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Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired‐end RAD sequencing

Overview of attention for article published in Molecular Ecology, February 2013
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Title
Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired‐end RAD sequencing
Published in
Molecular Ecology, February 2013
DOI 10.1111/mec.12239
Pubmed ID
Authors

Paul A. Hohenlohe, Mitch D. Day, Stephen J. Amish, Michael R. Miller, Nick Kamps‐Hughes, Matthew C. Boyer, Clint C. Muhlfeld, Fred W. Allendorf, Eric A. Johnson, Gordon Luikart

Abstract

Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300-400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 449 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 14 3%
Germany 3 <1%
Portugal 3 <1%
Netherlands 2 <1%
United Kingdom 2 <1%
France 1 <1%
Austria 1 <1%
Chile 1 <1%
Czechia 1 <1%
Other 6 1%
Unknown 415 92%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 132 29%
Researcher 97 22%
Student > Master 71 16%
Professor > Associate Professor 27 6%
Student > Doctoral Student 20 4%
Other 71 16%
Unknown 31 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 314 70%
Biochemistry, Genetics and Molecular Biology 50 11%
Environmental Science 28 6%
Earth and Planetary Sciences 3 <1%
Computer Science 3 <1%
Other 9 2%
Unknown 42 9%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 08 July 2013.
All research outputs
#15,403,045
of 24,417,958 outputs
Outputs from Molecular Ecology
#5,295
of 6,560 outputs
Outputs of similar age
#115,067
of 196,622 outputs
Outputs of similar age from Molecular Ecology
#52
of 87 outputs
Altmetric has tracked 24,417,958 research outputs across all sources so far. This one is in the 34th percentile – i.e., 34% of other outputs scored the same or lower than it.
So far Altmetric has tracked 6,560 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 11.5. This one is in the 17th percentile – i.e., 17% of its peers scored the same or lower than it.
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 196,622 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 39th percentile – i.e., 39% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 87 others from the same source and published within six weeks on either side of this one. This one is in the 39th percentile – i.e., 39% of its contemporaries scored the same or lower than it.