Color variations in brook and brown trout

[troutbert]

Has anyone seen any genetics studies regarding heritage strains versus hatchery genetics etc. of the wild brook trout in PA?

If so, please post the links or other information on those studies.

I have read these sorts of studies about brook trout in New York state and in the southern Appalachians, but never about brook trout in PA.

I went to a presentation by a Penn State Phd candidate who studied brook trout genetics, but the study did not deal with the heritage strain topic. And when asked about that, the researcher said that they did not know.

 

[troutbert]

How far upstream did brook trout retreat at the worst point after the landscape was logged?

When was that worst point? Immediately after logging? A year or two later? 5 years later? More?

And how would the brookie distribution at the worst point compare to the situation today, in freestone watersheds like Kettle Creek, or Pine Creek or Driftwood Branch Sinnemahoning?

From the book Vanishing Trout you get the idea that the brook trout retreated from the big water, i.e. the middle and downstream areas of streams like the Loyalsock.

But the author fished in the period from roughly the 1880s through the 1920s and he never gave any indication that the brookies were ever gone from the smaller streams.

 

[salmonoid]

troutbert wrote:
How far upstream did brook trout retreat at the worst point after the landscape was logged?

When was that worst point? Immediately after logging? A year or two later? 5 years later? More?

And how would the brookie distribution at the worst point compare to the situation today, in freestone watersheds like Kettle Creek, or Pine Creek or Driftwood Branch Sinnemahoning?

From the book Vanishing Trout you get the idea that the brook trout retreated from the big water, i.e. the middle and downstream areas of streams like the Loyalsock.

But the author fished in the period from roughly the 1880s through the 1920s and he never gave any indication that the brookies were ever gone from the smaller streams.

I would say that logging would have an immediate affect on warming the water, since the shading tree canopy was gone. But given how cool some of our forested streams are now, this might not have had immediate deterimental impact to the fishery. The time period 2-20 years after logging ceased in an area would be where I would see the major changes occurring. That would be the time for the greatest risk of fire, mass wasting of hillsides that are devoid of trees holding them together, increased runoff and erosion, and stream scouring events. Interesting side-thought is I wonder how the streams changed with the sudden influx of woody debris. Maybe this help offset all of the other potentially negative changes?

I can find little about PA genetic studies on brookies. There are a few theses but they cover only a handful of streams. NJ has a study for their state, but this seems like it would be an open area of research for PA.

 

[pcray1231]

How far upstream did brook trout retreat at the worst point after the landscape was logged?

It's very difficult to tell because records of small wild populations were not well kept at the time.

My best understanding is that in areas that were logged, the devastation was nearly "complete". Meaning, yes, most streams were wiped out at one point or another.

That said, it's important to note that the logging is not a single event, but rather progressed over a period of 30-40 years in a patchwork fashion. Imagine stream A and stream B, and they can be fairly close to one another. As stream A is being wiped out, stream B hasn't been touched yet. By the time they get to stream B, stream A is already recovering to some degree.

That's my mental image anyway. So it's not that they "retreat to the headwaters". But rather that as streams undergo fast changes, many fish die, and others leave. Those that leave may mix with other, still unaffected populations, where they probably were in too low a number to have much significant mixing effects. But some find a nearby empty stream which is once again capable of holding them, and re-seed it. Do this over and over with streams C, D, E, F, etc., and you just end up with once semi-unique populations mixing atogether and losing their uniqueness.

But between whole watersheds, less mixing. So afterward, Slate and Cedar runs may not have genetically unique populations anymore, but rather a combined genetic makeup of nearby populations. But the new mutt "strain" is still pretty unique from, say, brookies in the Allegheny drainage.

If you were to look for a genetically "pure" strain, in northern PA, you'd likely look for a pocket of virgin timber and a stream well isolated. SE PA may be a better place to look, as development was more gradual before the industrial age, and streams may not have been wiped clean. And limestoners, of course, where near their sources any warming and/or siltation issues are substantially diminished and populations may have survived just about anything.

 

[troutbert]

pcray1231 wrote:

My best understanding is that in areas that were logged, the devastation was nearly "complete". Meaning, yes, most streams were wiped out at one point or another.

What is that based on? Why do you think so? It's an interesting hypothesis, but is there any support for it?

 

[KenU]

In the Vanishing Trout, Charles Lose describes brook trout fishing just after the turn of the 20th Century. He describes how he and his Uncle caught brookies in the Loyalsock up to 20 inches in length. Kettle Creek and Sinnemahoning also produced brookies up to 20 inches. Aaccording to old angling literature; foot-long brookies were not uncommon. So they got pretty big in those days. They still achieve 12-inchesor more even in some of our small freestone streams. You guys know that!

Lose also writes about the logging era and how it devastated brook trout streams, but then goes on to describe how the streams were coming back by 1931. It is preposterous to think that all of our brook trout were 'wiped out' by the logging era. But they were certainly decimated.

Brookies survived because they have a very flexible genetic makeup. They have a large number of chromosomes , can breed at 2 years of age and at sizes as small as 5 inches. They survived in tiny tributaries and way up in headwater streams that stayed clear and cold. As the forest grew back, they drifted back down into the now cooler downstream waters. And brookies are well-known for their ability to quickly replace their numbers in temporarily flooded and drought decimated waters.

As for this mixing thing, recent studies have indicated that populations of brook trout, when moved into strange waters, can maintain their genetic identity for many generations. This means that they only interbreed with their own. How they accomplish this is not known, but it could be many things - each particular population may have evolved a different breeding strategy; different breeding time, or place; each population may have a different odor, etc. So when transplanted, wild populations may not readily interbreed with strangers.

There is still much to be learned about our only stream-dwelling salmonid. We really ought to be managing them with much more care than we are giving them now.

 

[BrooksAndHooks]

Very interesting stuff to say the least guys. I think it's fair to understand and respect the difference between a minor strain difference and the characteristics of fish in larger areas or water sheds. I don't think the difference is important enough to worry about but enough to understand and acknowledge.

 

[pcray1231]

My best understanding is that in areas that were logged, the devastation was nearly "complete". Meaning, yes, most streams were wiped out at one point or another.

What is that based on? Why do you think so? It's an interesting hypothesis, but is there any support for it?

The key add on to my comment was "but not all at the same point".

I base it on readings of fishing during the time period, likely including the one mentioned by Ken U, as well as some basic logic applied.

Were streams completely wiped out? A: Unknown. Likely yes, in many cases, and no, in many others. That's my own guess. It is known that yes, the vast majority of streams went through serious hardship, but not all at the same time. I'm not claiming there was a day where there were virtually zero brookies in all of NC PA. At any given time, you had streams yet to be logged, streams that were decimated (or eliminated), and streams that were already recovering, perhaps all within the Kettle Creek watershed.

Over 99% of the northern tier was clearcut in a few decades.

In any case, once hit it seems they did generally recover fairly quickly, as KenU states, and this seems to be backed up by stories of the day regarding the landscape. They called it the great brushpile, and fires became a major issue. Think of today. If you clearcut an area, in a year or two it's grown over in weeds. In 5-10 years it's packed with small trees, effectively ending the major erosion issues. In 20-30 years some of those trees are maturing while others are dying off, and it begins to resemble forest again.

Whether a given stream was completely eliminated, or significantly reduced, doesn't matter that much to the genetic history. If it's totally isolated, then it does, as it determines whether it'll recover at all. But most streams aren't totally isolated, rather they receive a handful of travelers from elsewhere on a regular basis.

The smaller the population, the more genetic influence that handful of newcomers has.

For example. A thought experiment. Geneticists have traced a time in human populations where we neared extinction, and were down to a very small population isolated to coastal Africa. Likely a few hundred individuals at most. As there was no outside influence, it diminished the gene pool, and it was a long time before we gained any diversity again. However, imagine there was also a population in China. At this low point in Africa, 2 dozen Chinese people showed up. Their influence on the genetics of the population would have been fairly significant, no? More significant than if the same 2 dozen Chinese people showed up to a thriving population of millions? Of course!

Now, in a few short years, the mixed African/Chinese population is recovering nicely again, but the Chinese population is on the ropes. A few Africans show up to China. Same logic applies. Both populations end up less "unique" than they were.

My claim (educated guess) is that the logging boom simply mixed things up. The genetics of the brookies in the Kettle Creek watershed likely survived and stayed largely in the Kettle Creek watershed. But no longer were the brookies in each little trib of Kettle Creek as unique as they had been prior to the logging boom.

 

[Eccles]

KenU wrote:
As for this mixing thing, recent studies have indicated that populations of brook trout, when moved into strange waters, can maintain their genetic identity for many generations. This means that they only interbreed with their own. How they accomplish this is not known, but it could be many things - each particular population may have evolved a different breeding strategy; different breeding time, or place; each population may have a different odor, etc. So when transplanted, wild populations may not readily interbreed with strangers.

That's interesting. I get the reproductive isolation bit but was unaware that this had been shown to such an extent for brook trout. Can you indicate which studies you are referring to?

 

[Eccles]

pcray1231
That's my mental image anyway. So it's not that they "retreat to the headwaters". But rather that as streams undergo fast changes, many fish die, and others leave. Those that leave may mix with other, still unaffected populations, where they probably were in too low a number to have much significant mixing effects. But some find a nearby empty stream which is once again capable of holding them, and re-seed it. Do this over and over with streams C, D, E, F, etc., and you just end up with once semi-unique populations mixing atogether and losing their uniqueness.

I can see your reasoning but isn't it more likely that isolation increases in the face of something like logging. Populations do move upstream to refugia, in this case as downstream is logged, and they are then marooned on an 'island' of habitat separated by lots of nasty uninhabitable stuff in-between them and the next headwater population (whether that has been logged yet or not). A small population on an island can be subject to all the inbreeding, drift, founder effects that increases differences between populations over time and can lead to speciation.

It might become even worse if, during the habitats recovery we notice there aren't many trout left and decide to move in another species to replace them. The invasive acts to exclude the headwater population from recolonizing its former range. Oh, wait...

 

[troutbert]

pcray1231 wrote:

My best understanding is that in areas that were logged, the devastation was nearly "complete". Meaning, yes, most streams were wiped out at one point or another.

What is that based on? Why do you think so? It's an interesting hypothesis, but is there any support for it?

The key add on to my comment was "but not all at the same point".

I base it on readings of fishing during the time period, likely including the one mentioned by Ken U, as well as some basic logic applied.

Were streams completely wiped out? A: Unknown. Likely yes, in many cases, and no, in many others.

I understand the "but not all at the same point" phrase.

But you are still asserting that many streams were likely completely wiped out by the logging. But, why do you think that is so?

Are there historical records of that happening? I've read a lot of the historical literature and never came across that.

Or is just based on the assumption that when watersheds were logged off, they must have had their brookie populations eradicated from that disturbance?

I don't think the evidence supports that. There have been clearcuts in modern times, in PA and in western states, and severe fires, that have damaged trout populations. But I've never read about any stream that had its trout population eradicated by logging.

There are photos and accounts of people fishing in the old splash dams. And Vanishing Trout talks about fishing in the time when nearly everything had already been cut over.

 

[Chaz]

Dwight there are several studies ongoing related to brook trout genetics. In one in PA, an AMD streams tributaries were sampled This stream is in either Clinton or Potter County. Cooks Run is one of the streams, but I don't recall which. Anyway the 2 tributaries were separated by the AMD for over 50 years, and the brookies in the 2 tributaries had unique DNA.

USGS has a study of brookies they conducted from several states in the mid-Atlantic Region, including PA, and they found they could separate out stains by all sorts of data. Maine Studied their brookies in detail and found over 400 strains.

I'm of the thought that most of the streams that have brookies now, have always had a population, my thinking on that is based on 2 things, 1) brookies didn't do well in the hatchery environment in the early days of fish culture and they don't survive stocking well, 2) even though the forests were clear cut the brookies in the far headwaters would have survived because the cold clean water was still there, and in many cases the far headwaters weren't reachable.

 

[Chaz]

I'd like to hear what you all think the reason is we still have any brookies in SEPA? Early on there was a very hard effort to clear the land for agriculture, yet we still have them in many SEPA. Streams, I know a couple of those streams were never stocked or only stocked once. So did those brookies survive?

 

[pcray1231]

But you are still asserting that many streams were likely completely wiped out by the logging. But, why do you think that is so?

A mix of reading history and logic. I don't "know" it to be so. My suspicion is that both elimination and mere reduction happened, and I don't know what % went each way. Given thousands of streams, I think it's a safe assessment.

Vanishing trout and other accounts do portray decimation of brookie populations in streams that were recently logged over. It does not address whether the populations wer temporarily eliminated, or just severely reduced. As we know, very small populations are more at risk for elimination due to events, such as pollution, a drought, disease, or a dude with a few worms who camps in that headwater region for a week or two.

Industrial processes, including logging, were much less resource conscious than they are today. All those little streams had narrow gauge railroad lines carved on their banks. They cut every tree in entire basins simultaneously, not just a patchwork array of clearcuts. They cut right to the banks, no buffer zones. The gasoline and other equipment they hauled up those railroads for the equipment were in leaky tanks. They built splash dams all over the place. They used strong chemicals to condition wood, and just hosed it down as clean up.

If fish populations retreat to the tiniest headwaters where the siltation and water quality are still ok, what happens when you get a drought and it dries up? Or a spill up there?

Either way, I don't see how the question of whether individual populations died off or merely took a hurting affects much today. I'd view the genetic impact on the large scale to be similar either way.

 

[pcray1231]

1) brookies didn't do well in the hatchery environment in the early days of fish culture and they don't survive stocking well.

This is true across the board. Lots of interesting hatchery history from where hatcheries started, in the Midwest (Wisconsin, Iowa, etc.).

No species did well. They captured wild fish and attempted to breed and raise them, and in the early years, struggled mightily to do so.

They wouldn't eat hatchery food. They'd run from hatchery workers. They'd run into walls and kill themselves. They weren't resistant to disease. They grew slowly and took too long to become sexually mature.

Interestingly, they thought it was learned behavior, so they started taking eggs instead of fish to raise. It did not help, even fish BORN in the hatcheries had these issues.

Though the early survival rates were low, there were survivors. They were mixed with survivors from other hatcheries. In a relatively short amount of time, "hatchery" strains were developed which were easier to maintain. As more states opened hatcheries, then hatchery strains were mixed and matched for various goals.

Of course, the hatchery strains didn't do as well once stocked. Over time, the hatchery strains grew more and more separate from wild strains.

Some states, including Wisconsin, are going back to wild strains in hatcheries, so that the stocked fish have a better chance of survival in the wild, and perhaps colonization. To do this, their more recent work involves changes to the hatchery raceways. They place rock bottoms and other cover in there. Fish densities have to be lower. Feed is changed, and they are fed by automatic feeders instead of people. It's needed to successfully raise a wild strain in captivity.

If that's not an interesting genetic study, I don't know what is! But it does lead to the concept that early hatchery trout were much more suited to the wild than today's hatchery trout. And hence much more likely to interbreed with existing wild fish or seed new populations.

Still, if streams were wiped out and re-colonized, I wasn't suggesting it was due to hatchery trout, but more often, probably nearby streams. A few travelers arriving to a healthy population = minor genetic effect. A few travelers arriving to a very poor population = major genetic affect. A few travelers arriving to an empty stream, but one which has recovered to the point where it can hold fish = seed a new population.

 

[JeffK]

Over in NJ about 35 streams were sampled in the brook trout genetics study by Pat Hamilton (who did lab work at ESSU). All the brookies could be identified to stream with 95% confidence and many appeared to be native strains. Some larger, heavily stocked sterams did have some hatchery genes. One brookie stream is within sight of Manhattan. These streams saw enormous abuse and the brookies still managed to survive.

One study underway now in the upper S Branch Rritan has marked brookies from the different brookie tribs. These streams are sampled a few times a year to get some measure of the movement of fish among the tribs. It will be interesting to see how that plays out. The upper valley here has a dilemma for dam removal. The section has an old dam that isolates browns from the very highest part of the drainage. Dam removal would cool the lower river, but would allow browns into a brooks only area. Browns make up 3/4 of the wild trout below the dam. What would you do?

 

[troutbert]

JeffK wrote:
The upper valley here has a dilemma for dam removal. The section has an old dam that isolates browns from the very highest part of the drainage. Dam removal would cool the lower river, but would allow browns into a brooks only area. Browns make up 3/4 of the wild trout below the dam. What would you do?

I'm not familiar with the dam or impoundment. But there may be ways to have cooler water without removing the barrier.

By creating a release from the bottom. On smaller dams you do not get a full cold tailwater like on the W Br Delaware. But, releasing water from the bottom gives you a cooler temperature than releasing from the top layer, even on small impoundments. Anyone who has ever gone swimming in a state park lake, or even a farm pond can tell you that the water 5 feet down is much cooler than the top layer.

Also, there are several ways the impoundment could be drawn down to a much smaller size, or drawn down completely, allowing for a narrow stream channel to flow through the old dam sediment, with the vegetation quickly growing along the channel. Either way, the warming of the water would be greatly decreased.

 

[troutbert]

Here's a link to the NJ study:

http://www.state.nj.us/dep/fgw/bkt_genetics.htm

 

[salmonoid]

You can get a general sense on the distribution of fish from the late 1800's through the early 1900's by reading the report of fisheries presented to the PA legislature. There is also some data in the US Bureau of Fisheries reports for these timeframes as well. There's no guarantee that if 2000 fish/eggs were shipped to someone for X stream that they actually survived or were stocked in X stream. But it gives you an idea of the distribution of fish at the turn of last century. And provides for an unnatural way to repopulate a recovering stream. For all the lamentation about stocking over wild fish today, back then, private citizens could request fish or fish eggs and they were sent to them, often by rail car, with no control on where they ultimately ended up.

US Bureau of Fisheries report 1919 (PA distribution of brook trout and eggs, other species listed as well).

Report of the State Commissioners of Fisheries, 1879/1880.

I often use these lists for researching possible origins of now wild populations of fish on streams. Stream names have sometimes changed, but its fun to try to piece together information from these historical resources. For instance, I found record of 3000 rainbow trout/eggs that were sent for a Shooks Mills Creek (likely a typo). No such stream name exists anymore but I likely drive over this stream every day - it's likely a small, nondescript stream near the former site of Shocks Mill (now Rowenna), with apparent sources in several limestone springs.

 

[BrookieChaser]

Thanks for the links, salmonoid. Unrelated, but I found it interesting that someone with my last name was a commissioner in PA during the 1879/1880 report.