Michael Crawford on anthropological genetics: DNA fingerprinting through history

Posted by Biome on 17th February 2014 - 0 Comments


DNA fingerprinting revolutionised the field of forensic science in the 1980s, however it went on to leave its mark across a far wider range of disciplines, including that of anthropological genetics. As part of a special series of articles on DNA fingerprinting brought together by Investigative Genetics, Michael Crawford and Kristine Beaty from the University of Kansas, USA, explored the evolving role of this innovative technique in anthropological genetics, published in their recent review. Here Crawford explains how the field of anthropological genetics has changed since his career began and the future of DNA markers in this area of research. A complete transcript of the interview can be viewed here.

 

What got you interested in anthropological genetics?

When I was a doctoral candidate in biological anthropology at the University of Washington-Seattle, USA, the field of anthropological genetics had not yet coalesced into a synthetic discipline. Most biological anthropologists of the 1950s and early 1960s were trained in morphological approaches to phylogeny, primate behavior and racial variation. My first exposure to population genetics came in 1963 in the form of Derek Roberts, a visiting biological anthropologist from Oxford University, UK. He applied Sewall Wright’s formulations on genetic drift to a genetic isolate in the southern Atlantic, Tristan da Cuhna (Nature 1968 , 220: 1084-1088). This research revealed how unique historical events and demographic structure impacts on the population and through the action of evolutionary forces. I was fascinated by this research, which now may be called anthropological genetics.

The following year, Derek Roberts returned to England but Stanley Gartler, a human geneticist at the University of Washington, USA, supervised my Master’s thesis on the application of biochemical genetics to non-human primate taxonomy and phylogeny. At that time a Regional Primate Research Center was established at the University of Washington, USA, and its director (Theodore Ruch) hired me as a ‘primate geneticist’ to conduct research on the genetics of the Macaque colony. In addition, an eminent medical geneticist, Arno Motulsky served as a mentor for my doctoral dissertation.

In 1970, I organized a conference at the School of American Research on the application of methods and theories of genetics to evolutionary questions of interest to biological anthropologists. An edited volume ‘Methods and Theories of Anthropological Genetics’, summarizing the proceedings was published in 1973 by the University of Mexico Press (Crawford MH, Workman PL, University of New Mexico Press, 1973). This volume helped synthesize anthropology and genetics into a field – anthropological genetics.

 

What is the focus of your research?

Two foci are prominent in my research: (1) causes and consequences of migration, the reconstruction of the human diaspora; (2) genetic-environmental interactions in the creation of complex phenotypes – morphological, behavioral and disease. These interactions are examined utilizing molecular and quantitative genetics, and a comparative approach through field investigations.

In 1977, I initiated a research program to reconstruct the peopling of the Americas based on genetic evidence. Morphology, blood groups and protein variation pointed to a Siberian origin of Native Americans. However, the Cold War prevented the direct testing of this origins hypothesis through the comparison of DNA markers on the Siberian side of the Bering Straits with Native American populations. In 1989, with the initiation of ‘perestroika’ (reconstruction) of the Soviet Union and with the collaboration of the Siberian Branch of the Soviet Academy of Sciences, I was able to conduct field investigations and obtain DNA samples from indigenous populations of Siberia.

To better understand the dynamics of migration and settlement of island populations from Siberia, a research program was initiated with Dennis O’Rourke and Dixie West on the Unagan (Aleut) populations of the Aleutian Archipelago. While O’Rourke focused on ancient DNA from Aleut burials, I sampled DNA from contemporary Aleuts residing on 11 of the islands of the Archipelago. Despite depopulation, relocation of western Aleuts to mainland Alaska, mtDNA sequences preserved the maternal genetic structure and reflected the prehistoric migration patterns.

My interests in quantitative genetics arose in 1964 during a summer institute in behavioral genetics at the University of California, Berkeley. Since that time, I have been dissecting the genetic-environmental variances in complex phenotypes. Currently, I have been collaborating with Ravi Duggirala from Texas Biomedical Research Institute, USA, and Mexican and US public health officials on the genetic-environmental interactions associated with risks of contracting clinical tuberculosis in Mexican Mestizo populations of Chihuahua (Tuberculosis 2013, 93, S71-S77).

I have also been conducting a 35 year longitudinal study on the genetics of biological aging in Mennonite communities of Kansas and Nebraska. This study demonstrated that biological aging (defined as the deviations from the prediction line in a stepwise multiple regression of physiological, genetic and biochemical markers) is a more reliable predictor of survivorship and life expectancy than chronological age. The heritability of biological age is approximately 50 percent, indicating that environmental factors play an equal role in survivorship (Crawford MH (Ed), Anthropology University of Kansas Press, 2000).

 

Do you think findings in anthropological genetics will impact other fields? And if so, how?

Anthropological genetics is currently impacting a number of different fields and disciplines: human genetics, genetic epidemiology, epidemiology and anthropology, paleontology and linguistics.

Anthropological genetics brings to the table the following approaches: (1) A broad bio-cultural perspective on genetic/environmental interactions in complex phenotypes, such as chronic diseases: diabetes, osteoporosis, cardiovascular disease, and hypertension. (2) A population sample is selected, instead of families of probands, sibships or monozygotic, dizygotic twins. (3) Small, reproductively isolated non-Western populations, instead of hospital samples from large cities often utilized by human geneticists. (4) The samples are usually from culturally homogeneous populations, thus, resulting in less statistical noise associated with the environment. (5) Sampling is representative of normal variation instead of clinical ascertainment. (6) Quantitative measures of the environment, instead of summarizing the environment as: E = 1 – Heritability (h2)(Hum Biol, 2000, 72(1), 3-13).

Field investigations in anthropological genetics provide a comparative dimension to a study or analysis. Research on urban, US samples may bring results that are misleading when dealing with complex phenotypes exposed to different environmental conditions. For example, the observed association between the APOE*4 allele and elevated cholesterol levels, established in US samples of European-American ancestry, was not verified in Central Siberian reindeer herding populations (Hum Biol. 1996, 68 (2), 231-244). Unique dietary patterns influence cholesterol levels and risk of cardiovascular disease in Evenki reindeer herders of Siberia with APOE*4 alleles.

Anthropological genetics can add a time dimension to evolutionary studies of human populations by applying archaeological evidence, historical reconstruction and genetic data. For example, because of an alliance between the Tlaxcaltecans of Central Mexico and the Spanish Conquisadores, a garrison from Tlaxcala was relocated into the adjoining Valley of Mexico in 1521. Similarly, 400 Tlaxcaltecan families were transplanted to northern Mexico in 1591 to establish a new colony of San Esteban de Nueva Tlaxcala (currently the City of Saltillo). Because Tlaxcaltecans were considered traitors and blamed for the fall of Mexico, these transplanted populations remained reproductively isolated for more than 400 years. A study of the contemporary populations offered a measure of evolutionary change and morphological micro-differentiation within a temporal frame (Crawford MH, Lawrence: University of Kansas Publications in Anthropology #7, 1976).

 

What do you think are the most seminal developments in the last 30 years that advanced the field of anthropological genetics?

From the 1970s to the present, the molecular revolution and developments in computers has had profound effects on anthropological genetics. The developments in methods of extracting, application of restriction enzymes, PCR amplification, manipulating and characterizing DNA has offered to the field of anthropological genetics powerful tools for testing hypotheses concerning population origins, affinities and history. The specificity of bacterial restriction enzymes identified variation in specific polymorphic sites. Distributions of restriction fragment length polymorphisms (RFLPs) were applied to the characterization of populations, their affinities and genetic structure. DNA fingerprints, developed by Alec Jeffreys, resulted in a major innovation in anthropological genetics and in forensic sciences. Sanger DNA sequencing methods and the establishment of the mtDNA Cambridge standards revealed normal mtDNA human variation and demonstrated that modern genomes resulted from a migration out-of-Africa of anatomically modern Homo sapiens replacing earlier hominin forms – such as Neanderthals from Europe and the Middle East.

Characterization of mtDNA haplogroups, NRY haplotypes and lineages provided the field of anthropological genetics with measures of sex specific migration and gene flow. While autosomal, recombining genetic marker can estimate parental population contribution, mtDNA and NRY provides gender-specific patterns of migration and gene flow. By focusing on Q, Q3 and C Y-chromosome haplotypes in Aleut populations, we were able to demonstrate that only 15 percent of the Aleut Y chromosomes are Native American. Eighty-five percent of the Y chromosomes of contemporary Aleut populations were the result of gene flow from Russian administrators and Scandinavian and English fishermen.

Development of laser based fluorescent detection of DNA and high throughput DNA sequencing resulted in the sequencing of the entire human genome, genome wide association studies for mapping genes and quantitative trait loci (QTLs). Refinement of sequencing techniques has resulted in the characterization of 600,000 year old Denisovan hominin form and challenged earlier theories of human evolution.

 

What do you think are the major open questions in anthropological genetics that remain to be answered?

The following are a few open questions among the numerous questions in anthropological genetics that remain to be addressed based on molecular genetic data:

What were the biological/genetic causes of the human diaspora, out-of-Africa, and when and why did Homo erectus and anatomically modern Homo sapiens expand to Asia, Europe, Oceania and the Americas? What role did DRD4 dopamine receptor alleles play in novelty seeking and migration? An association has been demonstrated between the distance to which a population has moved from its original location and the frequency of the dopamine receptor allele (Evol. & Hum Behavior. 1999, 20, 309-324). However, the magnitude of the variance explained by this association is low, and the roles of other neurotransmitters is yet to be tested.

What are the quantitative trait loci (QTLs) that influence specific complex chronic diseases? To date, association studies based on GWAS have identified numerous associations that explain a small proportion of the variance. Numerous spurious associations have been observed. Instead of associations based on samples of unrelated individuals, the use of extended families in genetic isolates followed by linkage analyses, and physiological functional studies appear to be most promising.

What role does epigenetic inheritance play on complex quantitative traits? Anthropological genetics offers experimental designs which examine DNA methylation based on migration and comparisons of parent-offspring living under diverse environmental conditions, diets and physical activities (Mosher MJ, New York Cambridge University Press, 2013, 101-132). This use of migrant models goes back to the 1900s with Franz Boas, who studied phenotypic variation in Jewish immigrants to the United States and compared them to populations in Europe where the immigrants resided and shared common environments. The migrant models are based on the principles of comparing relatives who migrated to different environments i.e. same genes-different environments or different genes-same environments.

 

With the advent of next generation sequencing and continued progress in related technologies, what questions can we now or soon answer that in the past would have proven too challenging?

With the recent developments in sequencing technology, researchers have been able to sequence DNA of entire ancient genomes from well-preserved skeletal materials dating back to as early as 600,000 years ago or hair samples from a 4,000 year old Paleo-Eskimo. Given such a time dimension, we should be able to ascertain the origins and evolution of specific chronic and infectious diseases from ancient DNA. Single nucleotide polymorphisms (SNPs) currently associated with contemporary diseases, such as type 2 diabetes mellitus, can be traced back to prehistoric Native American populations. Rasmussen et al sequenced DNA from hair of a 4,000 year old Eskimo, excavated from east Greenland. SNPs associated with metabolic diseases in contemporary populations were identified in the ancient DNA of this individual (Nature 2010, 463, (11), 757-762). For example: SNPs (rs1528133; rs2272383; and rs22723821) were identified in DNA associated with higher BMI in contemporary populations. Similarly, a SNP (rs2383207) associated with increased risk of heart disease in contemporary populations was identified in the Paleo-Eskimo of East Greenland. SNPs associated with cold adaptation (rs9493857, rs1042622 and rs751141) were also observed in the DNA of the PaleoEskimo. However, some of these associations may be spurious resulting from multiple comparisons and will require further physiological and functional analyses.

 

What do you think the role of DNA markers will be in future anthropological genetic research?

SNPs on a genome-wide level will be used to reconstruct human history, population affinities, genetic structure. However, greater precision will be possible as millions of markers will be available at lower costs. Use of uniparental markers, such as mtDNA or non-recombining Y chromosomes will continue to elucidate the history of either the maternal or paternal lineages. For example, the analyses of mtDNA in Aleut populations indicate only the presence of founding haplogroups A2 (A2a1a) and D2 (D2a1a) and are suggestive of no gene flow from European populations into the Aleutian Archipelago. In contrast, the Y chromosome markers, Q and Q3 occur in only 15 percent of the Aleut males, while European markers (R1b1, R1a1, I, J, N) occur at 85 percent throughout the Aleutian Islands. Autosomal STRs indicate that 40 percent of the Aleut gene pool is due to gene flow from Russia, England and Scandinavia(Hum Biol. 2010, 82(5-6), 695-717 ). The use of whole genomic sequencing will improve the accuracy of the measurement of gene flow, based on the characterization of the parental populations and the use of linkage disequilibrium (LD), and the sizes of the parental recombined segments in the mixed genome should provide the geographic regions from which the migrants originated. The sizes of the recombined regions in the admixed populations can estimate the chronology of the initial gene flow.

 

What challenges do you think lie ahead as technology pushes towards the field of anthropological genetics? How do you think these challenges can/will be addressed?

The characterization of the entire genome with circa three billion base pairs of DNA, will continue to offer major computational challenges. Scientists will have to be able to access super computers or ‘computer ranches’ (thousands of computer processors working in parallel). A computer ‘ranch’ facility at the Texas Biomedical Institute, USA, has proven to be highly successful in identifying genes for an assortment of complex diseases from approximately 30,000 exons and 3.5 billion base pairs that constitute the human genome. The AT & T Genomic Computer Center at the Texas Biomedical Institute, USA, focuses on the analyses of genetic data sets, made up of extended families or random samples representing specific populations. This computer cluster for human and genomic research utilizes thousands of processors working in parallel. Access to such super computers will permit the examination and analyses of whole genomes in large numbers of extended families with genes associated with disease susceptibility. This research, coupled with RNA studies should not only identify quantitative trait loci (QTLs) but also reveal their physiological functions.

One problem in future anthropological genetic research, independent of technological breakthroughs, will be access to populations for comparative purposes. Field research is becoming more difficult particularly in non-Western countries because of political instability, warfare, drug trafficking, terrorism plus the political baggage acquired by anthropologists during colonial administration. Future field investigations must be based on scientific partnership, cooperation and trust with the participating communities (Crawford MH, Cambridge University Press; 2007, 79-111).

 

More about the author(s)

Michael Crawford, Director of the Laboratory of Biological Anthropology, University of Kansas, Lawrence, USA.

Michael Crawford is Director of the Laboratory of Biological Anthropology and Professor of Anthropology and Genetics at the University of Kansas, Lawrence, USA, and Director of the International Consortium for the Study of Tuberculosis. He initiated and conducted field research programs across the globe, including; Alpine villages of Northern Italy, northern and central Mexico, Ireland, Belize, Guatemala, Honduras, India, Canada, Hungary, Siberia and the Aleutian Archipelago, amongst many others. Most of these research programs focused on the genetic structure of human populations, causes and consequences of human migration and the genetic epidemiology of chronic and infectious diseases. In addition, for 35 years he has directed a longitudinal study of biological aging and survivorship in Mennonite populations. Currently, Crawford is involved in a study of genetic susceptibility to tuberculosis in Mexican populations and the causes and evolutionary consequences of the successful colonisation of the coast of Central America by small group of forced migrants from St. Vincent Island.

Review

DNA fingerprinting in anthropological genetics: past, present, future

Crawford MH and Beaty KG
Investigative Genetics 2013, 4:23

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