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Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing

Overview of attention for article published in PLoS ONE, May 2015
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (98th percentile)
  • High Attention Score compared to outputs of the same age and source (97th percentile)

Mentioned by

news
6 news outlets
blogs
2 blogs
twitter
22 tweeters
facebook
2 Facebook pages
googleplus
5 Google+ users

Citations

dimensions_citation
15 Dimensions

Readers on

mendeley
54 Mendeley
citeulike
1 CiteULike
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Title
Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing
Published in
PLoS ONE, May 2015
DOI 10.1371/journal.pone.0125344
Pubmed ID
Authors

Rick W. A. Smith, Cara Monroe, Deborah A. Bolnick

Abstract

While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 54 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 2%
United States 1 2%
Unknown 52 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 21 39%
Researcher 11 20%
Student > Master 5 9%
Student > Bachelor 4 7%
Student > Postgraduate 3 6%
Other 10 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 32 59%
Biochemistry, Genetics and Molecular Biology 12 22%
Social Sciences 3 6%
Chemistry 2 4%
Medicine and Dentistry 2 4%
Other 3 6%

Attention Score in Context

This research output has an Altmetric Attention Score of 80. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 30 April 2019.
All research outputs
#197,852
of 13,094,645 outputs
Outputs from PLoS ONE
#3,964
of 140,888 outputs
Outputs of similar age
#4,386
of 232,834 outputs
Outputs of similar age from PLoS ONE
#153
of 6,192 outputs
Altmetric has tracked 13,094,645 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 98th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 140,888 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 12.0. This one has done particularly well, scoring higher than 97% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 232,834 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 98% of its contemporaries.
We're also able to compare this research output to 6,192 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 97% of its contemporaries.