iiinova — where your digital self keeps evolving

Iain A Malcolm @iainamalcolm.bsky.social · 06/08/2026

Fantastic work from the Freshwater Environment Team at S.G. Marine Directorate A big shout out to members of Fisheries Management Scotland who undertook the data collection that underpins the National Electrofishing Programme for Scotland and these analyses: #NEPS www.gov.scot/publications...

gov.scot

National Electrofishing Programme for Scotland (NEPS) 2023: status of juvenile Atlantic salmon and brown trout populations

The National Electrofishing Programme for Scotland (NEPS) is a statistical survey of freshwater fish populations and the pressures affecting them in Scotland, particularly water quality and genetic in...

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Iain A Malcolm @iainamalcolm.bsky.social · 06/08/2026

Escaped farmed #Atlantic #salmon can breed with wild populations with negative consequences for fitness. New paper assesses national & regional introgression pressures, integrating SNP marker panel, statistical survey of juveniles (NEPS) and novel stats approach 🧪🌏 academic.oup.com/icesjms/arti...

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Iain A Malcolm @iainamalcolm.bsky.social · 06/08/2026

A topologically correct Digital River River Network (DRN) underpins many statistical analyses. When landscape characteristics are added DRNs can support river temperature & ecological models. New open access DRN for Europe. Take a bow Andrew French & Phil McGinnity 👏🏻 zenodo.org/records/1436... 🧪🌏

zenodo.org

AMBER salmon: A digital river network containing reach-specific habitat variables related to the North-East Atlantic distribution of Atlantic salmon (Salmo salar)

Summary This dataset was collated through an offshoot of the AMBER project. One of the aims of AMBER was to evaluate the merits of different restoration actions proposed to reconnect Europe’s fragment...

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Iain A Malcolm @iainamalcolm.bsky.social · 25/07/2026

Brown trout populations are hard to assess due to their phenotypic plasticity, with life history strategies ranging from resident to anadromous (sea trout). Our latest paper provides a new assessment method for Scotland, based on juvenile electrofishing data. onlinelibrary.wiley.com/doi/10.1111/...

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Reposted by Iain A Malcolm

Dr. Jonathan Foley @globalecoguy.bsky.social · 28/06/2026

What *actually* works — right here, right now — to address climate change? Here you go. This is the result of thousands of hours of painstaking research and analysis from the Project Drawdown team.

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Reposted by Iain A Malcolm

Twlldun @twlldun.bsky.social · 25/06/2026

I’m not saying the debate in the U.K. has moved to the right, but Ed Miliband is basically seen as Pol Pot for aiming for a climate target first agreed to by…I think Theresa May’s government? Definitely Johnson’s. And this chat is going on during the middle of a record-breaking heatwave

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Iain A Malcolm @iainamalcolm.bsky.social · 09/06/2026

New paper on the potential effects of climate change and shrubification on river temperature in tundra environments. Where are temperatures likely to change most and how are underlying processes affected? 🧪 agupubs.onlinelibrary.wiley.com/share/QKHDEU...

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Iain A Malcolm @iainamalcolm.bsky.social · 27/02/2026

Provisional Atlantic #salmon catch statistics are out for Scotland. 2025 catches are likely to have been affected by extremely low summer flows. Nevertheless looking like a very poor year and possibly the worst recorded. www.gov.scot/publications... 🧪

gov.scot

Scottish salmon and sea trout fisheries: provisional statistics 2025

Provisional data on the number and weight of fish from Scottish salmon and sea trout fisheries.

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Iain A Malcolm @iainamalcolm.bsky.social · 01/02/2026

The Girnock & Baddoch index sites on Aberdeenshire Dee, Scotland, support some of the longest, most detailed salmon population datasets available. Latest data here. Flow affects inter-annual variability in female numbers, declining return rate drives trends. 🧪 www.gov.scot/binaries/con...

gov.scot

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Iain A Malcolm @iainamalcolm.bsky.social · 01/02/2026

New study: As lice pressure increased, the specific growth rate of returning fish declined. "Wild-origin fish had a greater return rate than hatchery-origin fish at all levels of lice infestation pressure, with the difference increasing with increasing pressure" academic.oup.com/icesjms/arti...

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Iain A Malcolm @iainamalcolm.bsky.social · 26/11/2025

#Northumberland coast, blow away the cobwebs and clear the mind.

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Iain A Malcolm @iainamalcolm.bsky.social · 14/11/2025

Transfer of genetic material from domesticated to wild salmon populations through fish farm escapes & interbreeding, is a significant risk to wild salmon populations. Identifying this pressure in wild populations requires the use of informative markers. New paper link.springer.com/article/10.1...

material.is

Material Video archive — Reykjavík, Iceland

Archive of videos from the Material Conference — Reykjavík, Iceland — by Joschi Kuphal & Brian Suda

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Iain A Malcolm @iainamalcolm.bsky.social · 09/11/2025

We do not have deliberate and politically driven reductions in long-term govt. science programmes in the UK. Nevertheless, budgetary constraints and a requirement to focus on immediate policy and regulatory data requirements are affecting the freswater data landscape nonetheless.

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Reposted by Iain A Malcolm

Nature Portfolio @natureportfolio.nature.com · 08/11/2025

From NASA to the National Institutes of Health, federal agencies conduct research that universities cannot. Agency scientists speak with Nature about the irreplaceable facilities, institutional knowledge, and training opportunities that the country is losing. 🧪

go.nature.com

Insiders warn how dismantling federal agencies could put science at risk

From NASA to the National Institutes of Health, federal agencies conduct research that universities cannot. Agency scientists speak out about the irreplaceable facilities, institutional knowledge and training opportunities that the country is losing.

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Reposted by Iain A Malcolm

CatchmentSci @catchmentsci.bsky.social · 14/08/2025

I’m delighted to share that our latest research has just been published in HESS. We developed an unsupervised workflow to estimate river surface velocities from videos. Testing on 11,000+ videos against 274 gauging measurements showed excellent agreement. hess.copernicus.org/articles/29/...

hess.copernicus.org

Unsupervised image velocimetry for automated computation of river flow velocities

Abstract. Accurate, long-term measurements of river flow are imperative for understanding and predicting a broad range of fluvial processes. Modern technological advances are enabling the development ...

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Iain A Malcolm @iainamalcolm.bsky.social · 14/08/2025

New paper on effects of captive rearing of Atlantic salmon on body morphology in context of stocking "Humanity often tries to engineer its way out of environmental crises. But nature isn’t easily replaced. Sometimes, the best solution is to give it the space to recover on its own" bit.ly/4oykzmy

theconversation.com

Wild salmon are the Zendayas of the fish world – what that tells us about conservation

Wild salmon look incredibly symmetrical but captivity makes them more lopsided, stressed and less able to survive in the wild.

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Iain A Malcolm @iainamalcolm.bsky.social · 28/07/2025

A fantastic job opportunity for someone to work at the interface between Atlantic salmon habitat modelling and management. Cutting edge research as part of an excellent project team.

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Iain A Malcolm @iainamalcolm.bsky.social · 21/07/2025

New recommendations for water regulation in England and Wales. In Scotland of course the water industry is publicly owned through Scottish Water.

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Iain A Malcolm @iainamalcolm.bsky.social · 19/07/2025

7. Logger calibration & QC are critical for the reliable assessment of river temperature trends. Failure to calibrate loggers can lead to spatio-temporal biases. These principles were core to the establishment of the Scotland River Temperature Monitoring Network #SRTMN www.gov.scot/publications...

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Iain A Malcolm @iainamalcolm.bsky.social · 19/07/2025

6. In the Girnock Burn, loggers deployed before March 1998 were positively biased while those deployed ca. 1998 to 2007 were negatively biased. The combined effect of these two biases is to moderate the observed temperature trends over the period ca. 1988–2010 relative to the true trend.

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Iain A Malcolm @iainamalcolm.bsky.social · 19/07/2025

5. Using the bias corrected time-series it was shown that winter temperatures (December–February) were largely stable. Temperatures in other months increased non-linearly. Increases were greatest in summer (June–August) & for daily maximum temperatures, followed by daily mean and minimum.

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Iain A Malcolm @iainamalcolm.bsky.social · 19/07/2025

4. We analysed trends in daily mean, max & min river temperature in the #Girnock Burn, the longest continuous sub-daily river temperature dataset in Scotland. Seasonal-Trend decomposition using Loess was undertaken on 1. raw & 2. bias corrected time-series to assess consequences for reported trends.

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Iain A Malcolm @iainamalcolm.bsky.social · 19/07/2025

3. There are few long-term sub-daily river temperature time-series. These are often comprised of multiple logger/sensor combinations. Technological developments have increased memory, sampling frequency, reporting resolution, and precision of data. However, these changes can also introduce biases

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Iain A Malcolm @iainamalcolm.bsky.social · 19/07/2025

2. Spatio-temporal biases can be introduced through changes in deployment location (micro-site) and methods (e.g. with or without shielding), or in the case of spot sample time-series through changes in the time or frequency of sampling. doi.org/10.1007/s102...

doi.org

Estimation of river and stream temperature trends under haphazard sampling - Statistical Methods & Applications

Long-term temporal trends in water temperature in rivers and streams are typically estimated under the assumption of evenly-spaced space-time measurements. However, sampling times and dates associated...

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Iain A Malcolm @iainamalcolm.bsky.social · 19/07/2025

1. Accurate (unbiased and precise) quality controlled data are essential for understanding and monitoring trends in river temperature. However, researchers often collate and analyse data without consideration of these issues. A new 📜 & summary🧵 onlinelibrary.wiley.com/doi/10.1002/...

onlinelibrary.wiley.com

The Influence of Equipment Bias on Reported Temperature Trends: Implications for River Temperature Monitoring Networks

River temperature is an important control on ecosystem health. Concerns around climate change impacts and availability of lower cost sensors have led to an increase in temperature monitoring of aquat....

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Reposted by Iain A Malcolm

Eva B. Thorstad @evathorstad.bsky.social · 22/06/2025

Do poor growth conditions at sea result in salmon returning to rivers to spawn at a younger or older age? New study shows that that rapid growth can lead to later maturation but maturation age can be influenced by shifts in growth during the marine migration link.springer.com/article/10.1... 🐟

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

13. EF data can provide accurate, catch independent estimates of abundance in rivers, provided they are collected & analysed using appropriate methods. By sampling multiple sites, assessment is possible at any scale. When combined with data on pressures this underpins evidence based management.

An photograph of early electrofishing in the 1960s by staff from the Freshwater Fisheries Laboratory in the Girnock Burn. Three people are standing in a river wearing waders shirts and ties. Staff variously holding nets, an early example of an anode and a bucket.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

12. NEPS surveys provide an opportunity to characterise environmental pressures at the time of survey, including water quality and introgression. This information can be used to understand the critical thresholds and effect sizes and target management.

16 panel plot of maps showing site-wise concentrations of ammonia, nitrate, nitrite and total nitrogen. Spatial patterns persist across years suggesting that these data are valuable indicators of inter-site variability and can be used to target management action.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

11. At low population densities, assessment becomes more challenging as the proportion of sites where fish are present decreases & relative inter-site variability in density increases. Occupancy provides another potential metric of population health if a suitable benchmark could be produced.

Four panel plot showing relationships between mean regional densities and occupancy (proportion of river network where fish are observed) for salmon and trout, fry and parr.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

10. At the national scale salmon fry densities varied among years with rod catch (proxy of adult abundance). This was less clear for salmon parr, due to the effects of covid lockdowns on rod catches in 2021. Trout fry densities exhibited signs of density dependence in relation to sea trout catches

Two panel plot showing relationships between rod catches, as an indicator of adult abundance (x axis), and national estimates of mean juvenile densities (y axis) for Salmon and Trout, fry and parr. Symbols separate lifestages, colours indicate NEPS survey years. 2021 is an outlier due to the effects of covid lock downs on angling effort and thus catches.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

9. Where habitats are saturated with juveniles (NEPS Grade 1) densities would be expected to remain fairly constant over time, independent of adult numbers due to density dependent competition (see Spey below). This was explored for a small number of catchments with longer-term multi-pass EF data.

Six panel plot with 3 rows and two columns. Left column shows the modelled partial effect of year on juvenile densities. Right column shows rod catches. Three rows show data for the Tweed, Dee and Spey. There are no significant trends in juvenile abundance on the Spey despite declines in rod catch, suggesting juvenile habitats remain saturated.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

8. At a national scale, Atlantic salmon densities increased with increasing Strahler river order (bigger rivers), while trout densities declined. In general, spatial patterns persisted between years shifting up or down depending on overall abundance.

Four panel plot with Strahler river order on the x axis and mean density on the y axis. Separate plots are shown for salmon and trout, fry and parr.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

7. Within the overall pattern of poor performance there was substantial regional variability. Fish stocks were assigned a Grade of 1-3 (1 healthy, 3 unhealthy) depending on performance against benchmark & uncertainty in abundance. Separate assessments were undertaken for each species & age class.

3-panel plot of maps showing regional performance in salmon stocks indicating by different shades of colour. Assessments were undertaken for fry and parr and then combined (overall).

3-panel plot of maps showing regional performance in trout stocks indicating by different shades of colour. Assessments were undertaken for fry and parr and then combined (overall).

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

6. At a national scale salmon fry (0 year old) & parr (>0 year old) juvenile densities were substantially & significantly below the benchmark indicating that available habitats are no longer fully occupied. Trout fry & parr densities were also below the benchmark, but not significantly for fry.

4 panel plot comparing national salmon and trout, fry and parr densities to the benchmark (densities expected if juvenile populations were fully occupying available habitat).

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

5. The NEPS 2023 report updates existing capture probability (P) models for Scotland, illustrating that P varies with species, lifestage, pass, organisation, habitat, day of the year & region. Importantly there are also long-term trends in P emphasising the need for continued multi-pass data.

Multi-panel plot showing how capture probability varies with species, lifestage, pass, organisation, habitat, region and time.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

4. NEPS consists of an ecosystem of spatial data, standardised sampling methods , statistical models (capture probability and expected densities) and a GRTS statistical survey. These are brought together to assess status & trends in Atlantic salmon and brown trout populations in Scotland's rivers.

Schematic showing how spatial data, historical electrofishing data and the NEPS survey are brought together to assess the status (health) of salmon and trout.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

3. Electrofishing (EF) data are commonly collected & accurate sources of information on ecosystem health, status & trends in diadromous fish. When collected to consistent protocols, with an appropriate survey, these data can provide reliable assessments across scales from sites to whole countries.

4 panel schematic showing how electrofishing data can be used to provide information on fish abundance and status at a range of spatial scales from individual sites to whole countries, informing policy and management decisions. Figure taken from NEPS 2021 report.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

2. Evidence based freshwater fisheries management requires a reliable understanding of the processes regulating fish populations, the status (health) of populations across a range of spatial scales, the environmental pressures acting on them and the efficacy of management actions.

Photograph of upland salmon stream in Scotland looking up onto Loch Nagar mountain range.

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Iain A Malcolm @iainamalcolm.bsky.social · 13/06/2025

1. Are you interested in assessing the status of Atlantic #salmon and brown #trout populations using electrofishing data? If so then this 🧵 is likely to be of interest to you. The latest report from the National Electrofishing Programme for Scotland #NEPS was published this week bit.ly/4jNrXH6 🧪🌎

Two people sampling fish in a small upland stream in Scotland using a traditional electrofishing backpack. One person carries the equipment and holds an anode and a hand net. The second person carries a net and bucket to help capture and hold fish that are caught.

Image showing front cover of the NEPS 2023 report

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Iain A Malcolm @iainamalcolm.bsky.social · 27/04/2025

Up above Loch Tummel. Time to go hunt for that pot of gold.

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Iain A Malcolm @iainamalcolm.bsky.social · 15/04/2025

Islay, distillery tour by bike. Time well spent in good company

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Iain A Malcolm @iainamalcolm.bsky.social · 12/03/2025

Protection & creation of riparian woodland is one of the few management options available to mitigate river temperature increases under climate change. "riparian buffers wider than 15 m protected against water temperature increases..." agupubs.onlinelibrary.wiley.com/doi/10.1029/...

agupubs.onlinelibrary.wiley.com

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Iain A Malcolm @iainamalcolm.bsky.social · 09/03/2025

Another day on the Northumberland coast😁

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