Ancient dna

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Ancient DNA (aDNA) is DNA isolated from ancient specimens. It can also be described as any DNA recovered from biological samples that have not been specifically preserved for future DNA analysis. Some examples include the analysis of DNA recovered from archaeological and historical material of skeletons or mummified tissues, collections or archives of medical samples, specimens from museums or historical herbaria, paleontological remains of animals or plants from the Holocene, marine and lake sediments, among others.

Unlike modern genetic analyses, ancient DNA studies are characterized by low DNA quality, which limits the scope of the analyses. Furthermore, due to the degradation of DNA molecules, a process correlated with factors such as time, temperature, and the presence of free water, exceeds the limits beyond which DNA is likely to survive.

Allentoft et al. (2012) attempted to estimate this limit by studying nuclear and mitochondrial DNA decay in Moa bones. DNA degrades exponentially. According to his model, mitochondrial DNA (mtDNA) degrades on average one base pair every 6,830,000 years at -5 °C. The decay kinetics have been measured through accelerated aging experiments where even plus the strong influence of storage temperature and humidity on DNA breakdown.

Nuclear DNA degrades twice as fast as mtDNA. As such, early studies reporting the recovery of much older DNA, for example from Cretaceous dinosaur remains, may have originated from sample contamination. As such, the first studies reporting the recovery of older DNA, for example from Cretaceous dinosaur remains, may have originated from a contaminated sample.

Reticulate DNA, 4000 years old, extracted from the liver of the ancient Egyptian priest Ankh-Nekht.

History of ancient DNA studies

The first study of what would be called aDNA was done in 1984, when Russ Higuchi and his colleagues at Berkeley reported that traces of DNA from a Quagga museum specimen not only remained in the sample more than 150 years later of the death of the individual, but they could not be extracted and sequenced.

Over the next two years, through investigations of natural and artificially mummified samples, Svante Pääbo confirmed that this phenomenon was not limited to recent museum specimens, but it appears that it can be replicated in a number of mummified human samples from thousands of years ago. However, the laborious processes required at the time to sequence DNA (via bacterial cloning) were an effective brake on the development of the field of ancient DNA.

Double amplification of the primer/primer by aDNA-PCR (jumping-PCR) can produce highly biased and inauthentic sequence artifacts. The nested PCR technique was used to overcome these deficiencies.

Single primer extension amplification (abbr. SPEX) was introduced in 2007 to address DNA damage from postmortem mutations.

Issues and bugs

DNA can contain a large number of mutations postmortem and these increase over time. Some regions of polynucleotides are more susceptible to this degradation, therefore sequencing data can evade the statistical filters used to check the validity of the information. Due to sequencing errors, great care must be taken when interpreting the size of a population. Substitutions resulting from deamination of cytosine residues are overrepresented in ancient DNA sequences. Another problem with ancient DNA samples is contamination with modern human DNA and by microbial DNA (most of which is not is old).

"Antediluvian" DNA

The post-PCR era triggered a flurry of publications from numerous research groups attempting to engage with aDNA. Recently, a series of incredible discoveries have been published, claiming that authentic DNA can be extracted from samples millions of years old, in the realm that Lindahl (1993b) called antediluvian DNA. Most of these claims were based on the recovery of DNA from organisms preserved in amber. Insects such as stingless bees (Cano et al. 1992a; Cano et al. 1992b), termites (De Salle et al. 1992; De Salle et al. 1993), wood gnats (De Salle and Grimaldi 1994), as well as plants (Poinar et al. 1993) and bacterial sequences (Cano et al. 1994) were extracted from Dominican amber from the Oligocene epoch. Older sources of weevils in coated amber from Lebanon, reportedly dating to the Cretaceous era, also produced authentic DNA (Cano et al. 1993). The recovered DNA is not limited to amber. Many preserved plant sediments dating to the Miocene have been successfully investigated (Golenberg et al. 1990; Golenberg 1991).

Later, in 1994 for international recognition, Woodward et al. reported the most exciting results to date - mitochondrial sequences of cytochromes b had apparently been extracted from dinosaur bones dating back more than 80 million years. When in 1995 two studies reported DNA sequences from a dinosaur extracted from a Cretaceous egg (An et al. 1995; Li et al. 1995), it seemed that this field would revolutionize the knowledge of the evolutionary past of the earth. Even these extraordinary years were capped off by the claimed recovery of 250-million-year-old Halobacterium sequences, extracted from Halite.

Unfortunately, a critical review of the ancient DNA literature asserted throughout the development of the field that few studies as of 2002 were successful in amplifying DNA from remains older than hundreds of thousands of years.

A greater appreciation of the risks of contamination and studies on the chemical stability of DNA from the environment have led to concerns being raised regarding the previously reported results. The dinosaur DNA turned out to be a human Y chromosome, while the encapsulated DNA reported to be from Halobacterium has been criticized due to its similarity to modern bacteria, hinting at possible contamination.

A 2007 study suggests that these bacterial DNA samples could not have survived from ancient times, instead they may be the long-term product of their low-level metabolic activity.

Ancient DNA studies

Despite the problems associated with 'antediluvian' DNA, a wide and growing range of DNA sequences have been published from a range of animal and plant taxa. Tissues examined include artificially or naturally mummified animal remains, bones (c.f. Hagelberg et al. 1989; Cooper et al. 1992; Hagelberg et al. 1994), paleofeces, alcohol-preserved specimens (Junqueira et al. 2002), rodent shell mounds, dried plants (Goloubinoff et al. 1993; Dumoulin-Lapegüe et al., 1999) and, recently, animal and plant DNA extractions directly from soil samples.

In June 2013, researchers announced that they had sequenced the DNA of a 560-780,000-year-old horse, using material taken from a leg bone found buried in frozen ground in the territory of Yukon in Canada. In 2013, a German group reconstructed the mitochondrial genome of an Ursus deningeri over 300,000 years old, showing that authentic ancient DNA can be preserved for hundreds of thousands of years outside of permafrost.

Ancient DNA studies of human remains

Due to the anthropological, archaeological, and public interest directed toward human remains, it is natural that they receive a similar amount of attention from the DNA community. Due to its obvious signs of morphological preservation, many studies use mummified tissue as a source of ancient human DNA. Examples include specimens preserved naturally, for example those preserved in ice, such as the Ötzi (Handt et al 1994.), or by rapid drying, such as mummies from the high altitudes of the Andes(Montiel et al. 2001), as well as various sources of artificially preserved tissue (such as chemically treated mummies from ancient Egypt).

However, mummified remains are a limited resource, and most studies of human aDNA have focused on extracting DNA from two sources that are far more common in the archaeological record - bones and bones. teeth. Recently, other sources have also produced DNA, including paleofeces (Poinar et al., 2001) and hair (Baker et al. 2001, Gilbert et al. 2004). Contamination remains a major problem when working with ancient human material. In November 2015, scientists reported the discovery of a 110,000-year-old fossil tooth, containing the DNA of the Denisovan hominid, an extinct species of human in the genus Homo.

ADNA analysis of pathogens and microorganisms using human remains

The use of degraded human samples in DNA analysis has not limited the amplification of human DNA. It is reasonable to assume that for a period of time post mortem the DNA of any microorganism present in the sample may survive. These include not only pathogens present at the time of death (either causing long-term infections or death), but commensals and other associated microbes. Despite several studies that have reported limited preservation of this DNA, for example, the lack of preservation of Helicobacter pylori in ethanol-preserved specimens dating back to the XVIII, more than 45 published studies report the successful recovery of ancient pathogen DNA from human samples dating back more than 5,000 years and as long as 17,000 years ago in other species. In addition to the usual sources of mummified tissue, bone and teeth, such studies have also examined a number of other tissue samples, including calcified pleura (Donoghue et al. 1998), paraffin-embedded tissue, and tissues fixed in formalin.

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