Technical Considerations (Bottlenecking / SNPs / Old DNA)

—–Original Message—–
From: Dennis Kenji Shiozawa
Sent: Monday, December 13, 2010 9:46 AM
To: ‘David & Carmela Kortum’
Subject: RE: Alvord Cutthroat Trout

David and Carmela,

Re- your question about translocated populations and their  retention of alleles – if they come from a rare (likely bottlenecked) population, the population will have a reasonable probability of being relatively homozygous … compared to a more abundant population.  How much difference you find between the parental or source population and the translocated population will likely depend on the number of fish transferred and their genetic makeup (this is another bottleneck event), and then any genetic drift that may occur in the translocated population.  We are conducting a study for the NPS and NDOW on a series of populations of Bonneville cutthroat trout and will be looking at precisely that question with one population of BCT that was established from another location.  We are planning to use microsatellites at this point (because they have been widely used), but are also considering developing SNPs to do the same.  We are about half done with the standard introgression screen so early next year we will start the microsatellite or SNPs work.  We have been discussing a next gen sequencing run to develop the SNPs, or we may just go to the literature for a more limited subset.

Dennis

BYU - Dennis Shiozawa, Professor of Integrative Biology

From: David & Carmela Kortum; Tuesday, November 23, 2010 1:58 PM

To: ‘Dennis Kenji Shiozawa’  RE: Alvord Cutthroat Trout

Dennis,

Thank you for your reply to our email and for your genetics work with preserved fish collections (and all of your work with trout genetics).

We hope, perhaps even expect, that in due time there will be methodologies developed that will provide for competent analysis of extremely antiquated specimens.  With pioneering work such as yours to help pave the way, perhaps some more significant breakthroughs are ‘just around the corner.’

Regarding the study that we are currently involved in – the primary analysis slated at this time is nuclear – though mitochondrial analysis could, perhaps, shed some light on the challenging “genetic soup” that we’re confronted with.  Both methodologies have been discussed, but nuclear seems to be on the table at the present.

…Mary Peacock (UNR) is involved in the analysis – with funding ostensibly approved – and UMMZ tissue specimens requested, or being requested.

A probable challenge with these specimens would be the temperatures at time of acquisition, and the shipping and etc. involved.  Establishing a genetic baseline for Oncorhynchus clarki alvordensis would seem to be just one of numerous challenges regarding how to truly assist this remnant population.

We greatly appreciate your input.  I’ll mention the proteinase K to Mary.  My understanding is that she has had some success in extracting useable DNA from museum specimens in the past.  Perhaps your techniques will also be helpful for this project.

One last question, regarding an aspect of this circumstance that you may, or may not, be able to answer (but it never hurts to ask):  To the best of your knowledge — regarding translocated trout populations, from specific (rare) parental stock — over a period of a few decades do the alleles tend to remain consistent – so that the “genetic baseline” will be a consistent identifier for the translocated population?

Thank you again for taking to the time to reply to our previous questions (and to the one above).  We would be glad to hear of any other developments with your work that might be germane, and please don’t hesitate to contact us with any questions or considerations.

Respectfully,

David and Carmela Kortum

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About kortumofdiscovery

Kortum of Discovery (a slight play on Lewis & Clark's Corps of Discovery) is a family team that is Affirming the Exceptional Beauty of Nature, one Adventure at a Time. With a focus toward rare and endangered species in the Great Basin and American west: discoveries, unique methodologies, and many “tall tales to tell” are continually being shared around the campfire!
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