Archaeogenetics is the study of ancient DNA using various molecular genetic methods and DNA resources. This form of genetic analysis can be applied to human, animal, and plant specimens. Ancient DNA can be extracted from various fossilized specimens including bones, eggshells, and artificially preserved tissues in human and animal specimens. In plants, ancient DNA can be extracted from seeds and tissue. Archaeogenetics provides us with genetic evidence of ancient population group migrations, The ancient DNA cross referenced with the DNA of relative modern genetic populations allows researchers to run comparison studies that provide a more complete analysis when ancient DNA is compromised.
Archaeogenetics receives its name from the Greek word arkhaios, meaning "ancient", and the term genetics, meaning "the study of heredity". The term archaeogenetics was conceived by archaeologist Colin Renfrew.
In February 2021, scientists reported the oldest DNA ever sequenced was successfully retrieved from a mammoth dating back over a million years.
Early work
Ludwik Hirszfeld (1884–1954)
Ludwik Hirszfeld was a Polish microbiologist and serologist who was the President of the Blood Group Section of the Second International Congress of Blood Transfusion. He founded blood group inheritance with Erich von Dungern in 1910, and contributed to it greatly throughout his life. He studied ABO blood groups. In one of his studies in 1919, Hirszfeld documented the ABO blood groups and hair color of people at the Macedonian front, leading to his discovery that the hair color and blood type had no correlation. In addition to that he observed that there was a decrease of blood group A from western Europe to India and the opposite for blood group B. He hypothesized that the east-to-west blood group ratio stemmed from two blood groups consisting of mainly A or B mutating from blood group O, and mixing through migration or intermingling.
Arthur Mourant (1904–1994)
Arthur Mourant was a British hematologist and chemist. He received many awards, most notably Fellowship of the Royal Society. His work included organizing the existing data on blood group gene frequencies, and largely contributing to the genetic map of the world through his investigation of blood groups in many populations. Mourant discovered the new blood group antigens of the Lewis, Henshaw, Kell, and Rhesus systems, and analyzed the association of blood groups and various other diseases. He also focused on the biological significance of polymorphisms. His work provided the foundation for archaeogenetics because it facilitated the separation of genetic evidence for biological relationships between people. This genetic evidence was previously used for that purpose. It also provided material that could be used to appraise the theories of population genetics.
William Boyd (1903–1983)
William Boyd was an American immunochemist and biochemist who became famous for his research on the genetics of race in the 1950s. During the 1940s, Boyd and Karl O. Renkonen independently discovered that lectins react differently to various blood types, after finding that the crude extracts of the lima bean and tufted vetch agglutinated the red blood cells from blood type A but not blood types B or O. This ultimately led to the disclosure of thousands of plants that contained these proteins. In order to examine racial differences and the distribution and migration patterns of various racial groups, Boyd systematically collected and classified blood samples from around the world, leading to his discovery that blood groups are not influenced by the environment, and are inherited. In his book Genetics and the Races of Man (1950), Boyd categorized the world population into 13 distinct races, based on their different blood type profiles and his idea that human races are populations with differing alleles. One of the most abundant information sources regarding inheritable traits linked to race remains the study of blood groups. and Dense Stereo Reconstruction. Tools used include knives, brushes, and pointed trowels which assist in the removal of fossils from the earth.
To avoid contaminating the ancient DNA, specimens are handled with gloves and stored in −20 °C immediately after being unearthed. Ensuring that the fossil sample is analyzed in a lab that has not been used for other DNA analysis could prevent contamination as well. Bones are milled to a powder and treated with a solution before the polymerase chain reaction (PCR) process.
DNA preservation is difficult because the bone fossilisation degrades and DNA is chemically modified, usually by bacteria and fungi in the soil. The best time to extract DNA from a fossil is when it is freshly out of the ground as it contains six times the DNA when compared to stored bones. The temperature of extraction site also affects the amount of obtainable DNA, evident by a decrease in success rate for DNA amplification if the fossil is found in warmer regions. A drastic change of a fossil's environment also affects DNA preservation. Since excavation causes an abrupt change in the fossil's environment, it may lead to physiochemical change in the DNA molecule. Moreover, DNA preservation is also affected by other factors such as the treatment of the unearthed fossil like (e.g. washing, brushing and sun drying), pH, irradiation, the chemical composition of bone and soil, and hydrology. There are three perseveration diagenetic phases. The first phase is bacterial putrefaction, which is estimated to cause a 15-fold degradation of DNA. Phase 2 is when bone chemically degrades, mostly by depurination. The third diagenetic phase occurs after the fossil is excavated and stored, in which bone DNA degradation occurs most rapidly. One of the more common methods utilizes silica and takes advantage of polymerase chain reactions in order to collect ancient DNA from bone samples.
There are several challenges that add to the difficulty when attempting to extract ancient DNA from fossils and prepare it for analysis. DNA is continuously being split up. While the organism is alive these splits are repaired; however, once an organism has died, the DNA will begin to deteriorate without repair. This results in samples having strands of DNA measuring around 100 base pairs in length. Contamination is another significant challenge at multiple steps throughout the process. Often other DNA, such as bacterial DNA, will be present in the original sample. To avoid contamination it is necessary to take many precautions such as separate ventilation systems and workspaces for ancient DNA extraction work. The best samples to use are fresh fossils as uncareful washing can lead to mold growth. Coming to a consensus on which methods are best at mitigating challenges is also difficult due to the lack of repeatability caused by the uniqueness of specimens. The general process for extracting DNA using the silica-based method is outlined by the following: Some issues with PCR is that it requires overlapping primer pairs for ancient DNA due to the short sequences. There can also be "jumping PCR" which causes recombination during the PCR process which can make analyzing the DNA more difficult in inhomogeneous samples.
Methods of DNA analysis
DNA extracted from fossil remains is primarily sequenced using Massive parallel sequencing, which allows simultaneous amplification and sequencing of all DNA segments in a sample, even when it is highly fragmented and of low concentration. and was found to be powerful in analyses of aDNA because it avoids potential loss of sample, substrate competition for templates, and error propagation in replication.
The most common way to analyze an aDNA sequence is to compare it with a known sequence from other sources, and this could be done in different ways for different purposes.
The identity of the fossil remain can be uncovered by comparing its DNA sequence with those of known species using software such as BLASTN. Apart from that, species identification can also be done by finding specific genetic markers in an aDNA sequence. For example, the American indigenous population is characterized by specific mitochondrial RFLPs and deletions defined by Wallace et al.
aDNA comparison study can also reveal the evolutionary relationship between two species. The number of base differences between DNA of an ancient species and that of a closely related extant species can be used to estimate the divergence time of those two species from their last common ancestor.
Applications
Human archaeology
Africa
Modern humans are thought to have evolved in Africa at least 200 kya (thousand years ago), with some evidence suggesting a date of over 300 kya. Examination of mitochondrial DNA (mtDNA), Y-chromosome DNA, and X-chromosome DNA indicate that the earliest population to leave Africa consisted of approximately 1500 males and females. Genetic evidence shows that occupation of the Near East and Europe happened no earlier than 50 kya. Cavalli-Sforza's analysis of genetic-geographic patterns led him to conclude that there was a massive influx of Near Eastern populations into Europe at the start of the Neolithic. The Indian gene pool has contributions from earliest settlers, as well as West Asian and Central Asian populations from migrations no earlier than 8 kya.
Much work has been done to discover the extent of north-to-south and south-to-north migrations within Eastern Asia. Native American mtDNA haplogroups have been estimated to be between 15 and 20 kya, although there is some variation in these estimates. The Indigenous people of Australia and New Guinea are phenotypically very similar, but mtDNA has shown that this is due to convergence from living in similar conditions.
Domestication of animals
Archaeogenetics has been used to study the domestication of animals. By analyzing genetic diversity in domesticated animal populations researchers can search for genetic markers in DNA to give valuable insight about possible traits of progenitor species. These studies also reveal evidence about the details of early farmers. Genetic studies have shown that all dogs are descendants from the gray wolf, however, it is currently unknown when, where, and how many times dogs were domesticated.