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Old 07-07-2014, 01:58 PM   #1
EminentJunkie
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Post REQUEST: any NGS evolutionary genomics for non-model taxa

Hello all- I'm having trouble finding papers in the realm of evolutionary biology that involve NGS techniques. I'm writing a proposal, but I need to get a sense of the state of the field in evolutionary biology that's powered by genomics and transcriptomics, and I'm mostly finding a lot of functional studies.

Thanks for any help/direction!

EJ
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Old 07-14-2014, 11:16 AM   #2
mbblack
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Try going to http://www.ncbi.nlm.nih.gov/ and searching the SRA data base with key words like "evolutionary" or "population" and you will get hits to datasets for human, bacteria, virus and others. Then, look in those datasets for the references to publications, such as this one: http://www.biomedcentral.com/content...08-9-6-r94.pdf

or this one: http://www.biomedcentral.com/content...148-10-387.pdf

A simple web search of a string like "next generation sequence evolutionary biology" will readily return many hits too, for everything from benthic invertebrates to birds and bacteria. Try different key words in place of "evolutionary biology" like "population biology", "microbial diversity", "metagenomics", or "phylogenetics" as well.

Honestly, from my simple couple of minutes searching, the sort of literature you are looking for is readily available and easily found but you just have to try different query strings to see what you get. Once you get a few recent papers, then just start using their cited literature lists.
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Old 07-14-2014, 12:00 PM   #3
jgibbons1
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These are a bit dated but should help:
http://mbe.oxfordjournals.org/content/26/12/2731.long
http://onlinelibrary.wiley.com/doi/1...nticated=false
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Old 07-15-2014, 09:24 AM   #4
SNPsaurus
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Many RAD-Seq projects have an evolutionary bent to them:

http://bfg.oxfordjournals.org/conten...6/416.abstract
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Old 07-20-2014, 02:54 PM   #5
EminentJunkie
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@mbblack you're absolutely right. My searches were misdirected and now I'm not having any problems at all. Thanks for the advice.

And SNPsaurus you're right- do you work with RADseq at all? My boss is looking to do RAD genotyping within the next 6 months.
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Old 07-20-2014, 08:00 PM   #6
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We do genotyping by sequencing as a service, but with a method we call nextRAD. I developed the original RAD-Seq, and nextRAD is our new method that uses selective priming PCR instead of restriction enzymes to pick the loci to be sequenced. It gives the same kind of data as RAD (pile-ups of reads at 10,000s of loci). Send an inquiry to me at eric@snpsaurus.com when you start thinking about the scope of the project and we can help.
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Old 07-20-2014, 08:19 PM   #7
EminentJunkie
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Oh jeez I just realized who I was talking to. Thanks for your input, I'll do that.
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