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Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico.

ABSTRACT: The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n?=?9; A.D. 800-1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n?=?5; A.D. 1200-1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speakers. The five Paquimé and Convento individuals belong to haplogroups C1c1a, C1c5, B2f and B2a which, are found in contemporary populations in North America and Mesoamerica. We report the first successfully reconstructed ancient mitogenomes from Central America, and the first genetic evidence of ancestry affinity of the ancient inhabitants of Greater Nicoya and Casas Grandes with contemporary Isthmo-Columbian and Greater Southwest populations, respectively.

SUBMITTER: Morales-Arce AY

PROVIDER: S-EPMC5741722 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico.

Morales-Arce Ana Y AY Hofman Courtney A CA Duggan Ana T AT Benfer Adam K AK Katzenberg M Anne MA McCafferty Geoffrey G Warinner Christina C

Scientific reports 20171222 1

The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput se ...[more]

PMID: 29273718

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Project description:ObjectivesArchaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis.Materials and methodsExtracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing.ResultsFull mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth.DiscussionDental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.

Project description:ContextThe COVID-19 pandemic has affected all sectors and human activities around the World.ObjectiveIn this article we present a first attempt to understand the immediate impact of COVID-19 and the sanitary measures taken by governments on farming systems in Central America and Mexico (CAM).MethodsThrough a review of information generated in these initial months of the COVID-19 pandemic (webinars, blogs, electronic publications, media) and 44 interviews with key informants across the region, we have identified the main impacts felt by different types of farming systems in the region.Results and conclusionsFrom corporate agricultural production systems, to small and medium scale entrepreneurs and smallholder subsistence farm households, all types of farming systems were impacted, more or less severely, by the different measures implemented by governments such as reduced mobility, closure of public and private venues and restrictions in borders. Larger corporate farming systems with vertical market integration and high level of control or coordination within the supply chain, and smallholder or subsistence farming systems with important focus on production for self-consumption and little external input use, were both relatively less impacted and showed greater adaptive capacity than the medium and small entrepreneurial farming systems dependent on agriculture as their primary income and with less control over the upstream and downstream parts of their supply chain. All types of farming systems implemented a series of mechanisms to cope with the COVID-19 pandemic including the development of alternative value chains, food and agricultural products delivery systems and the exponential use of digital means to communicate and maintain the viability of the different agricultural systems. Collective action and organization of farmers also proved to be an important coping mechanism that allowed some farmers to acquire inputs and deliver outputs in the context of restricted mobility, price volatility, and general uncertainty. Some features of the CAM region played an important role in mediating the impact of COVID-19 and associated sanitary measures. We identify as particularly relevant the nature of agricultural exports, the current structure of the agricultural sector, the diversified livelihood strategies of rural households, and the importance of mobility for rural livelihoods.SignificanceThe results presented focus only in the immediate effect of COVID-19 pandemic and the mechanisms implemented by farmers in the first months. Whether these impacts and response mechanisms will result in a transformation of the farming systems towards greater resilience and sustainability is still an open question.

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Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico.

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Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico.

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