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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

The data shown below were compiled from readership statistics for 392 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 16 4%
Germany 3 <1%
Portugal 3 <1%
Chile 2 <1%
United Kingdom 2 <1%
Brazil 2 <1%
Netherlands 2 <1%
Czechia 1 <1%
France 1 <1%
Other 7 2%
Unknown 353 90%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 123 31%
Researcher 86 22%
Student > Master 62 16%
Professor > Associate Professor 26 7%
Student > Bachelor 18 5%
Other 77 20%
Readers by discipline Count As %
Agricultural and Biological Sciences 300 77%
Biochemistry, Genetics and Molecular Biology 38 10%
Environmental Science 25 6%
Unspecified 21 5%
Computer Science 3 <1%
Other 5 1%

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
#7,104,288
of 12,354,212 outputs
Outputs from Molecular Ecology
#3,225
of 4,162 outputs
Outputs of similar age
#67,730
of 143,835 outputs
Outputs of similar age from Molecular Ecology
#19
of 45 outputs
Altmetric has tracked 12,354,212 research outputs across all sources so far. This one is in the 40th percentile – i.e., 40% of other outputs scored the same or lower than it.
So far Altmetric has tracked 4,162 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 8.7. This one is in the 19th percentile – i.e., 19% 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 143,835 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 50% of its contemporaries.
We're also able to compare this research output to 45 others from the same source and published within six weeks on either side of this one. This one is in the 46th percentile – i.e., 46% of its contemporaries scored the same or lower than it.