Brief communication: DNA from early Holocene American dog

Tito, Raúl Y.; Belknap, Samuel L.; Sobolik, Kristin D.; Ingraham, Robert; Cleeland, Lauren M.; Lewis, Cecil M.

doi:10.1002/ajpa.21526

Cited by 30 publications

(17 citation statements)

References 32 publications

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“…DNA extraction was performed in a dedicated ancient DNA facility in accordance with established contamination control precautions and workflows, as previously described (28) (SI Appendix, section 2). Following decalcification and digestion, two DNA extraction methods were compared: (i) phenol-chloroform separation followed by purification and concentration using a MinElute PCR Purification kit (Qiagen) (28) and (ii) salting out followed by purification and concentration using a QIAamp DNA Mini Kit (54). For 3 of the 12 individuals, DNA extraction was performed using both methods.…”

Section: Methodsmentioning

confidence: 99%

Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc

Jeong

Ozga

Witonsky

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×-7.25×, mean 2.16×) and mitochondrial genomes (20.8×-1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.Ancient DNA | population genetics | high altitude | EGLN1 | EPAS1

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Section: Methodsmentioning

confidence: 99%

Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc

Jeong

Ozga

Witonsky

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

155

142

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“…Ideally, coprolites provide a view of how humans and microbes coevolved in response to different environments over time, including responses to both natural and cultural change. Previous molecular analyses of coprolites have been used to retrieve dietary information [12], [13]. However, the potential for retrieving ancient microbiome data is confounded by continuing microbial activity, environmental contamination, degradation and other post-depositional processes.…”

Section: Introductionmentioning

confidence: 99%

Insights from Characterizing Extinct Human Gut Microbiomes

et al. 2012

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In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.

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“…The mtDNA HVR1 PCR amplification was completed using previously established protocols (Grier et al 2013;Tito et al 2011). Agarose gels stained with ethidium bromide were used for visualization of HVR1 PCR products.…”

Section: Methodsmentioning

confidence: 99%