Genetic Facts should not be Overlooked in Pursuit of the Truth


For decades now, genetic science has continuously been breaking new ground regarding the ability to identify specific trout species and their ancestral lineages.

Though we are currently still without the ultimate identifiers that would tell the story of the Alvord cutthroat trout and their history, we are not entirely without clues and genetic facts that should give us pause for thought, and some clear understanding, where the trout from Guano Creek are concerned.

These clues infer a genuine prospect where Alvord cutthroat trout origins are concerned; and they irrefutably tell the story of what these rare trout are not.


No one knew more about alvordensis than Dr. Behnke.  From verifying the meristic characteristics of alvordensis; researching many historical records about these trout; and foraying into native alvordensis habitat in the search for any remnant of the trout – few researchers challenged Dr. Behnke’s knowledge and claims on the subject.

Yet over these years we have experienced a range of responses from personnel within ODFW regarding these trout and Dr. Behnke’s declaration that phenotypical alvordensis were present in this stream . . .

Some assert “this phenotype” is found in several Alvord Basin streams: “There are other populations of alvordensis hybrids in the Alvord Basin that display this phenotype . . . .   Alvord Basin streams do not have special angling regulations to protect the LCT x rainbow hybrids.”

(Please note that they state “LCT”/Lahontan cutthroat trout rather than mention Alvord cutthroat trout, and they reference hybridization with rainbows; not hybridization among divergent strains of cutthroat trout – as has been the case within Guano Creek.)

And other biologists have been prone to deny the existence of Alvord phenotypes in any stream, including Guano Creek: Their thought is that the hybridization in this stream is simply LCT x rainbow hybrids, and that there is no “mystery” or any hint that trout were ever translocated here – except for those in ODFW’s records.

Though ODFW’s own sampling projects have not produced palpable rainbows in Guano Creek; their opinion is that Guano Creek was originally a redband trout stream, connected to Catlow Lake.  Waterfall stretches in the canyon, and a marsh deemed to be impassible, might contest that claim; yet these barriers may not always have been so formidable . . .

It is possible Guano Creek was the farthest southern stream with Catlow redband trout.

Yet, whatever the ancient historical aspect of the stream may have been, we should not let that affect our thinking such as to deny contemporary reality.


We’ve tried, but we have not found Alvord phenotypes – anyplace – except in this one stream. We have fished the Trout Creek system to its headwaters, and found solid rainbow strain trout – with no visible expression of alvordensis.

However, there have been trout in Guano Creek that have clearly expressed the phenotype of the Alvord cutthroat trout.

And now, there is specific genetic information that may constrain the opinions that have been so common regarding these trout and their adoptive stream that Dr. Behnke identified as a their surrogate home.


We’ve asked a few questions regarding origins of the Alvord cutthroat trout in Questions from the Pluvial Past.  And we’ve seen evidence that boils down to few possibilities in The End of the Innocence or the Beginning of an Answer?

Without the answers to be finally provided by genetic analysis of the Alvord cutthroat trout specimens at the University Of Michigan Museum Of Zoology we are still in that dilemma.  Yet recent analysis by Victoria L. Pritchard, John Carlos Garza and Mary Peacock of the University of Nevada, Reno may shed light regarding the limited prospects and possibilities of alvordensis origins.

(I find it amazing that this brief article was evidently in peer review for nearly a full year, before it was finally accepted and recently released.)

For those of you with access to technical articles via Springer Link, it may be possible to download a copy of this Conservation Genetics article, located at:

Conservation Genetics: SNPs reveal previously undocumented non-native introgression within threatened trout populations DOI 10.1007/s10592-015-0712-6


The Abstract (thesis) deals with the prospect of introgression into native trout taxa from: “rainbow trout (Oncorhynchus mykiss) and cutthroat trout of the Yellowstone evolutionary lineage (O. clarkii subspp.)”

The Introduction states: “Introgressive hybridization as a result of anthropogenic movement of taxa is a threat to many species of conservation concern.  Ongoing interbreeding between native and non-native individuals can replace a pure population with a hybrid swarm (Allendorf et al. 2012).  Even small amounts of non-native genetic material might increase the extirpation risk of a population via outbreeding depression (Edmands 2007).”

. . .

Of course, we all know that to be true . . . . This is what led to the extirpation of the Alvord cutthroat trout from Trout Creek Oregon and Virgin Creek Nevada.

. . .

The article goes on to state that all strains of cutthroat trout are fully inter-fertile with other Oncorhynchus (rainbow) trout. And the article states that “Historically, cutthroat trout from the Alvord Basin may have been transplanted to Guano Creek, Oregon (Behnke 2007). Hence, this stream may hold a remnant of this ‘extinct’ lineage; however it has also received Lahontan cutthroat trout from at least two other locations (ODFW 2005). Conversely, Lahontan cutthroat trout from the neighbouring Coyote Lake sub-basin were transplanted into fishless streams in the Alvord Basin in the late twentieth century (Peacock et al. 2011).”

I applaud the intellectual honesty here; that there is acknowledgement of Dr. Behnke’s thoughtful conclusion that Alvord cutthroat trout were transplanted from Trout Creek to Guano Creek, and acknowledgement that (at least some of) the streams that Coyote Lake sub-basin (Willow/Whitehorse Cr.) trout were transplanted into were not really fishless.

. . .

At the conclusion of the Abstract, it notes that of 33 waters tested for specific Yellowstone cutthroat trout markers, three of the test populations “contained much genetic material of the Yellowstone lineage. This included one population proposed to be a remnant of an extinct cutthroat trout lineage.

This article also describes the challenges in identifying trout that may be recipients of what is tantamount to a hybrid-swarm from multiple sources, and then goes on to summarize:

“Our study had three aims: (i) to examine whether results from SNPs were congruent with those from other genetic markers; (ii) to examine whether historical introductions of Yellowstone cutthroat trout or related subspecies threaten the genetic integrity of Lahontan cutthroat trout populations; and (iii) to further investigate the putative ‘Alvord cutthroat trout’ remnant population in Guano Creek.


“Three populations were inferred to contain genetic material from the Yellowstone lineage: Three Mile, Little McCoy, and Guano Creeks (Table 1; Fig. 1). Yellowstone cutthroat trout mtDNA was documented in Three Mile Creek in 1985 (Sevon et al. 1999). Subsequent genetic analyses, investigating introgression from rainbow trout only, identified the population as ‘pure’ Lahontan, however we recently questioned this classification (Sevon et al. 1999; Pritchard et al. 2013). The Little McCoy Creek population in the Alvord Basin was founded in 1980 by a transplant from Willow Creek in the Coyote Lake Subbasin (Peacock et al. 2011). We found no evidence of Yellowstone lineage alleles within Willow Creek, nor within adjacent Alvord Basin populations, most of which were established in the same year from the same source population. This suggests either the existence of a trout population in Little McCoy Creek prior to transplantation, or a subsequent introduction. The presence of non-Lahontan genetic material in Little McCoy Creek may explain the elevated microsatellite diversity previously observed in pooled Alvord Basin transplant populations when compared with pooled Coyote Basin source populations (Peacock et al. 2011).”

Guano Creek, suggested to harbour a remnant population of ‘Alvord cutthroat trout’, contained a large amount of genetic material from the Yellowstone lineage. This is most likely the result of undocumented Yellowstone cutthroat trout stocking. Nevertheless, we note that only two of our markers discriminate Yellowstone cutthroat trout from other members of the Yellowstone lineage. It follows that an evolutionary origin of ‘Alvord cutthroat trout’ within the Yellowstone rather than the Lahontan lineage would cause remnant Alvord genotypes, such as those proposed to be present in Guano Creek, and possibly also present in Little McCoy Creek, to assign to the Yellowstone cluster in the STRUCTURE analysis. Such an evolutionary affiliation appears unlikely, as trout in the neighbouring Coyote sub-basin are of Lahontan lineage and the two basins were intermittently connected during the Pleistocene (Carter et al. 2006). However, it has been suggested that the Coyote sub-basin populations are themselves transplants (Peacock and Kirchoff 2007). Genetic analysis of Alvord Basin museum samples and remnant hybridized cutthroat trout populations present there would further illuminate this issue.”


Again — the intellectual honesty extant in this brief article is greatly appreciated.

Admittedly, there are aspects regarding the Alvord cutthroat trout that we do not know at this time.  And admittedly; there are aspects regarding the history of Guano Creek – and the trout there that are there, and how they got there, that we do not know at this time.

This article either presents the “smoking gun” indicating the heredity of the Alvord cutthroat trout — or else it “drives the nails in the coffin” regarding the prospect that there were usable Alvord cutthroat trout phenotypes that could have been saved and perpetuated from this small stream in SE Oregon.

Ultimately, there is only one way to settle dispute and verify either side of the question.


Embedded below are illustrations from the study results revealed in the article, showing Lahontan genetics, Rainbow genetics, and Yellowstone genetics, for 33 waters analyzed:

RT-YCT-LCT Charts“Fig. 1 Proportion of ancestry from the three reference populations, as estimated for each test individual using STRUCTURE. Test populations are ordered by Geographical Management Unit (GMU): a Eastern GMU; b Northwestern GMU including Coyote Lake Basin, and Guano Creek; c Western GMU. LCT Lahontan cutthroat trout, YCT Yellowstone lineage, RT rainbow trout.”

There are striking observations that the article notes from these results. “All but one of the 28 populations previously classified as pure Lahontan cutthroat trout were inferred to be free of rainbow trout ancestry in our new analysis.” (Exception: Cascade Lake)

The preponderant strain of trout in Guano Creek is Yellowstone cutthroat trout heritage. There are not sufficient Rainbow SNP’s in the mix of genetics for the trout from Guano Creek to yield perceptible rainbow characteristics.

Of course, this would explain why the trout samplings ODFW has undertaken since 1992 have not yielded any discernible rainbow characteristics.  And, this could also validate Dr. Behnke’s conclusion that there was already a well-established cutthroat population in the creek before the introduction of other trout by ODFW began.


There are only a couple of choices here.

• Either Alvord cutthroat trout were adapted as a sub-species from early Yellowstone cutthroat trout heritage . . .

• Or, Yellowstone cutthroat trout were transplanted to this basin at a very early date.

Though we have seen trout in Guano Creek that seemed to “shout” that they were Yellowstone cutts: there have also been trout that seem to defy explanation; other than that they were of Alvord cutthroat trout heritage.

It is extremely odd that ODFW would conclude that the trout that were propagated from Guano Creek parents were rainbow hybrids, when there are not enough rainbow alleles in the population to reproduce rainbow characteristics. The study reveals that the Guano Creek trout are comprised of 52% Yellowstone ancestry, 45% of Lahontan ancestry, and just 3% Rainbow ancestry.

Perhaps I should add that the specimens an ODFW biologist extracted from the stream in 2008, that were used for this study, were a broad, comprehensive, indiscriminate mix; i.e. an objective cross-range of trout from this stream that would provide an accurate analysis or summation of what the trout in this stream are comprised of.

The conclusion, and the whole outcome, from the Alvord phenotype hatchery propagation project seems very anomalous indeed, since the parents would have likely been from 97% cutthroat lineage.


There are other reasons that I suspect that alvordensis may have been derived from very early strains of Yellowstone cutthroat trout. But there are too many unanswered questions that pervade this subject — and that need to be answered — before any genuine, ultimate, conclusion can be drawn.


As was alluded in the last post: regarding any issue, our belief or unbelief- often shapes our actions.  If we believe Alvord phenotypes still exists in Guano Creek, then our actions will be to preserve the phenotypes at all costs.  However if we do not believe the possibility then it becomes easy to dismiss these trout or their progeny as just being rainbow hybrids.

If Dr. Behnke is correct — that what remains of the Alvord genetic legacy is found in this small stream — then these trout should have been safeguarded with care.

Interestingly, Little McCoy Creek is in the native Alvord cutthroat trout range.   It does cause one to wonder if there were not a remnant of alvordensis that had survived up until the stocking of these east-side Steens Mountain streams . . .  Little McCoy Creek is not a stream that would have seemed to have been a ‘first choice’ for a Yellowstone introduction.

Of Three Mile Creek, Quinn River System, Nevada — it should have indigenous Humboldt cutthroat trout. Yet it is interesting to note that it is about the same distance to this stream from Virgin Creek, as Guano Creek is from Trout Creek.  In fact, Three Mile may be even closer to Trout Creek than Guano Creek itself is.


All of the above stated; it is equally true that Yellowstone cutthroat trout were distributed across the west by assorted methods of transportation.  Although these are some of the most remote streams and basins in the country, it is within the realm of possibility that Yellowstone cutts found their way to these isolated range-land streams.

There is one element of scientific recourse that is yet to be accomplished in order to answer the unanswered questions . . . .   And to be a determining factor regarding future activity where the Alvord cutthroat trout is concerned.

That one element of scientific recourse, as stated in the analysis by Victoria L. Pritchard, John Carlos Garza and Mary Peacock, is that “Genetic analysis of Alvord Basin museum samples and remnant hybridized cutthroat trout populations present there would further illuminate this issue.


It seems unclear whether a “remnant hybridized cutthroat trout population” will persist in Guano Creek – through the throes of this devastating drought that has affected SE Oregon and several other western states . . .

For this author, it truly seems that the darkest hour has come with the loss of the Guano Creek hatchery progeny and the devastating drought affecting this stream, and the entire region of SE Oregon and beyond.

Though I am hoping & seeking any miracle to put the wind back into the alvordensis sails.

. . .

Surely, it has become hyper-imperative to find the means to perform genetic analysis of the Alvord cutthroat trout specimens at the University Of Michigan Museum Of Zoology  in order to prevent any further loss of the prospect for revival of any remnant population of alvordensis and finally have answers for questions that otherwise cannot be ascertained.

. . .

© Kortum of Discovery, May 2015

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 ***** Creek Sampling, Fisheries Biology and Genetics, Observations, Progress - Reply - Response - Status and tagged , , . Bookmark the permalink.

1 Response to Genetic Facts should not be Overlooked in Pursuit of the Truth

  1. Rick Haley says:

    Dear Kortum of Discovery – I have followed this topic only at a distance and sporadically, and do not know the **** Creek system other than looking at a map despite having probably been close by it in the 70s (when I was a fisheries student at OSU, ironically). I did have some correspondence with Dr. Behnke years ago, calling his attention to a post elsewhere that he probably had already seen. Is there no chance of the survival of the phenotype downstream of the area that dried up? This has been a difficult topic all along and I appreciate your attention to it.

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