Ancient DNA confirms a local origin of domesticated chenopod in eastern North America

Kistler, Logan; Shapiro, Beth

doi:10.1016/j.jas.2011.08.023

Cited by 36 publications

(24 citation statements)

References 27 publications

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“…Thus, there is no longer any reason to speculate about the true ages of specimens that might have been subject to postdepositional movement in spite of lack of obvious disturbance or mixing of the strata in which they were buried. Especially when a great deal of effort will be made to extract ancient DNA from archaeological material, it is imperative to ensure that the suspected antiquity be verified, as was done by Erickson et al (2005), Kistler and Shapiro (2011), and Kistler et al (2014) during their pioneering studies of ancient Lagenaria and Chenopodium DNA.…”

Section: Refining Methods and Integrating Techniquesmentioning

confidence: 99%

Agricultural origins from the ground up: Archaeological approaches to plant domestication

Langlie

Mueller

Spengler

et al. 2014

American J of Botany

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The timing, geographical locations, causes, and consequences of crop domestication have long been major concerns of archaeologists, and agricultural origins and dispersals are currently more relevant than ever to scientists seeking solutions to elusive problems involving food insecurity and global health disparities. Perennial research issues that archaeologists continue to tackle include (1) thinking outside centers of origin that were based on limited and insufficient past knowledge; (2) distinguishing between single and multiple domestications of specific crops; (3) measuring the pace of domestication; and (4) decoupling domestication from agricultural economies. Paleoethnobotanists have expanded their toolkits to include analysis of ancient and modern DNA and have added increasingly sophisticated techniques in the field and the laboratory to derive precise chronological sequences to assess morphological changes in ancient and often fragmentary archaeobotanical remains and to correctly interpret taphonomy and context. Multiple lines of archaeological evidence are ideally brought together, and whenever possible, these are integrated with information from complementary sources. We discuss current perspectives and anthropological approaches to research that have as their goals the fuller and broader understanding of ancient farming societies, the plants that were domesticated, the landscapes that were created, and the culinary legacies that were passed on.

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Section: Refining Methods and Integrating Techniquesmentioning

confidence: 99%

Agricultural origins from the ground up: Archaeological approaches to plant domestication

Langlie

Mueller

Spengler

et al. 2014

American J of Botany

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“…Notably, the M29‐12‐2 and M29‐12‐3 samples generated endogenous rates similar to the mixed sample in both total mapping rate and unique mapping rate. In comparison with the respective mapping rates in published ancient plant samples, the high total mapping and unique mapping rates of our single‐seed samples indicated the sufficient endogenous content of DNA reads generated by current single‐seed DNA extraction and sequencing methods (Kistler and Shapiro, ; Kistler, ; Fernández et al ., ).…”

Section: Resultsmentioning

confidence: 59%

“…DNA extraction from archeological, especially paleobotanical, plant specimens and further high‐throughput sequencing have been accomplished using different protocols (Kistler and Shapiro, ; Li et al ., ; Kistler, ; Fernández et al ., ). In our case, we developed a pipeline integrating the optimized PTB ( N ‐phenacylthiazolium bromide) and guanidine hydrochloride DNA extraction from single wheat seeds and subsequent compatible whole‐genome shotgun sequencing with Illumina HiSeq X10.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic and population structural inference from genomic ancestry maintained in present‐day common wheat Chinese landraces

Ding

Zhang

et al. 2019

The Plant Journal

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Summary Hexaploid common wheat is one of the most important food crops worldwide. Common wheat domestication began in the Fertile Crescent of the Near East approximately 10 000 years ago and then spread west into Europe and eastward into East Asia and China. However, the possible spreading route into and within China is still unclear. In this study, we successfully extracted DNA from single ancient wheat seeds and sequenced the whole genome of seven ancient samples from Xiaohe and Gumugou cemeteries in Xinjiang, China. Genomic inference and morphological observation confirmed their identity as hexaploid common wheat grown in prehistoric China at least 3200 years before present (BP). Phylogenetic and admixture analyses with RNA‐seq data of modern hexaploid wheat cultivars from both China and Western countries demonstrated a close kinship of the ancient wheat to extant common wheat landraces in southwestern China. The highly similar allelic frequencies in modern landraces of the Qinghai‐Tibetan plateau with the ancient wheat support the previously suggested southwestern spreading route into highland China. A subsequent dispersal route from the Qinghai‐Tibetan plateau margins to the Yangtze valley was proposed in this study. Furthermore, the common wheat populations grown in the Middle and Lower Yangtze valley wheat zones were also proposed to be established by population admixture with the wheat grown in the Upper Yangtze valley. Our study reports ancient common wheat sequences at a genome‐wide scale, providing important information on the origin, dispersal, and genetic improvement under cultivation of present‐day wheat landraces grown in China.

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“…melanospermum and their relative 226 frequency in archaeological remains is indicative of the degree of seed selection by past cultivators (35,36). The presence of dark seeds (#15,18) in archaeological food processing places suggests the 228 prolonged use of a combination of domesticated and weed chenopod grains by past populations in Northwest Argentina (37), a feature also observed elsewhere in the Americas (36,38). 230…”

Section: Inference Of Local Demographic Historymentioning

confidence: 99%

Discontinuities in quinoa biodiversity in the dry Andes: an 18-century perspective based on allelic genotyping

Winkel

Aguirre

Arizio

et al. 2018

Preprint

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History and environment shape crop biodiversity, particularly in areas with vulnerable human 36 communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of 38 quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 40 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based 42 analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish 44Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process 46 occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries-a time of agricultural intensification well before the Inka and Spanish conquests-and then between the 13th 48 century and today-a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply 50 losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural 52 trajectories. 54

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Ancient DNA confirms a local origin of domesticated chenopod in eastern North America

Cited by 36 publications

References 27 publications

Agricultural origins from the ground up: Archaeological approaches to plant domestication

Agricultural origins from the ground up: Archaeological approaches to plant domestication

Phylogenetic and population structural inference from genomic ancestry maintained in present‐day common wheat Chinese landraces

Discontinuities in quinoa biodiversity in the dry Andes: an 18-century perspective based on allelic genotyping

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