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SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

Overview of attention for article published in Molecular Ecology Resources, July 2016
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  • Good Attention Score compared to outputs of the same age (71st percentile)
  • Above-average Attention Score compared to outputs of the same age and source (52nd percentile)

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7 tweeters
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1 Facebook page

Citations

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11 Dimensions

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88 Mendeley
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Title
SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate
Published in
Molecular Ecology Resources, July 2016
DOI 10.1111/1755-0998.12560
Pubmed ID
Authors

Gretchen H. Roffler, Stephen J. Amish, Seth Smith, Ted Cosart, Marty Kardos, Michael K. Schwartz, Gordon Luikart

Abstract

Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5,321 candidate adaptive genes associated with known immunological, metabolic, and growth functions in ovids and other ungulates. We selectively targeted 8,161 exons in protein-coding and nearby 5' and 3' untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (O. canadensis) exon capture data and directly from the domestic sheep genome (O. aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2,350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP-chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (LOSITAN and BayeScan), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation, and temperature, suggesting local environmental adaptation. The 3 methods demonstrated consistent support for natural selection on 9 genes with immune and disease-regulating functions (e.g., Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signaling pathways (e.g., KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP-chip genotyping using low quality samples in a non-model species. This article is protected by copyright. All rights reserved.

Twitter Demographics

The data shown below were collected from the profiles of 7 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 88 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 4 5%
Brazil 1 1%
Unknown 83 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 21 24%
Student > Ph. D. Student 21 24%
Student > Master 12 14%
Student > Doctoral Student 8 9%
Student > Bachelor 7 8%
Other 19 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 50 57%
Biochemistry, Genetics and Molecular Biology 15 17%
Unspecified 11 13%
Environmental Science 8 9%
Earth and Planetary Sciences 3 3%
Other 1 1%

Attention Score in Context

This research output has an Altmetric Attention Score of 4. 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 04 April 2017.
All research outputs
#3,182,708
of 12,543,614 outputs
Outputs from Molecular Ecology Resources
#426
of 895 outputs
Outputs of similar age
#73,463
of 261,285 outputs
Outputs of similar age from Molecular Ecology Resources
#27
of 55 outputs
Altmetric has tracked 12,543,614 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 895 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 9.0. This one has gotten more attention than average, scoring higher than 52% 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 261,285 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 71% of its contemporaries.
We're also able to compare this research output to 55 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 52% of its contemporaries.