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The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human

Overview of attention for article published in BMC Genetics, January 2012
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (87th percentile)

Mentioned by

blogs
1 blog
twitter
4 tweeters

Citations

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27 Dimensions

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45 Mendeley
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2 CiteULike
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Title
The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human
Published in
BMC Genetics, January 2012
DOI 10.1186/1471-2156-13-52
Pubmed ID
Authors

Qiaoping Yuan, Zhifeng Zhou, Stephen G Lindell, J Higley, Betsy Ferguson, Robert C Thompson, Juan F Lopez, Stephen J Suomi, Basel Baghal, Maggie Baker, Deborah C Mash, Christina S Barr, David Goldman

Abstract

As a model organism in biomedicine, the rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate. Although a draft genome sequence was completed in 2007, there has been no systematic genome-wide comparison of genetic variation of this species to humans. Comparative analysis of functional and nonfunctional diversity in this highly abundant and adaptable non-human primate could inform its use as a model for human biology, and could reveal how variation in population history and size alters patterns and levels of sequence variation in primates. We sequenced the mRNA transcriptome and H3K4me3-marked DNA regions in hippocampus from 14 humans and 14 rhesus macaques. Using equivalent methodology and sampling spaces, we identified 462,802 macaque SNPs, most of which were novel and disproportionately located in the functionally important genomic regions we had targeted in the sequencing. At least one SNP was identified in each of 16,797 annotated macaque genes. Accuracy of macaque SNP identification was conservatively estimated to be >90%. Comparative analyses using SNPs equivalently identified in the two species revealed that rhesus macaque has approximately three times higher SNP density and average nucleotide diversity as compared to the human. Based on this level of diversity, the effective population size of the rhesus macaque is approximately 80,000 which contrasts with an effective population size of less than 10,000 for humans. Across five categories of genomic regions, intergenic regions had the highest SNP density and average nucleotide diversity and CDS (coding sequences) the lowest, in both humans and macaques. Although there are more coding SNPs (cSNPs) per individual in macaques than in humans, the ratio of dN/dS is significantly lower in the macaque. Furthermore, the number of damaging nonsynonymous cSNPs (have damaging effects on protein functions from PolyPhen-2 prediction) in the macaque is more closely equivalent to that of the human. This large panel of newly identified macaque SNPs enriched for functionally significant regions considerably expands our knowledge of genetic variation in the rhesus macaque. Comparative analysis reveals that this widespread, highly adaptable species is approximately three times as diverse as the human but more closely equivalent in damaging variation.

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 45 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 7%
France 1 2%
Unknown 41 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 33%
Researcher 14 31%
Student > Master 4 9%
Student > Bachelor 3 7%
Student > Doctoral Student 2 4%
Other 5 11%
Unknown 2 4%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 49%
Biochemistry, Genetics and Molecular Biology 10 22%
Environmental Science 2 4%
Neuroscience 2 4%
Medicine and Dentistry 2 4%
Other 7 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 10. 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 27 February 2013.
All research outputs
#1,971,815
of 15,748,907 outputs
Outputs from BMC Genetics
#83
of 978 outputs
Outputs of similar age
#15,581
of 127,497 outputs
Outputs of similar age from BMC Genetics
#1
of 1 outputs
Altmetric has tracked 15,748,907 research outputs across all sources so far. Compared to these this one has done well and is in the 87th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 978 research outputs from this source. They receive a mean Attention Score of 3.8. This one has done particularly well, scoring higher than 91% 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 127,497 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 87% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them