Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and Is DNA Leaching a Factor?

Abstract

In recent years, several studies have reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even in the absence of macrofossils) in order to obtain genetic "profiles" from past environments. One of the hazards associated with this approach, particularly in nonfrozen environments, is the potential for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from sediments up to 3300 years old at 2 cave sites in the North Island of New Zealand. These sites are ideal for this purpose as the presence or absence of DNA from nonindigenous fauna (such as sheep) in sediments deposited prior to European settlement can serve as an indicator of DNA movement. Additionally, these strata are well defined and dated. DNA from sheep was found in strata that also contained moa DNA, indicating that genetic material had migrated downwards. Quantitative polymerase chain reaction analyses demonstrated that the amount of sheep DNA decreased as the age of sediments increased. Our results suggest that sedimentary aDNA is unlikely to be deposited from wind-borne DNA and that physical remains of organisms or their ejecta need to have been incorporated in the sediments for their DNA to be detected. Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for.

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

“…Furthermore, subclade C has, so far, been found only among New World mammoths (27)(28)(29). This finding provides support for a local origin of the sedaDNA sequences at Stevens Village, which is compatible with previous reports that sedaDNA is not readily transported over long distances (12,13). Importantly, we obtained PCR products of the expected length from six of the 39 modern control samples using the same primers and amplification conditions as were applied to the ancient samples; the remaining control samples produced no PCR products of the expected length.…”

“…to leave its DNA traces behind in the sediments, and thus why its DNA is not expected to be found in each layer (12,13). Interestingly, mtDNA of mammoth and horse could be obtained from a single layer dated to between Ϸ10,500 and 7,600 yr BP (Fig.…”

“…Previous studies have shown that mitochondrial DNA (mtDNA) putatively derived from the feces, urine, epidermal cells, and hair of a diverse range of vertebrates may be preserved for long periods in suitable sedimentary environments, such as those in the Arctic, even in the absence of identified macrofossils (12)(13)(14)(15)(16). This so-called ''sedimentary'' ancient DNA (sedaDNA) has been shown to be of local origin (12,13,17), requiring an animal to have been physically present at the site for its DNA to be deposited (13).…”

“…This so-called ''sedimentary'' ancient DNA (sedaDNA) has been shown to be of local origin (12,13,17), requiring an animal to have been physically present at the site for its DNA to be deposited (13). Although leaching of DNA may occur between layers in nonfrozen depositional settings (13), several studies have demonstrated that this problem does not appear to affect either perennially frozen sediments (17)(18)(19)(20) or sediments frozen recently (15). Furthermore, in cases where strata have remained undisturbed, DNA extracted from modern surface sediments at localities in the Arctic and temperate regions has yielded the genetic signatures of extant fauna only (12,16), which suggests that DNA is not readily reworked from older deposits and incorporated into younger deposits.…”

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

“…Recent developments in the combined use of high-throughput sequencing 14 and metabarcoding approaches enable the assessment of the biodiversity of current ecosystems using extracellular DNA that is contained in environmental samples 15,16 . DNA from a variety of taxa, including faecal bacteria, plants and domestic mammals, has been successfully extracted and sequenced directly from natural archives (frozen soils, cave sediments and lake sediments), even in the absence of visible macrofossils [17][18][19][20][21][22][23][24][25] . The application of DNA metabarcoding to lake sediments has also proven its potential to trace past vegetation cover 22 .…”