Improved methods for the extraction of ancient DNA (aDNA) from museum artifacts, ice cores, archeological or paleontological sites, and next-generation sequencing technologies have spurred this field.
It is now possible to detect genetic drift, ancient population migration and interrelationships, the evolutionary history of extinct plant, animal and Homo species, and identification of phenotypic features across geographic regions.
[3] With the development of the Polymerase Chain Reaction (PCR) in 1983, scientists could study DNA samples up to approximately 100,000 years old, a limitation of the relatively short isolated fragments.
With these data we can create a distribution representing a size decay curve that enables a direct quantitative comparison of fragmentation across specimens through space and environmental conditions.
In order to separate endogenous and exogenous fractions, various methods are employed: By now many studies in different fields have led to the conclusion that present-day non-African population is the result of the diversification in several different lineages of an ancestral, well-structured, metapopulation which was the protagonist of an out-of-Africa expansion, in which it carried a subset of African genetic heritage.
[7] Besides that, in many cases ancient DNA has allowed to track historical processes which have led, in time, to the actual population genetic structure, which would have been difficult to do counting only on the analysis of present-day genomes.
Migration to new habitats, new dietary shifts (following the transition to agriculture) and building of large communities led to the exposure of humans to new conditions that ultimately resulted in biological adaptation.
Nowadays the “light skin” alleles of these genes are fixed in Europe but they reached a relatively high frequency only fairly recently (about 5000 years ago).
[7] Thus, even in the case of lactase-persistence there is a huge time delay between the onset of a new habit and the spread of the adaptive allele and so milk consumption may have been restricted to children or to lactose-reduced products.
However, it is difficult to directly correlate particular ancient genome changes to improved resistance to particular pathogens, giving the vastness and complexity of the human immune system.
For example, researchers have discovered that all strains of Yersinia pestis before 3600 years ago were lacking the ymt gene, which is essential for the pathogen to survive in the intestine of fleas.
[10] Many non-hominin vertebrates - ancient mammoth, polar bear, dog and horse - have been reconstructed through aDNA recovery from fossils and samples preserved at low temperature or high altitude.
Mammoth studies are most frequent due to the high presence of soft tissue and hair from permafrost and are used to identify the relationship and demographic changes with more recent elephants.
[1] The analysis of ancient genomes of anatomically modern humans has, in recent years, completely revolutionized our way of studying population migrations, transformation and evolution.
[1] As we do not possess ancient DNA coming from the time and the region inhabited by the original ancestors of present-day non-African population, we still know little about their structure and location.
[7] Bioethics in paleogenomics concerns ethical questions that arise in the study of ancient human remains, due to the complex relationships among scientists, governments and indigenous populations.
In fact, ancestors’ remains are usually considered legally and scientifically as “artifacts”, rather than “human subjects”, which justifies questionable behaviors and lack of engagement from communities.