Ancient plant DNA in archaeobotany

Plant diaspores, tissues and wood are preserved in natural and anthropogenic sediments. Also, over the past centuries, plants have been collected in herbaria. These plant remains carry macroscopic and molecular information, making them a rich source for reconstructing past plant use, agriculture, diet or vegetation—they are thus proxies for past economies, ecology, migrations or trade. This article focuses on the application of ancient DNA analyses from plants excavated at Holocene archaeological sites. A short methodological section is added to illustrate possibilities and limitations of ancient DNA research in plant

Ancient DNA in Archaeologically Charred Zea Mays L: Prospects and Limitations

Plant remains are an integral part of any archaeological investigation given the large role they play in ancient subsistence economies, medicinal practices, technologies and folklore. However, despite new developments in ancient genetics, research in plant ancient DNA (aDNA) is a relatively young and untouched discipline accounting for less than 7% of all aDNA analyses published in academic literature. As a result, paleoethnobotanists, archaeologists and geneticists have not understood the feasibility and limitations of each other’s field. Few are aware that DNA extraction from charred plant remains is rare and without any kind of standard or working protocol. The possibilities of retrieving aDNA from charred Zea mays L. is considered in this study using modern maize for polymerase chain reaction (PCR) optimization and combining purification methods on ancient samples (1150-1250 AD), resolving the question of whether or not archaeologically charred plants are a viable source for genetic material. The confirmed positive results generate questions about the added-value of maize and how knowledge of genetic attributes can contribute to the growing field of archaeology and ethnobiology while demonstrating the value of these findings as they pertain to the treatment of charred floral remains by archaeologists and First Nation communities

The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains

The majority of archaeological plant material is preserved in a charred state. Obtaining reliable ancient DNA data from these remains has presented challenges due to high rates of nucleotide damage, short DNA fragment lengths, low endogenous DNA content and the potential for modern contamination. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three different laboratories, presenting the largest HTS assessment of charred archaeobotanical specimens to date. Rigorous analysis of our data-excluding false-positives due to background contamination or incorrect index assignments-indicated a lack of endogenous DNA in nearly all samples, except for one lightly-charred maize cob. Even with target enrichment, this sample failed to yield adequate data required to address fundamental questions in archaeology and biology. We further reanalysed part of an existing dataset on charred plant material, and found all purported endogenous DNA sequences were likely to be spurious. We suggest these technologies are not suitable for use with charred archaeobotanicals and urge great caution when interpreting data obtained by HTS of these remains

The ancient DNA and archaeobotanical analysis suggest cultivation of Triticum aestivum subsp. spelta at Yumuktepe and Yenikapı Pottery Neolithic sites in Turkey

Archaeobotanical materials subject to aDNA analysis were recovered from Yumuktepe and Yenikapı, two important archaeological sites in Anatolia and date back to the Pottery Neolithic Period i.e., 7th millennium BC. Many charred ancient seeds representing various cereal species including a great number of wheat grains were documented in mentioned sites. Among the cereal seeds, charred wheat samples were tentatively identified as Triticum aestivum subsp. spelta L. or Triticum new glume wheat (NGW) or atypical emmer or naked wheat in Yumuktepe and Yenikapı showed similarities with the morphological characteristics of T. aestivum subsp. spelta wheat, but it was difficult to reach a firm conclusion. This study aimed to provide genetic data to enable more precise identification of charred wheat seeds using an ancient DNA (aDNA) approach. aDNAs were successfully extracted from the representative charred seeds of T. aestivum subsp. spelta or NGW or atypical emmer or naked wheat. The PCR amplification of 26SrDNA and IGS gene regions with aDNA was carried out and sequenced. The expected product sizes of IGS 158 bp for the D genome and 87 bp for the A or B genomes and DNA sequence comparisons with other wheat species revealed that T. aestivum subsp. spelta or NGW or atypical emmer or naked wheat samples included the D genome from Aegilops tauschii and is more likely to be T. aestivum subsp. spelta. The discovery of T. aestivum subsp. spelta grains in the Yenikapı and Yumuktepe suggest that the cultivation of hexaploid wheat was widespread. Further, spelta hulled wheat, which is the progenitor of the hexaploid wheat, might have been cultivated in these settlements. © 2022, The Author(s), under exclusive licence to Springer Nature B.V

Novel substrates as sources of ancient DNA: : prospects and hurdles

Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively “novel”. Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized

In the human past, is the perennial consumption of starch a deep or shallow phenomenon?

In the human past, is the perennial consumption of starch a deep or a shallow phenomenon? Recent research has argued that digestible carbohydrates, rather than just meat, were necessary to accommodate the metabolic demands of the evolving human brain. This argument is supported by genetic and biological evidence that Homo sapiens was especially adapted to a starch diet within the Palaeolithic, making starch consumption a deep phenomenon. Yet there is no deep time archaeological evidence of starch consumption by early humans. A significant body of evidence attests to the increasing starch diet of humans from the Upper Palaeolithic, through the advent of agriculture into the present day where cereals represent 70% of worlds energy intake. Without archaeological evidence of regular early human starch consumption, this appears to be a shallow phenomenon on the timescale of human evolution. Based on botanical evidence from Klasies River and Blombos Caves, among the earliest human Middle Stone Age (MSA) occupation sites of South Africa, this thesis makes three key arguments: firstly that cooked roots and tubers provided a high quality starch diet for MSA hunter-gatherers from at least 120 thousand years ago in the Cape region; secondly, that pounded, cooked tuber remains and mixed plant food ‘recipes’ from two hearths (85 kya and 81 kya) at Blombos Cave represent a consistent subsistence strategy through climatic change, one hearth dating to a warm interglacial cycle and the other to a very cold glacial cycle; thirdly, that cooking and processing roots and tubers represent a dietary mainstay for MSA hunter-gatherers in this region for at least the 55 ky span of the hearths sampled. The collection and analysis of these data involved an innovative extension of method to overcome difficult preservation conditions. The analysis also benefited from the creation of a regional parenchyma modern reference collection and co-operation with geoarchaeologists to understand the micro-context of each hearth, especially at Klasies River. Combined these method extensions have provided better quality data analysis. This research offers evidence of the earliest yet known evidence of early human consumption of cooked and processed starchy plants from the MSA of the Cape coast of South Africa. The findings conclude with the hypothesis that perennial starch consumption is a deep phenomenon in the evolution of Homo sapiens. The further question must be: How deep is the phenomenon in the ancestors of Homo sapiens?The PhD was fully funded by the Arts and Humanities Research Council. The fieldwork was funding by RCUK and Jesus College Fieldwork Fund

Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains

Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities