Pursuing The Best Courses of Action . . .

—–Original Message—–

From: Mary M Peacock
Sent: Tuesday, October 05, 2010 11:30 AM
To: David & Carmela Kortum; ‘Helen Neville’; ‘Shannon Hurn’
Subject: RE: Alvord Phenotype SE Oregon, Museum Specimens, Strategy…

Dear Dave, Carmela, Helen and Shannon – I had gone on the Michigan site a couple of years ago and only found 4 pure Alvord samples so this 83 is a real surprise!  The online access to the fish collection is down for the moment but I will check this out.  I have additional good news I spoke with Lisa Heki at USFWS and she is willing to fund this work within a genetic monitoring program we already have set up.  I will receive an additional funding within the next couple of months. In the meantime I will request samples from the museum.  I am not sure what the best approach is to preserving the Alvord phenotypes in ***** would be other than moving them to other streams.  The genetic analysis will certainly let us know how pure these fish are.  The USFWS and Oregon Game and Fish would have to weigh in on any transplant program.

Mary M. Peacock, Ph.D.,  Associate Professor, Department of Biology, MS 314, Ecology, Evolution and Conservation Biology Graduate Program, University of Nevada, Reno – Reno, Nevada 89557

UNR - Mary Peacock - Associate Professor / Co-Director

—–Original Message—–

From: David & Carmela Kortum, Tuesday, October 05, 2010 12:36
To: ‘Mary Peacock’; ‘Helen Neville’; ‘Shannon Hurn’; ‘Markle, Douglas F – FW’; ‘Patrick Trotter’; ‘Joe Tomelleri’; ‘Richard Mayden’; ‘Casey Dillman’
Subject: RE: Alvord Phenotype SE Oregon, Museum Specimens, Strategy…

Hello Mary, and Helen, Shannon & All;

Thank you for your reply, and for the willingness to pursue activity to verify the genetic composition of the ***** Creek trout that exhibit the Alvord phenotype.

A few considerations have occurred to Carmela and I — that seem best shared with the team.  Being a bit uncertain about where to begin — please accept our apology if these items are not necessarily in order of “priority.”  They are simply “observations” that hopefully will be helpful to us all, so that we may all be similarly apprised . . .

Please know that we greatly appreciate the involvement and the important value that each team member brings to the table.


When Dr. Behnke noted these trout in 2006, he indicated that there were Alvords among the trout in ***** Creek.   Experience on the stream would indicate that the Alvord phenotypes in ***** Creek are in a minority status — perhaps about one in twenty of the trout in ***** Creek exhibit exceptional alvordensis characteristics — a somewhat higher percentage allowing for characteristics that would indicate some hybridization.  (Though hybridization would seem to be inevitable, most of the trout in ***** are, in general, identifiable as Willow/Whitehorse/Humboldtensis or as Henshawi Lahontans.  There may also be other trout types in the mix—but the Humboldtensis and Henshawi tend to dominate the system.)  If the 26 samples from 2008 were simply taken as they came up from the shocker, there may be just a few Alvord phenotypes in that mix.

It is understandable why Dr. Behnke said “Simplify, simplify, simplify” and that “genetic research can go on indefinitely because new techniques are continually being developed.  Genetic and other proposals to better characterize the ***** Creek trout can be done after a transplant is made.  There are no logical reasons that they should be a pre-requisite for a transplant.”  His thought was to secure the best of the phenotypes for translocation.   No doubt, there is wisdom in finding the most expedient solution.

It is unfortunate that the few remaining “uninhabited” streams in the Alvord Basin seem to have extreme fluctuations in flow from spring to fall, and present a rather hostile environment for the prospect of preserving and saving these trout.  If Oregon does not have a suitable fishless stream, are there streams in Nevada (or even another state) that would be suitable to receive the most promising phenotypes?   What efforts can or should be initiated to verify compatible systems — oxygen levels, temperatures, etc?

(If the habitat were more favorable, perhaps a translocation project for the most promising Alvord phenotypes could already be in the works.    . . . But, then again, perhaps ***** Creek really is the most suitable remaining habitat for these trout.  Could a resident “selective breeding” program for the Alvord phenotypes in ***** Creek work?)

The plight for the Alvord phenotypes in the ***** System is almost certainly in a more precarious state than it was four years ago when Dr. Behnke first discovered them (and suggested that a restoration project be initiated as soon as possible).  Can we afford to let more years go by without making significant progress in a restoration project?  The Alvord phenotype in the ***** System may become simply history, without expedient action.  What will it take?  Who needs to be involved?  Where is it best to go from here?


The five samples taken for TU this year were fairly selectively taken.  Even with these samples, close examination might indicate some hybridization.  Perhaps only one would seem to defy any evidence of hybridization (based on the strict characteristics determined from the Hubbs collection).  Yet these all exhibited general Alvord characteristics.

There are some Alvord phenotypes that seem optimal.  Perhaps it is possible that the alvordensis tend to spawn a bit later than typical Lahontans:  The reason this is postulated is that there were trout exhibiting the Alvord phenotype caught on July 26th that were still in “spawning shock” from the most recent spawning event.  All in all, this seems a bit late in comparison with other cutthroat species that we’ve noted spawning (including other cutthroat types in the ***** System).

Regarding specimens from Virgin Creek in the 80’s — [via Tol and French (1988), and Bartley and Gall (1991)] Patrick Trotter notes that using allozyme electrophoresis (the workhorse method at the time), they found one unique allele (absent from other cutthroat subspecies and rainbow trout).  This was a rare form of phosphoglycerate kinase-2 enzyme, Pgk-2(55), that they detected in the 1985 specimens, but not in those collected in 1986.  Perhaps some 1984 fin clips were also taken by Nevada Dept. of Wildlife?

. . . Dennis Shiozawa checked BYU’s files, and they have three fish from Virgin Creek, collected in 1985 (Pop # 1338, BYU Accession #s 56977-56979) and they may have fin clips collected in 1994 (pop# 270 BYU Accession # 95362-95365).  (. . . Would not the fin clips from 1994 most likely have been secured with ethanol?)

Additionally, there are still 83 non-hybridized specimens at the University of Michigan, Museum of Zoology (please see attached spreadsheet).  If we’re hoping to find a genetic baseline for Alvordensis, perhaps these would provide the best potential source for non-introgressed Oncorhynchus clarki alvordensis DNA material. (?)   Douglas Nelson confirmed for us that the Hubbs material (as is the case for almost all the specimens in the UMMZ collections) was originally fixed in the 10% formalin solution, and then transferred to 70% ethanol for long term storage.


As Carmela and I have attempted to communicate; it would seem that a “genetic time clock” is ticking for the remnant of Oncorhynchus clarki alvordensis in ***** Creek.  We surely don’t know how long that clock will tick.  . . . It is perhaps a bit miraculous that Alvord phenotypes still persist in ***** Creek (with the known cutthroat trout that have been introduced in the late 50’s and 60’s).

In reality, the mystery and dilemma of the Alvord phenotype in ***** Creek may be even more unique — and in some ways even more challenging — than the restoration of the California Condor, the Idaho Redfish Lake Sockeye Salmon, or other similarly endangered species.

The alvordensis in ***** Creek are where they “are not supposed to be.”   It was through transplants of trout into systems where they “are not supposed to be,” that led to the extirpation of the Alvord Cutthroat Trout; and yet it may be that similar transplants (whether by the military, or homesteaders, or even Indians) could be the “saving grace” for the Alvord Cutthroat Trout — or at least its phenotype — for future generations to experience, appreciate and enjoy.

It is with the sense of urgency that we have the possibility of preserving — virtually resurrecting — an “extinct” species of trout that we look for input and direction from all of you, who are genuine experts in the field . . .  Does the extreme minority status of the Alvord phenotypes in the system indicate the need for a greater sense of urgency?  Does the relative abundance of museum specimens change the “game plan?”   Should there be an accelerated effort to map the genome for Oncorhynchus clarki alvordensis?  It seems that it would be beneficial for all if we can come to a “consensus” on what the best next (genetic or other) activities are that should be pursued . . . and outline the plan.

Carmela and I will do what we can in terms of generating support, interest (and revenue).   WNTI and similar resources are almost certainly the optimal direction to look toward for funding, though we are also looking toward organizations that may share the interest of native trout enthusiasts and nature lovers on this subject.  Via combined efforts and shared resources, we believe that the goal of protecting, preserving and ultimately restoring the Alvord Cutthroat Trout (phenotype if not genotype) is attainable.

No doubt, whatever course is taken, it will surely require some thinking “out of the box;” and may even necessitate new scientific methodologies in order to be successful.   Perhaps we need a sound “plan B,” if we reach an impasse regarding funding.   Yet, as Dr. Behnke has stated; “the costs of extinction far outweigh the ‘costs’ of preservation.”

We look forward to hearing any additional thoughts regarding preserving and restoring the remnant alvordensis from ***** Creek (based on the 83 University of Michigan, Museum of Zoology specimens — or our concern as to the minority status of the Alvord phenotypes in ***** Creek — or any other thoughts you’d like to share).

Thank you again for your considerate interest, and your investment of time in pursuing this worthy goal.


David and Carmela Kortum

—–Original Message—–
From: Mary M Peacock
Sent: Monday, September 13, 2010 3:09 PM
To: Helen Neville; David & Carmela Kortum
Cc: Shannon Hurn
Subject: RE: Alvord Phenotype SE Oregon

Hi Dave and Carmela – Helen cced me on your email thread with her. She and I discussed some potential avenues to at least narrow down whether ***** Creek trout may be Alvords.

1. We can run the samples I have (26 from early 2000’s) and the 5 Helen sent me on hybrid loci to see if they are introgressed with rainbow trout and/or Yellowstone cutthroats.

2. Use the suite of Lahontan cutthroat trout loci we have in our lab on the (few) museum samples to look for unique variants. However I have to add that isolating DNA from museum samples is difficult at best due to the formaldehyde they were preserved in and you can not always get useful data for a lot of genetic loci.  For instance we screened 10 loci on Lahontan museum samples and were only able to use data from 4 of the loci. So it is challenging to work with museum preserved specimens.

3. Compare the ***** Creek samples to the four museum specimens to look for unique genetic variants

4. Compare the ***** Creek samples to Lahontans which have been sampled from throughout their range and possible other cutthroat trout to see how different they are.

As I had discussed with you in earlier emails there are only (few) museum preserved specimens for the entire species. This isn’t much to work with. Although I absolutely think this is worth pursuing I have no funding to do it. All of my funding is for work on Lahontans and I have a multitude of projects on them as well as a number of other non-trout and non-fish projects. As a result I have not gotten to any additional analyses specifically addressing the Alvord cutthroat trout issue for the 26 ***** Creek samples that were collected by ODFW earlier and for which I have genotypes for at 20 Lahontan cutthroat trout loci. If ODFW or Trout Unlimited or some other funding agency could provide funding to pursue this project I could take on a student to work on it but this would require a substantial investment in terms of lab costs and support for the student and/or lab technician if we went that route. We could be looking at $10-20k which would cover lab costs and a student stipend. We should work together to try and find funding for this as my lab would be the perfect place to do it as we have so much data on Lahontans already.

Mary M. Peacock, Ph.D., Associate Professor, Department of Biology, MS 314, Ecology, Evolution and Conservation Biology Graduate Program, University of Nevada, Reno – Reno, Nevada 89557

UNR - Mary Peacock, Associate Professor | Co-Director

—–Original Message—–
From: Helen Neville, Monday, September 13, 2010 10:12 AM
To: David & Carmela Kortum
Cc: Mary M Peacock; Shannon Hurn
Subject: RE: Alvord Phenotype SE Oregon

Hi Dave and Carmela,

Thanks for sending all the information and photos, I was really sad not to be able to make that adventure, so these are great to see.   The main issue in terms of who does what on genetic analyses is what markers the different labs have for either diagnostic tests (which require museum samples or other historical samples) or comparative analyses.

I don’t have a lab here so don’t do any lab work myself, so I sent the fin clips down to Mary Peacock at UNR, who has been working on the genetics of Lahontan cutthroat trout for many years and had previously analyzed some of the earlier samples Shannon sent to her.  I think her plan at this point was to run them on a set of loci we use to look at hybridization to determine their purity and see if any odd alleles pop up at those loci that might indicate the uniqueness of these fish.  She is also planning to compare these clips to samples she has from other LCT populations range-wide, including Willow Whitehorse.  This won’t demonstrate whether or not they are Alvords, as that would take some historical samples of Alvords, but would demonstrate whether or not they are highly distinctive from other LCT pops, which would be one more line of evidence.

I’m not sure what Rick has going on in his lab, in terms of the types of analyses/markers he would want to run, but I’m sure Mary could sub-sample the samples he has and send him DNA or fin clips, if he’s interested.   If he has other approaches than Marys that would add different insight, that would be great to have as well

I’ve cc’d Mary on here so she can chime in, and can get in touch with Rick, as she’s the one doing the lab work and analyses for this.

Feel free to get back to me/all with any comment/insights or further questions, and thanks for your great work and info!! Take care, Helen

Helen Neville, Ph.D., Research Scientist, Trout Unlimited, 910 W Main Street, Suite 342, Boise, ID 83702

TU - Helen Neville - Research Scientist

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!
This entry was posted in Fisheries Biology and Genetics, Observations, Progress - Reply - Response - Status. Bookmark the permalink.

One Response to Pursuing The Best Courses of Action . . .

  1. Kortum says:

    The diversity and complexity of this northern Great Basin ecosystem defies easy description… Perhaps the photo journals will convey more than just words can say: the desert is not barren.

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