Beneath the Surface > March 2014

Apologies for the derth of updates recently but it's been all hands to the pumps recently to get the data into a single, coherent whole as the Carron Restoration Project nears the end of it's current funding run.

However, this recent push has unearthed some interesting trinkets:

The data shows a statistically significant swing on the Carron from a majority male, grilse catch to a majority female, Multi Sea-Winter salmon catch. While these majorities may appear to be very narrow the trend is definitely significant and several different analyses of different aspects of the catch data have all pointed toawrds the same conclusion.

Future work on the Carron might look at tracking this trend and seeing if it is a complete reversal or part of longer periodic cycle that may swing back the other way given enough time ...

The work that Eric and Mark are doing with the modelling and genetic analyses are also starting to show some exciting, preliminary results. The genetic analyses, in particular, look like they might be showing several distinct genetic groups in the river and future work on this may be able to categorise these groups as stocked or unstocked/ wild, as belonging to a particular family (something which will help us to track how many stocked fish are returning to the river), or even as belonging to a particular part of the river (prooving or disprooving the idea local genetic populations).

These are certainly exciting times for the Carron ...
Posted: 9/18/2014 4:15:09 PM by Matthew Curran | with 0 comments

Apologies for not getting more information out sooner but I had some technical difficulties posting updates last week (internet rather website in origin). The short statement posted last week was a test that seems to have worked...

These last few weeks I've been continuing to work on the analysis of the screw trap data and have started to look at the electrofishing data. In particular, I've been looking running statistical analyses of the numbers of fish recorded as having damage and the samples taken from the river in the April 2014 electrofishing survey.

For a larger image of this graph click here.

This graph appears to show that the mean number of damaged fish in each year is different. In fact, if you look at the error bars on the graph you can see that they all overlap except those on the 2012 bar. So the only clear relationship we can take from here is that the samples collected in 2012 show a larger number of damaged fish than any other year.

If you examine deeper; a t-test for different means shows that all years are different except 2010/ 11 and 2009/ 13. Again the graph would seem to bear this out as the actual bars for 2010/ 11 and 2009/ 13 certainly group close together when compared to the other graphs. However, assuming that the damage data is not normally distributed, a chi2 analysis of the data suggests that none of the years are significantly different to each other. However, chi2 becomes unreliable when there are large numbers of zeroes in the dataset (as there are here) so these results must be viewed with caution. Indeed the next step for the analysis will be to test for normalcy in the data and re-test with a different non-parametric test such as the Mann-Whitney U-test.

Unfortunately, while we can to a degree quantify these relationships, we cannot explain them. Because of limitations in the data collected we cannot say why 2012 showed so much more damage than any other year. Lacking data on predator numbers or movements we cannot say if there were more adult or juvenile predators that year (or both), nor can we cannot link the damage to a particular species. Flow data does not correlate with damage. In fact, for the six years of the study four show no correlation between flow and the percentage of damaged fish, one shows a weak negative correlation and one a strong negative correlation suggesting that the fish are not being damaged by the riverine environment (discussed previously on the 21.08.2014).

While we may never be able to explain the increase in 2012, future work using juveniles density surveys, predator surveys, flow and substrate studies, may allow us to identify an explanation for the observed relationship. With this data in hand it may be possible to compare the identified contributing factors the historical data to explain patterns seen in the the earlier study years.

I've also been looking at the Electrofishing data. Starting with the 2014 electrofishing data, I've been able to identify one site where the ratio of the juveniles length to weight is significantly different to the other sites. The lowest site of the survey, where the River Taodail merges with the Carron, gave rise to juveniles that were skinnier than the other fish in the river (confirmed with a Mann-Whitney U-test). Is this due to the low position in the river? The influence of the Taodail? Does the ratio held true year on year? Is the ratio associated with a genetic difference in the fish? Or was it a one-off due to something specific to this year? Future electrofishing surveys should continue to takes weights of juveniles captured and include this site again, perhaps even traveling up the Taodail to see if the fish in the Taodail are morphologically/ genetically different from those in the Carron. Perhaps comparative habitat surveys may help shed some light on these differences.

Finally, initial observations of this same data seemed to show that the fish being caught in the Coulags River were, on average, both bigger and heavier than those elsewhere in the river. This needs a bit more analysis as while the Coulags has some of the longest and heaviest fish in the survey sample, the ratio between length and weight remained similar to the other sites (except the Taodail site obviously). This might suggest that the weight of the fish is increasing in line with the length of the fish (more research needs to be done to see if there is an accepted model relating weight gain to length), therefore the ratio will remain the same regardless of the actual size/ weight of the fish. Or it might indicate that the Coulags produces bigger fish. Point to not here is that the survey was performed in April and there may be something about the Coulags that allows it to produce larger fish at that point of the year.

Future work for me will be to look at the length and weight data to see if there is any significant differences there (rather than in the ratios). future work for the project may be to look at the Coulags to try and determine why it produces bigger fish, or whether the growth rate is different here and the fish all end up the same size eventually.
Posted: 9/1/2014 10:21:48 AM by Matthew Curran | with 0 comments

This week I continued to look at the scale damage observed in the smolts captured by the screw trap sited at Brabourne's pool on the River Carron.

One of the things that the project would like to do going forwards is to monitor the numbers of piscivorous birds on the river as this seems the most likely cause of the damage seen in these small fish (damage by seals or otters would be much more devastating to the fish). As there are no records of bird sightings or numbers to date it is impossible to try and relate the two factors to each other a this time, except to say that adult and juvenile birds have been seen on the river and smolts are getting damaged.

Examples of smolts from the screw trap with scale damage.

What I was able to do was explore whether the smolts might have been being damaged in fast-flowing water. By comparing the levels of damage to the strength of the water flow it's possible to estimate the likely impact of the flows on the smolts.

For a larger image of this graph click here.

For a larger image of this graph click here.

Bearing in mind that the data for the screw traps is incomplete due to the need to remove it from the river when the flow is very high to prevent it from being damaged; the graphs actually seem to show that there are less damaged smolts when the flow rate of the river is high. This can be seen in the examples above where the flow rate (green line) peaks either side of the peak incidence of scale damage.

However, this data does support Bob's observation that the damage is greater in lower, calmer flows and may even bear out his idea that piscivorous birds on the river have an easier time catching fish in these water conditions. If we could get collect the quantitative data on bird numbers/ sightings on the Carron and match this up with the damage and flow data, the three things together could perhaps tell us exactly what's going on...
Posted: 8/22/2014 2:26:43 PM by Matthew Curran | with 0 comments

This is the second Thursday update using the format of a monthly overview of the project progress so far. Office moves, summer holidays and software updates have all resulted in progress being very slow for the last six or seven weeks. However, despite this some progress has been made and this is detailed below...

Assessment of potential relationships between juvenile salmon stocking and the rod catch on the River Carron
The data in this paper has been lagged to give a better representation of the relationship between the numbers of fish stocked and the number of fish in the rod catch. The statistics have been completed – Spearman’s rank correlation, regression analysis and residual plots. To date, all of the analyses are giving a strong relationship. However, the data still needs to be further lagged as the current transformations do not take into account differing proportions of S1 and S2 smolts in the population or the different proportions of S1 and S2 smolts that will mature into grilse or Multi Sea-Winter (MSW) fish. The residuals also indicate better fit between the trend line and the data in the early stocking effort therefore the data will be split in half and pre and post 2004 data subjected to statistical tests separately.
The data in it's current form has now been split into a set of pre-2004 and post-2004 data with the aim of seeing if there is a stronger correlation in the earlier years of the stocking programme than in the later years; a possible indication that the stocking had a greater impact in the early part of the programme which is often seen to be the case. While the analysis of the complete dataset demonstrates a strong correlation, neither the pre-2004 nor the post-2004 datasets show any correlation.
The question of the proportions of S1, S2 and S3 smolts assumed to be present in the data will have to be determined by calculation as no details of an overarching, general proportion has be found in the literature or in communication with other academic institutions. To this end the screw trap and electrofishing data will be used to determine if there is any bimodality in the samples which may indicate differing age classes, this will be combined with scale readings (to be performed be me following training with specialist input where needed).
An initial attempt to calculate proportions of S1, S2, S3 and S4 smolts from the screw trap data generated mixed results – proportions in three years were clearly and easily calculated but beyond these, proportions calculated in one year could not be reliably transferred to other years. This leaves the electrofishing and scale reading data as the only methods likely to generate usable smolt age proportions.
I will be contacting Andrew Duncan in the near future to discuss possible ways of proving whether the lagging transformations performed have improved the fit of the data to the trend and, if so, by how much.

Mark and recapture (Panjet) study
The recapture data has been looked at quite thoroughly in terms of looking at possible correlations and all of the possible biases in the data. So far we have been able to show a weak correlation between the number of fish marked and the number of fish recaptured and between the number of fish marked and total catch for each year. This data also shows that the proportion of the marked fish in the recapture and total catch record stays fairly constant. Analysis shows no significant relationships in the factors that could potentially bias or confound the study – the catch composition does not show greater numbers of males than females or grilse than MSW adults, nor does that data suggest that fish show any preferences in movement direction after initial capture and marking. The analysis did indicate a possible trend in the data towards a reversal from a majority male catch to a majority female catch – this observation will be examined further in a linked, but separate, small scale paper looking to see if proportions of grilse and MSW adults and size of angled fish are also changing in line with the change from male to female fish. I am also looking into development of GIS maps that will show the distribution of where fish were captured and re-captured.

Assessment of River Carron smolt run
So far this data has been organised and graphed to show a three day running mean of smolt numbers against date and river level observations made by Bob. I have already received information from SEPA on the daily flows and rainfall for the Carron which will be related to this smolt run data to see if we can see patterns between rainfall, river level and smolt numbers. Work has also begun on looking at difference between smolt damage in different years and this will be statistically analysed once the organisation and clarification of the data is complete.
Following discussion with Bob Kindness, it has become clear that there is no quantitative data on predator sightings available to compare with the instances of fish damage. Discussions have been had abaout obtaining photographs of damaged fish, although again, there are not many of these available for analysis.
The SEPA data for flow, rainfall, temperature and river level have been recieved and subjected to initial analysis by plotting this information on graphs alongside the smolt number data and moon phase data (see example below).

For a larger image of this graph click here.

Use of coded wire tags to assess the relative impacts of Salmon smolting in the wild or the hatchery
The data for this section has been “cleaned up” to some extent to allow it to be analysed. The data has been further reorganised to allow relationships to be explored but discussion with Andrew Duncan indicates that creation of a mixed model on ‘R’ may be the best way to look for significant patterns and interactions in the data. To that end I am liaising with Andrew to organise attendance on an ‘R’ course covering, or his assistance with, the development of a mixed model and the analysis of the data is on hold until the course of action has been decided upon.
So far no further progress has been made on this as we are waiting for Andrew to return from the college summer vacation before discussing the possibility of him taking over the development of the mixed model entirely as he is likely to be able to generate it faster and more effectively than myself and would avoid the loss of time incurred by attendance on the training course.

Determination of the distribution of juvenile salmon in the River Carron catchment
So far no analysis has been started for the electrofishing data but I have organised a GIS training session with the Inverness College GIS trainer aimed specifically at creating maps that will show the Carron electrofishing data.
The GIS training is progressing but slowly due to office moves, software updates, and holiday and research commitments of both Dr de Raad (GIS trainer) and myself. My decision to effectively start over from first principles rather than trying to repurpose material already available has also meant that the process has taken longer but should produce a more accurate and fit-for-purpose product at the end. The skills obtained in the training will allow comprehensive GIS maps to be generated for many of the sections of this report as the restoration project continues.
The fish obtained by Murray Stark and myself during an electrofishing survey in April have now been processed, and information gathered from this fish will be added into the electrofishing data to help build the picture of the River Carron as well as adding into the genetic picture of the river.

Using genetic analysis to determine the relative abundance of wild and stocked Salmon in the River Carron
The cataloguing of the samples will be complete by 23.07.2014 and the first batches will be sent to the genetics lab by 01.08.2014. The results of these tests will be analysed by Mark Coulson now that he has accepted a place with the RLI. The cataloguing of the samples is now complete. The final decision on which samples will be shipped to the genetics laboratory will be made on Tuesday 19.08.2014 before the samples are then packaged and shipped that afternoon.
Mark Coulson has now joined the team and has already begun analysing 358 samples generated as part of an electrofishing survey carried out by Eric Verspoor and Jonah Tosney in October 2012. When compared to samples taken from fish known to have been stocked by Bob Kindness, these samples will begin to illuminate the relationships between wild and stocked fish in the Carron.

Initial assessment of gravel movements in the River Carron catchment
The analysis in this section has not yet been started but contact has been made with Richard Tipping at Stirling University to obtain copies of three student dissertations based on data collected in the summer of 2013 for inclusion in the final report.
Following discussions between Professor Tipping and Melanie Smith; Professor Tipping has agreed to provide a short summary of the three dissertations for inclusion in this report.

Carron population modelling
This section has not yet been started.

Species other than Atlantic Salmon
This section has not yet been started.

Posted: 8/14/2014 5:43:24 PM by Matthew Curran | with 0 comments

Firstly my apologies for not posting anything for a while but between vacations and training courses I've not had any new material to post.

That changed last week; Eric and I spent Tuesday and Wednesday processing juvenile salmon gathered from the River Carron during an electrofishing survey on the 3rd and 4th of April. Below are pictures of all the fish processed over these two days as an illustration of the size of the task:

(Note: some of these fish look to have damaged fins but this may well be an artifact of thawing these frozen specimens.)
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In all 336 fish were lengthed and weighed, and had scale and tissue samples taken. And this isn't even the end of the process! Now all of this information has been gathered, it needs to be processed.

Over the next few months the scales will be read as part of the stocking investigation to allow us to determine the age ranges of the Carron population. The length data will be combined with electrofishing data collected over many years to try to map the distribution of juveniles in the river. Examination of this length data may also be able to shed some light on how many age classes co-exist in the river at a given time; by looking for distinct groups of sizes and comparing the findings to the literature we can estimate the range of ages present in the river.

Finally, the tissue samples will be used to look at the genetics of the fish in river. This will allow us to determine what proportions of the juveniles found in river surveys are of completely wild origin, which have been stocked from the hatchery and what proportion (if any) are a mix of the two.

Watch for these results over the coming months...
Posted: 8/12/2014 4:50:15 PM by Matthew Curran | with 0 comments

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