Evolutionary Genetics, Molecular Anthropology and Forensic Genetics
Dr Maziar Ashrafian Bonab
Evolutionary Genetics is the broad field of studies that attempts to account for human evolution in terms of changes in gene and genotype frequencies within human populations. Four evolutionary forces (mutation, random genetic drift, natural selection, and gene flow) acting within and among populations cause micro-evolutionary change and these processes are sufficient to account for macro-evolutionary patterns, which arise in the longer term from the collective action of these forces. That is, given very long periods of time, the micro-evolutionary forces will eventually give rise to the macro-evolutionary patterns that characterize the higher taxonomic groups. Thus, the central challenge of Human Evolutionary Genetics is to describe how the evolutionary forces shape the patterns of biodiversity observed in modern human populations.
Molecular anthropology is a field of anthropology in which genetic analysis is used to determine evolutionary links between ancient and modern populations, as well as between contemporary species. By examining DNA sequences in different populations, molecular anthropologists can figure out how closely related those populations are. Certain similarities in genetic makeup let molecular anthropologists determine whether or not different groups of people belong to the same haplogroup, and thus if they share a common geographical origin. This is significant because it allows anthropologists to trace patterns of migration and settlement, which gives helpful insight as to how contemporary populations have formed and progressed over time. Molecular anthropology has been extremely useful in establishing the connection between modern humans and other primates. While there are clearly many morphological similarities between humans and chimpanzees, for example, not many would have guessed that the two have roughly 98 percent of their DNA in common. Such information is useful in searching for common ancestors and coming to a better understanding of how humans evolved.
Forensic Genetics is a new discipline including several techniques such as genetic fingerprinting, DNA testing, DNA typing, and DNA profiling; used to distinguish between individuals of the same species using only samples of their DNA. Two humans will have the vast majority of their DNA sequence in common. Genetic fingerprinting exploits highly variable repeating sequences called minisatellites. Two unrelated humans will be likely to have different numbers of minisatellites at a given locus. In STR profiling, which is distinct from DNA fingerprinting, PCR is used to obtain enough DNA to then detect the number of repeats at several loci. It is possible to establish a match that is extremely unlikely to have arisen by coincidence, except in the case of identical twins, who will have identical genetic profiles. Genetic fingerprinting is used in forensic science, to match suspects to samples of blood, hair, saliva or semen. It has also led to several exonerations of formerly convicted suspects. It is also used in such applications as identifying human remains, paternity testing, matching organ donors, studying populations of wild animals, and establishing the province or composition of foods. It has also been used to generate hypotheses on the pattern of the human diaspora in prehistoric times.
Osteoarchaeology and palaeopathology: Human and animal bones are amongst the most common finds on archaeological excavations of all periods and can provide abundant information about past human populations, diet, economy, society and the natural world. Palaeopathology is the study of ancient diseases. It is useful in understanding the history of diseases, and uses this understanding to predict its course in the future.
We are using the methods of modern molecular genetics to investigate questions that anthropologists are interested in concerning the origin, relationships, history, structure and migration patterns of human populations. Depending on the question, we analyze variation in mitochondrial DNA, Y-chromosome DNA and/or autosomal DNA in either contemporary populations or ancient specimens.
1. Molecular Genetic Variation in the Middle East
We are conducting a comprehensive analysis of mitochondrial, Y-chromosome, and autosomal DNA variation in 23 different populations from Iran and neighbouring groups, to address questions concerning the influence of linguistic and geographic barriers on genetic variation in these populations and to further our understanding of the origins of Iranian populations. We are also attempting to retrieve and analyze DNA from Bronze and early Iron Age human remains from the Iran to address questions of genetic diversity and the continuity of human populations in this region.
2. Genetic Perspectives on the Aryan Race
We are interested in the history of human populations in Middle East, from the time of the Neolithic Evolution ~11,000 years ago (the origin of agriculture in the Fertile Crescent) until the arrival of Aryans to the Iranian Plateau ~4,000 years ago. In the winter of 2003, we collected 2610 fresh blood samples from 23 ethnic groups in Iran and neighbouring countries, as part of a project entitled: “Genetic polymorphism of modern and ancient population of Iran”; which aims to form a unitary model of the human settlement of Iran and Middle east.
In addition to using mtDNA and Y chromosome of these samples in order to gain an understanding of the maternal and paternal histories of Iranian populations, we will investigate patterns of variation in the autosomal microsatellite loci of these samples in order to discern relationships between Iranians and other populations. More specifically, we will examine the genetic relationship between Persian speaking groups and non-Indo-European speakers in the region in order to learn more about how languages and genes have spread and interacted in this region of the world.
3. Developing autosomal markers for population genetic studies
Over the last decade, interest in Single Nucleotide Polymorphisms studies (SNPs) has steadily grown. SNPs as a genetic marker are becoming especially useful in forensic genetics, admixture mapping, and structured-association mapping. SNPs have promising advantages over other kind of markers, for example Short Tandem Repeats (STRs), such as high-throughput analysis, uniform distribution along and large coverage of the human genome. Autosomal SNP markers also promise to be useful concerning the analysis of patterns of genetic variation to reconstruct the evolutionary history of human populations. We aim to apply high-throughput, large scale SNP genotyping on our Middle eastern samples for a more comprehensive estimation of genetic admixture, migration and colonization processes, the structure and relationship of Iranian populations. We aim as well to move one step forward into the future of genetic markers by studying new polymorphisms, such as copy number variation in the human genome.
4. Forensic DNA Analysis
The literature for forensic DNA analysis has expanded rapidly in the past few years as various technologies and genetic markers have been adopted and validated. During 2003 to 2005, more than 1600 papers were published regarding DNA markers that are applied to human identity testing. New methods for detecting, preserving, extracting, and quantifying DNA are continually being developed and are aiding recovery of DNA from biological material found at crime scenes. Real-time PCR has been introduced as an important tool to aid DNA quantization especially with samples containing low amounts of DNA template.
Tandemly repeated DNA sequences are widespread throughout the human genome and show sufficient variability among individuals in a population that they have become important in several fields including genetic mapping, linkage analysis, and human identity testing. These tandemly repeated regions of DNA are typically classified into several groups depending on the size of the repeat region. Minisatellites (variable number of tandem repeats, VNTRs) have core repeats with 9-80 bp, while microsatellites (short tandem repeats, STRs) contain 2-5 bp repeats.
Short tandem repeat (STR) typing of autosomal markers with fluorescence-based detection is now almost universally used in forensic DNA laboratories worldwide. The ABI 310 and ABI 3100 genetic analyzers, which are the primary instrument platforms for STR typing, have been reviewed along with issues surrounding sample preparation, detection, and interpretation of STR profiles. Commercial STR kits enable routine multiplex amplification of as many as over 20 STR markers in a single assay. Protocols for analyzing DNA samples with commercial STR kits have been described. A large portion of the literature involves reporting STR allele frequencies from various populations.
We are trying to develop a multiplex PCR and SNP typing assay for 13 SNPs from the mitochondrial Genome that help separate samples containing the most common HVS-I and HVS-II mtDNA sequence in Iranian populations. In addition, we are trying to create the first Y-STR multiplex capable of simultaneous amplifying of the original European extended haplotype loci as well as some suitable markers for Middle Eastern Populations.
5. Ancient DNA analyses
More than 2 decades ago, DNA sequences were isolated from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140 and 2400 year-old specimens. However, ancient DNA (aDNA) research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace.
The use of aDNA in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA.
In our aDNA lab, we use a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of Restriction Fragment Length Polymorphisms (RFLP), quantitation of target DNA, amino acid racemization, and amino acid quantitation.
We have a large collection of ancient human, animal and plant remains (7,000 to 1,200 years old) from several ancient sites in Middle East and UK (from British Heritage). As well as our current projects for retrieving aDNA from our ancient samples (in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts) for our studies we are trying to design new strategies for isolation and extraction of ancient DNA from archaeological samples.