Wednesday, December 18, 2013

Cutthroat genetics for the layperson

     I thought I'd give folks a rundown of the current state of affairs in the world of cutthroat trout genetics. It is a very confusing situation. I get asked by anglers a lot about where they can go to catch a cutthroat that is native or genetically pure. The answer to that question is quite complicated and involves a lot of history. The story that I'll give you has some generalities and glosses over some details but this is an endless rabbit-hole if you get bogged down in exploring every detail. You have to take this slowly, piece by piece, for it to make sense, and hopefully I can succeed in making it understandable.
     We have to start with the world as we knew it before 2007. Up to that point we understood that there were three subspecies of cutthroat trout native to Colorado: the Rio Grande, the Greenback, and the Colorado River. Their distributions are shown below:
    Credit for all the graphics in this post goes to Kevin Rogers.  In the map above, the green area is where the Greenbacks were native (east of the Continental Divide), and so on. This is a very clean and understandable distribution of subspecies, split out along drainage divides. It is important to keep in mind that especially with Greenbacks and Colorado River cutthroat, it is basically impossible to differentiate between the two in the field. Rio Grande are a little more different than the other two, but still there is a lot of visual overlap in the appearance of all three of these subspecies. So up to this point, the fish's LOCATION has been just as important as its appearance in identifying which subspecies it belongs to.
     Greenbacks were thought to be extinct until 1957, when an isolated population was found. Other remnant populations were found in 1965 and 1970. There were no stocking records in existence for the streams where these fish were found, and the best science at the time identified them as being Greenbacks, native to the Arkansas and South Platte. This led to several decades of conservation and reclamation work in the Akansas and South Platte river basins, to reestablish populations of these fish using progeny taken from these remnant populations that were found.
     So everything was moving along more or less swimmingly until 2007. A Geneticist from CU named Jessica Metcalf published a paper that rocked the world of cutthroat genetics. She used a new technique called AFLP - Associated Fragment Length Polymorphisms - to look at the genetics of our cutthroats in a higher level of detail than anyone ever had before. This is one very important thing to be aware of when trying to follow this progression: these genetic techniques are on the cutting edge of the technology that's available, so every decade or so there are new tools available that reveal things that we have never been able to see before. Here is the abstract from her paper:

Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations


Accurate assessment of species identity is fundamental for conservation biology. Using molecular markers from the mitochondrial and nuclear genomes, we discovered that many putatively native populations of greenback cutthroat trout (Oncorhynchus clarkii stomias) comprised another subspecies of cutthroat trout, Colorado River cutthroat trout (Oncorhynchus clarkii pleuriticus). The error can be explained by the introduction of Colorado River cutthroat trout throughout the native range of greenback cutthroat trout in the late 19th and early 20th centuries by fish stocking activities. Our results suggest greenback cutthroat trout within its native range is at a higher risk of extinction than ever before despite conservation activities spanning more than two decades.

     This paper identified a number of populations on the east slope that appeared to be Colorado River cutthroat when looked at with the new analysis. Up until that point our understanding was that these populations were Greenbacks. So the stories started hitting the popular media that seemingly incompetent biologists had been stocking "the wrong fish". What this paper did was redefine what the "right fish" and "wrong fish" are, and again, you can't tell by looking at them in the field.
     So here is what the situation looked like after the 2007 study:

     On this chart, the blue populations are what were referred to as "Lineage CR" - presumably Colorado River cutthroats. The green populations are "Lineage GB" - presumably greenbacks. We're now calling them Blue Lineage and Green Lineage, for reasons I'll explain below. But it was a major blow to find out that some of these east-slope populations did not appear to be Greenbacks after all. Especially Apache Creek down south - that was one of the original populations "rediscovered" when it was believed that Greenbacks were extinct.
     Now you have to start considering what happened with fish stocking historically in Colorado. In the early 1900's, many millions of eggs were harvested from Trappers Lake and stocked all over the state. At that time, a cutthroat was a cutthroat and all fish were considered the same from Yellowstone south. Distinct subspecies of the fish had not been recognized.  In fact, during a period when the Trappers Lake cutthroat population appeared to be struggling, Yellowstone cutthroat were stocked into Trappers to bolster the population. Up until that point, Trappers was the largest intact remaining population of pure Colorado River cutthroats, but once those Yellowstones went in, that was no longer the case.
    Another problem with that period in history is that for a long time we weren't aware of much in the way of stocking records. There was a "dark age" of fish stocking history in Colorado from about 1900 or so to 1950. Fish were dumped all over the place and no records were kept - apparently. However, Chris Kennedy, one of our colleagues who works for the U.S. Fish and Wildlife Service, has done a ton of spectacular historical forensics work and uncovered many old stocking records that were not previously known. Some of them were in old ledger books buried and literally forgotten in the basement of the state archives. He has pieced together a stocking history that shows that at least 26 million fish were reared and stocked from Trappers Lake all over the state, just from the years 1914-1925 (see below). This is also new information to us.

     One of the things that the 2007 study didn't really highlight is the fact that one Lineage GB population was found west of the divide, in the Gunnison Basin. You can see that one in the figure above. The presence of the Lineage CR fish east of the divide was easily explained by the new historical stocking information available to us, but there was no historical explanation for east slope fish moving west - we are not aware of that taking place on any large scale historically.
     So, in the aftermath of this study, we continued collecting genetic samples and using AFLP analysis for as many of our cutthroat populations as we could. In particular we were looking for more occurrences of Lineage GB fish popping up west of the divide. Sure enough, we found a lot of them - as illustrated here:

     In a few years' time, we had identified over 60 populations on of Lineage GB fish on the west slope. Remember that these are the fish that Metcalf's 2007 paper was treating as Greenbacks, native to the east slope. If they were native to the east slope, why would we find so many populations of these fish on the west slope? Also, here's another interesting thing: we're finding these populations all over the west slope EXCEPT for in the Yampa and White River basins (and the San Juan but that's a different story). To this day we still have not identified a single Lineage GB population from either of those drainages - everything is Lineage CR. So this has become an ever-larger question.
     Enter Chris Kennedy again with his historic investigations. He and others have also found old records of a lot of fish being raised from lakes on the Grand Mesa. In fact, from 1899-1909, we now have records that at least 29 million fish were hatched from Grand Mesa lakes and stocked all over the state, including many places on the east slope.

     So now, a new theory emerges: what if the differences that we're seeing between Lineage GB and Lineage CR fish is a difference WITHIN Colorado River cutthroats - that is, Lineage GB fish are native to the Colorado and Gunnison watersheds, and Lineage CR are native to the Yampa and White. Our historical stocking records support this theory. And if we're defining Greenback cutthroat as the fish native to the Arkansas and South Platte, then if this theory is true, Lineage GB does NOT equal Greenback. That is why we have started calling Yampa/White cutthroats "Blue Lineage" and Colorado/Gunnison cutthroats "Green Lineage", to move away from the Greenback name.

    I'm about half way through this story, so I'm going to stop it here and pick it up next week. Please be sure to let me know if you have any questions, either in the comments or by emailing me at If something is unclear to you, I guarantee you it's unclear to other people as well and I should try to do a better job explaining.

To be continued . . . 


  1. Hey Jon, Awesome article. It's great to see lots of this info laid out for people. I do have one question. With the amount of undocumented stocking, how finite are we about Metcalf's museum samples that are used as the baseline to her work? Thanks for taking the time to detail this out.

    1. Great question. The museum samples are so valuable because they were collected by explorers and surveyors BEFORE, and sometimes well before, any aquaculture of any kind was taking place in Colorado. So the possibility of the museum samples coming from fish that had been stocked or moved is nil. I'm not sure I understand your question correctly. What you may be asking about, is how sure are we of the locations where the samples were collected. I haven't seen the original documentation myself, but as far as I know these are samples that we are sure about the locations. I believe I remember hearing about other museum specimens that exist that were not used for exactly that reason - that the precise location where they had been collected was unclear. So that problem ruled out some specimens for the museum study. The fish that were used were fish that we are sure about. Hopefully that answers your question.

  2. Hi Jon. Shared this series of articles on the Facebook Page and just sent it out in the newsletter for Rocky Mountain Fly Fisher. Great information and thanks for making this available. It really helped people understand what is going on and what the situation is and isn't.
    Josh Rickard

  3. Cool, thanks Josh. Glad to hear about someone making use of it.