Sunday, December 29, 2013

Cutthroat genetics, part 2

     So, where we left off, our cutthroat researcher Kevin Rogers, along with others, put forth the theory that Green lineage fish represent the Colorado River cutthroats native to the Gunnison and Colorado, and Blue lineage fish are the Colorado River cutthroats native to the Yampa and White. When the new genetics information was combined with historical information, this was the theory that best explained what we were seeing.
     Now a couple of new questions arise. If this theory is true, is there any way to prove it? Also, if it is true, where does that leave the true Greenback - the fish native to the South Platte? Does it even exist  any more or is it actually extinct?
     Enter Jessica Metcalf again, and the Museum DNA project. As it turns out, a handful of early surveyors collected fish specimens from Colorado rivers and streams, spanning the period from 1856 to 1889. The specimens still exist, in places like the Smithsonian. For the first time in history, we have the technology to extract DNA from those specimens, perform the same AFLP analysis on the samples, and compare those results to today's populations. Metcalf published her findings in 2012:

Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout


Many species are threatened with extinction and efforts are underway worldwide to restore imperilled species to their native ranges. Restoration requires knowledge of species' historical diversity and distribution. For some species, many populations were extirpated or individuals moved beyond their native range before native diversity and distribution were documented, resulting in a lack of accurate information for establishing restoration goals. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native diversity and distribution for cutthroat trout in the Southern Rocky Mountains. We assembled a large archive of historical records documenting human-mediated change in the distribution of cutthroat trout (Oncorhynchus clarkii) and combined these data with phylogenetic analysis of 19th century samples from museums collected prior to trout stocking activities and contemporary DNA samples. Our study of the trout in the Southern Rocky Mountains uncovered six divergent lineages, two of which went extinct, probably in the early 20th century. A third lineage, previously declared extinct, was discovered surviving in a single stream outside of its native range. Comparison of the historical and modern distributions with stocking records revealed that the current distribution of trout largely reflects intensive stocking early in the late 19th and early 20th century from two phylogenetically and geographically distinct sources. Our documentation of recent extinctions, undescribed lineages, errors in taxonomy and dramatic range changes induced by human movement of fish underscores the importance of the historical record when developing and implementing conservation plans for threatened and endangered species.

     So, there are a few big game-changers here. First, the sentence about six divergent lineages. Remember the old traditional model that I described at the beginning of the last post, about the three ranges of Greenback, Colorado River, and Rio Grande cutthroats? That is out the window now. Gone. It has been replaced by this:

     We have six historic lineages of cutthroats that are definitely distinguishable from each other genetically. Two of them are believed to be extinct - the fish native to the Arkansas River (historically referred to as the Yellowfin), and the fish native to the San Juan - which were never named. There is only one population in the state - alas, in the world - that matches the historic Greenbacks collected from the South Platte watershed. So in the span of a few years, we've gone from thinking (erroneously) that we had a good  number of Greenback populations up and down the east slope, to now knowing that we only have one population that resembles the fish that were there originally. This is a huge setback for Greenback recovery.
     Even before this study was complete, our cutthroat researcher Kevin Rogers had the foresight a few years ago to realize that there was something important about this single unique population, and had already been working with our hatchery managers to build a captive broodstock of these fish in our hatchery system. So we have these fish in captivity to guard against something catastrophic happening to the stream where they live, such as a large fire and/or extreme flooding. 
     We're hopeful that our Durango counterpart, Jim White, will manage to find a San Juan lineage population somewhere, but there aren't many stones still unturned in his part of the state.
    Notice that we're being careful not to call them subspecies. This whole issue is a perfect example of the quesiton of how exactly to define a subspecies. Geographic separation is the most commonly stated element defining subspecies. But are these subspecies or strains? Ultimately, these questions are up to the US Fish and Wildlife Service, because they are the entity that determines what populations warrant protection under the Endangered Species Act. The jury is still out on that but we are expecting some direction soon.
     Another question that arises, and one that certain sectors of the angling public definitely ask is, who cares? Why does this matter? Well, to some people it doesn't matter. But, if we've got populations of fish that are unique in the world and are still persisting in the drainages that they have lived in since the last ice age, isn't that valuable? If we are doing things that are leading to the extirpation of some or all of those populations, shouldn't we do everything we can to reverse those declines that we caused? For me, the answer to both of those questions is an emphatic "Yes."
     I'll wrap it up with a nice shot (taken by Kevin Rogers) of a fish from one of my native populations. This is a population Green lineage fish, in the Colorado River basin, that does not carry a Grand Mesa haplotype - which means that we have every reason to believe that this is the aboriginal fish, occupying this stream successfully since long before our time. There aren't very many of those populations, and everything I do in terms of cutthroat conservation from here going forward will radiate out from these fish in this stream.
     Thus ends the first year of this blog, and I'm happy with the level of success. We'll end up at right about 16,000 views for the year, which may not sound like a lot but I wasn't as consistent as I could have been so I'm happy with that. The whole purpose of this is to do a better job conveying information to the folks I work for (you) and so please be sure to let me know of any topics you'd like to see me cover, either in the comments or via email at Here's to a good 2014.

1 comment:

  1. Good read.
    Glad to see restoration for these fish being done near my house on Bear Creek.