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 onset of the palaeoanthropocene in Iceland: Changes in complex natural systems

This study was financially supported by the Carnegie Trust for the Universities of Scotland, the National Science Foundation of America (through grant 1202692 ‘Comparative Island Ecodynamics in the North Atlantic’ and grant 1249313 ‘Tephra layers and early warning signals for critical transitions’) and the Leverhulme Trust (Study Abroad Fellowship to AJD).Pre-industrial human impacts on the past environment are apparent in different proxy records at different times in different places. Recognizing environmentally transformative human impacts in palaeoenvironmental archives, as opposed to natural variability, is a key challenge in understanding the nature of the transition to the Earth’s current ‘Anthropocene’ condition. Here, we consider the palaeoenvironmental record for Iceland over the past 2.5 ka, both before and after the late ninth century human settlement (landnám). The Scandinavian colonization of the island was essentially abrupt, involving thousands of people over a short period. The colonization triggered extensive changes in Icelandic ecosystems and landscapes. A volcanic ash known as the Landnám tephra was deposited over most of Iceland immediately before the settlement began. The Landnám tephra layer thus provides a uniquely precise litho-chrono-stratigraphic marker of colonization. We utilize this marker horizon as an independent definition of the effective onset of the local palaeoanthropocene (which is conceptually related to, but distinct from, the global Anthropocene). This allows us to evaluate proxy records for human impact on the Icelandic environment and to assess how and when they show transformative impact. Based on this analysis, we consider the implications for understanding and defining the Anthropocene in those areas of the Earth where such a clear independent marker of the onset of significant human impacts is lacking.PostprintPeer reviewe

A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world’s most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130–1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals