health 102(5):936-945.

In this paper, Krieger explains how discrimination based on racial/ethnic origins affects health of the racial/ethnic minorities.  She uses a bio-cultural approach to understand the interactions between social aspects (social structure, economic and social derivation, individual’s life-long experience of racism, and individuals’ cognitive aspects) and biological aspects of race (physical traits and exposures to toxins, hazards, and pathogens).  This approach incorporates the temporal (life-cycles starting in utero to the end of life) and spatial (from individual to global level) aspects that affect minority health.  While incorporating the wide variety of aspects of minority individuals and societies into her theoretical framework, she focuses on the causal relationship between discrimination and health, so she sees health inequality is manifestation of social inequality.

But we really need to look at these tables from her paper to understand the social context.

Table 1 Analyzing US Racial/Ethnic Health Inequities in Context

There are more African Americans living at poverty level, unemployed, and without health insurance compared to European Americans.  Infant mortality rate is much higher among African Americans, and more African American self-report having poor health status.  Minority groups are underrepresented in the congress and state legislature.

Table 3 Postelection National Poll Results for Statement on Racial Discrimination, November 3-7, 2010

However, so many white Americans and Tea Party and Republicans agree that “Today discrimination against Whites has become as big a problem as discrimination against Blacks and other minorities.”

The core concept in her approach is embodiment of social inequality.  I believe the concept of embodiment came from habitus, idea developed by Pierre Bourdieu, a French social theorist who also talked about social capital.  Embodiment is one of the core aspects of habitus, and I believe it means that people’s e experience, material word, and social structure are incorporated deep into one’s cognition.  Krieger develops this concept further to reflect biological aspects related to health inequality.  Because of discrimination, racial minorities are more likely to be exposed toxins, hazards, and pathogens and surfer from economic and social deprivation and inadequate medical care, so racial minorities are more likely to have worse health condition.

I believe embodiment is the concept that we should explore in our research and could be very useful to analyze social determinants of health.  For example, we can use this idea to analyze the relationship between fast food culture and health.  In the U.S. fast food restaurants are fun place for kids and provide quick and inexpensive food for teenagers and adults.  It is culturally acceptable to go to fast food restaurant regularly, if you do not have time and money.  The food tastes good for kids and fills adults’ stomach for a long time.  Over time, we develop the taste for fast food, and going to fast food restaurant became an integrated part of people’s life and cognition.  People who grow up with fast food restaurants now have children and take them there regularly.  It is not surprising if these children prefer French fries over vegetables.  Because of targeted marketing and economic condition, low-income individuals, and many of them are racial/ethnic minorities, are more likely to be exposed to these high fat high calories diet.

While she focuses on racial discrimination as one of the causes of health inequality, her ecosocial approach seems to be a holistic framework for analysis of social determinants of health.  Human and our societies are very complex, we need a framework as holistic as possible to capture multidimensional aspects of human societies (social determinants of health, racism, etc.) and human biology (health).

Because her focus in this paper was explaining the causal relationship between discrimination and health, she did not explain how this framework can be used to reduce health inequality.  If we can identify the social issue related to racism and health that we hope to fix, how can we use this approach to develop a strategies for intervention?

Why I am interested in genetic epidemiological study of prostate cancer: Is prostate cancer disparities due to gene or environment?

Prostate cancer is the most common cancer among men in the U.S., and African American men have 63% higher incidence compared to European American men.  Prostate cancer incident rate was 228.8 cases per 100,000 in African American men from 2005 to 2009, while the incidence rate was 140.3 per 100,000 in European American men (DeSantis et al. 2013).  Globally, African descent men have high incidence and mortality (Rebbeck et al. 2013), and incidence of prostate cancer is rising in African countries.  Only established risk factors for prostate cancer are age, family history, and race/ethnicity, and the cause for disparities in prostate cancer incidence is still not well understood.

Environmental and social/cultural factors may play roles for increasing prostate cancer risk among African descent men, but the causal relationship of any environmental and social/cultural factors with prostate cancer risk is not well demonstrated.  Many suggest that diet likely plays roles for Pca risk.  For example, differences in serum vitamin D levels between African Americans and European Americans have been well demonstrated, and some suggested that differences in vitamin D levels may explain prostate cancer disparities.  However, epidemiological studies, mainly conducted in people of European descent, show inconsistent results.

Access to health care, socioeconomic status, neighborhood derivation, and other socio-cultural factors affect stage and tumor grade at the diagnosis, treatment choice, and mortality, but these factors may not explain the difference in prostate cancer incidence.

On the other hand, there is strong evidence for genetic factors that explain increased incidence in African Americans.  Admixture mapping identified loci at 8q24 region showing association between African genetic ancestry and prostate cancer risk (Freedman et al. 2006).  Admixture mapping takes advantage of long-range linkage disequilibrium (LD) in recently admixed populations such as African Americans and Hispanic Americans, and with use of ancestry informative markers (AIMs) that have large allele frequency differences between ancestral populations, fewer number of markers is required to capture genomic variation than genome wide association study (GWAS).  This approach is powerful, when the prevalence of disease is different between two populations and used to identify genomic region that are associated with many diseases that have different prevalence between populations (Batai and Kittles 2013).  Association of 8q24 variants with prostate cancer has been replicated in African Americans, Caribbeans, and West Africans.  In addition, GWAS among African American identified a novel locus at 17q21 associated with Pca (Haiman et al. 2011).

GWAS among European and Asian populations identified number of prostate cancer susceptibility loci, but the replication of GWAS identified loci in AA has been difficult (Batai et al. 2012), and we have a lot of work ahead of us to understand how genetic factors affect prostate cancer risk in African American men


Batai K, and Kittles RA. 2013. Race, Genetic Ancestry, and Health. Race Social Problems 5:81-87.

Batai K, Shah E, Murphy AB, Newsome J, Ruden M, Ahaghotu C, and Kittles RA. 2012. Fine-Mapping of IL16 Gene and Prostate Cancer Risk in African Americans. Cancer Epidemiology Biomarkers & Prevention 21(11):2059-2068.

DeSantis C, Naishadham D, and Jemal A. 2013. Cancer statistics for African Americans, 2013. CA: A Cancer Journal for Clinicians 63(3):151-166.

Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, Penney K, Steen RG, Ardlie K, John EM et al. . 2006. Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proceedings of the National Academy of Sciences 103(38):14068-14073.

Haiman CA, Chen GK, Blot WJ, Strom SS, Berndt SI, Kittles RA, Rybicki BA, Isaacs WB, Ingles SA, Stanford JL et al. . 2011. Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21. Nature Genetics 43(6):570-573.

Rebbeck TR, Devesa SS, Chang B-L, Bunker CH, Cheng I, Cooney K, Eeles R, Fernandez P, Giri VN, Gueye SM et al. . 2013. Global Patterns of Prostate Cancer Incidence, Aggressiveness, and Mortality in Men of African Descent. Prostate Cancer 2013:12.

Race, Genetic Ancestry, and Health: A Direction for Anthropological Genetics in the 2010’s?

Batai, K. and R. A. Kittles (2013). “Race, Genetic Ancestry, and Health.” Race and Social Problems 5(2): 81-87.

In June 2013 edition of Race and Social Problems journal, we published this review article.  I think, for anthropologists who have a training in genetics, it is an interesting direction that we should explore more.  When I was almost done with my dissertation work, I began to think what I could do after I got my degree.  I was dissatisfied with anthropological genetics.  Although I was excited to investigate human genetic variation and evolution and had fun learning and teaching (I am still interesting in these topic and continue to explore), I felt “so what?”  I understand the importance of understanding migration history and genetic variation in the world, but I felt that anthropologists and many people, mostly wealthy people, are interested in human past and variation mostly only for their intellectual interests.  Who really care about our findings?  Are they really useful knowledge?

Then, I began thinking about using anthropological perspectives and methods to help other people.  I contacted my current mentor, Dr. Rick Kittles, to see if I could do genetic research on health disparities.  I learnt genetic epidemiology, a study of roles of genetics in determining or influencing disease risk in families or populations.  In the genetic epidemiology, a lot of population genetics knowledge and methods are applied to the basic epidemiological research design.  More recently, genetic epidemiologists are showing interests in gene and environment interactions.  Here, environment refers to lifestyle and socio-cultural factors.  Gene and environmental interactions is basically what anthropologists call “bio-cultural perspective,” but genetic epidemiologists think more statistically.

In the U.S., we see a great racial health disparities.  Differences in access to health care and health screen can explain a part of health disparities, but there are more complex, genetic, biological, and socio-cultural factors that are intertwined with ‘race.’  Anthropologists are trained to understand this complex relationship.  We can bring different insights in the genetic research of health disparities from scientists who were trained in other fields, and we can contribute to biomedical science in unique ways.

Vitamin D level in traditional societies in Africa

Luxwolda, M. F., et al. (2012). “Traditionally living populations in East Africa have a mean serum 25-hydroxyvitamin D concentration of 115 nmol/l.” British Journal of Nutrition 108(09): 1557-1561.

I was very excited to find this article.  Anthropologists say that people with dark pigmentation in the equatorial areas can have optimal serum vitamin D levels, but I have not been able to find any good paper showing the serum vitamin D levels in African people who still live in traditional societies.  I was always wondering what is the natural variation in serum vitamin D levels in Africa.

In this paper, Luxwolda et al. (2012) report that the Massai pastoralists and Hadzabe hunter-gathers have high serum vitamin D concentrations.  They measured serum 25(OH)D, a major circulating form of vitamin D in the blood, in 35 Massai and 25 Hadzabe and found that mean serum 25(OH)D levels was 47.7 ng/mL for the Massai and 43.7 ng/mL for the Hadzabe.  Although sample size was very small, nobody was vitamin D deficient (<20 ng/mL).  The Massai and Hadzabe people spend most of their days in the sun and do not have excess clothes covering their body.

As an anthropologist, I am interested in vitamin D level, first because of vitamin D hypothesis of skin color (see here) and second because of link between low vitamin D and health disparities.  The authors says that serum vitamin D levels observed should be similar to vitamin D levels in African populations before the Out-of-Africa event.  If so, traits, such as skin color, vitamin D binding proteins, and enzymes in vitamin D metabolic pathway, that help maintain optimal levels of serum vitamin D (more than 40 ng/mL?) should have been positively selected outside of Africa.  They also note that it is not clear, if observed vitamin D levels should be a target optimal level in the westernized societies.

Bantu expansion in East Africa: mtDNA variation in two Bantu-speaking ethnic groups (Taita and Mijikenda)

Batai K, Babrowski KB, Arroyo JP, Kusimba CM, Williams SR. 2013. Mitochondrial DNA diversity in two ethnic groups in Southeastern Kenya: Perspectives from the northeastern periphery of the Bantu expansion. American Journal of Physical Anthropology 150 (3):482–49. 

My article from my dissertation project was published on the March issue of American Journal of Physical Anthropology.  We found a great genetic diversity in small Bantu-speaking ethnic groups in southeastern Kenya, the Taita and Mijikenda.  The Taita was genetically similar to the Turkana, Nilo-Saharan-speaking ethnic group in Kenya.  The Mijikenda showed mtDNA variation between the Central African Bantu populations and Northeastern East African populations.  The migration rates between different ethnic groups estimated using MIGRATE were high, and gene flow between different ethnic groups from different language families were common in East Africa.  The results suggest that the Bantu-speaking groups chose many different strategies as they arrived or after they arrived in East Africa.  Probably, the Taita incorporated local females into their group through inter-ethnic marriage and ethnohistorical studies support this data.  On the other hand, the Mijikenda maintained close ties with other Bantu-speaking groups.

In this paper, I wanted to show that although Bantu languages are very homogeneous, the Bantu speaking populations are genetically very heterogeneous and show great differentiation, especially in East Africa.  Although language differences can reduce rates of gene flow, I believe that language difference is not that important, and language and gene have different evolutionary processes.