What do we learn from ancient DNA sequencing?

- with usefulness, educational and cultural aims -

Outputs of sequencing fossil DNA, often referred to as ancient DNA (aDNA), provide a wealth of valuable information on various aspects of biology with practical benefits, of evolution and the history of species, including the human species. You will find here are some key insights giving you an overview of their significance.

Les résultats du séquen?age de l'ADN fossile, souvent appelé ADN ancien (aDNA), fournissent une mine d'informations précieuses sur divers aspects de la biologie, avec des avantages pratiques, de l'évolution et de l'histoire des espèces, y compris l'espèce humaine. Vous trouverez ici quelques éléments clés qui vous donneront une vue d'ensemble de leur importance.

Origin and human migration history:

Fossil DNA sequencing makes it possible to trace the migratory movements of ancient human populations. For example, it has revealed details of the migrations of early Homo sapiens out of Africa and their dispersal across Europe, Asia and the Americas. The unraveling of the timeline of our genetic evolution, can help us to predict how we might evolve into the future.

For example, we have learned from ancient DNA sequencing when appeared mutations and where they stand today within human populations. The ability to digest milk in adulthood is related to the persistent production of a natural specialized protein called lactase, able to split the sugar (lactose) naturally present in milk into two simple sugars. Some populations lost this ancestral evolutionary advantage and are now lactose intolerant. These human groups no longer produce lactase from adulthood. Furthermore, migration of human supports the idea that lactase persistence co-evolved with the cultural adaptation of dairying as a gene–culture coevolution process of farming of milk producing cattle. This suggests that cultural processes can change the human selective environment and thereby can affect which genotype(s) survive and reproduce.

Ancient DNA sequencing has also helped to identify direct evidence of interbreeding between Homo sapiens and other human species such as Neanderthals and Denisovans, providing insights on the genetic heritage of modern populations. Human beings, today, carry up to 4% Neanderthal DNA and these genes can influence skin pigmentation, hair and immunity. Ancient Neanderthal and Denisovan specific mutation still subsist today. Identified differences in circadian regulation genes between modern humans and ancestral ones support the idea that actual variations in human chronotypes – how easy you rise up early in the morning - come from ancient interbred between modern and ancestral human groups.

?In short, fossil DNA sequencing is a valuable window on the past, offering detailed and often surprising insights into the history of life on Earth. It fills gaps in our knowledge and answers fundamental questions about our origins and evolution.

Evolution, adaptation, genetic diversity and population structure

?Ancient DNA sequencing helps us to understand how species, including humans, have adapted over time when subjected to different environments. Such changes are attended by evolution or disappearance of organisms, or else their migration to areas where they can survive. Thus, adaptation leading to specific diet changes or to disease resistance or else to genomic reorganization can occur according to time over several thousands of years. Changes can be identified in comparison to actual organisms thanks to ancient DNA sequencing.

LinkedIn?

Domesticated cotton varieties grown in Africa, in North and South Americas are the result of natural DNA reorganization of several lineages from a common ancestor relative to time during periods of fast changes and periods of stability. These reorganizations range from local rearrangement up to doubling of the entire genome through individual chromosome duplication. Ancient genome sequencing can shed light on crop evolution and domestication of plants. Information obtained aim at varietal improvement connected with a specific area, diet or culture. The biological capacities of species are revealed, as well as the selective pressures that have shaped these changes. Results of the analyses can contribute to the creation of new varieties with specific new properties (drought resistance, earlier blooming…).

Reconstructing the history of diseases

By now, paleo-microbiologists can extract fragments of microbial DNA from centuries-old skeletons. The DNA is then reconstructed, allowing scientists to diagnose a disease hundreds or even thousands of years after the person's death. Thus, technology is changing how we view and understand our past and can help the development of novel cures.

Sequencing ancient DNA of pathogens makes possible to trace the history of infectious conditions and study their evolution. For example, the DNA of ancient bacteria responsible for plague and tuberculosis has been sequenced to understand their origins and evolution. At the

when European traders and colonists were enslaving Africans and transporting them thousands of miles to the Americas, the cruel conditions on ships allowed infections to spread rapidly. The ancient DNA analyses from the teeth of victims of time-distant outbreaks, reveal they were infected with hepatitis B virus and human B19 parvovirus. Rather than a European origin as previously thought, the researchers found that the viruses likely originated in Africa.

?Reconstructing of diseases spreading using DNA sequencing results is striking. Until recently, the European syphilis outbreak which happened just after the return of Columbus and his crew from their first trans-Atlantic voyage was referred to at the time as from the 'New World'. But at least three separate strains of Treponema pallidum, the pathogens causing syphilis, were identified in skeletons and coffins of individuals died in early-to-late 15th century. The results suggest that syphilis was already circulating in Europe before Columbus return from his maiden voyage. In fact,

‘’We know [now] that the spread of pathogens is connected to trade routes," say Schuenemann et al.

It turns out that syphilis has been re-emerging globally in the last few decades. While resistance to penicillin has not yet been identified, an increasing number of strains fail to respond to the second-line antibiotic azithromycin. Results of DNA sequencing of ancient pathogens contribute to draw a new evolutionary scheme of the pathogens from a common ancestor after the 15th century, allowing ultimately to understand from when current infections appeared. They allow developing new active antibiotic compounds against this pathogen family as well.

Human-environment interaction

By analyzing the fossil DNA of animal and plant species, scientists can reconstruct past ecosystems and understand the interactions between humans and their environment, including the impact of human activities on animal and plant populations. Results will enlighten present and future projects aiming at reducing and avoiding loss of biodiversity.

Sequencing fossil DNA makes it possible to identify and classify species that are now extinct, broadening our knowledge of past biodiversity. This includes human species such as Neanderthals and Denisovans, as well as prehistoric animals such as mammoths.