April 2025 - Tracing Hidden Waters: Uncovering the Past Landscapes of the Three Lakes

Tucked into the hills of West Cork, the Three Lakes site may seem like a quiet corner of Ireland’s natural landscape. But beneath the still surface of Middle Lake, a complex story is buried — one that I am exploring through palaeoecological research using sedimentary ancient DNA (sedaDNA).

My aim is to uncover how biodiversity has changed here since the last glaciation, more than 16,000 years ago. But to understand that ecological history, I first need to understand the landscape itself: how it was formed, how it drains, and why it has remained so relatively undisturbed through millennia of climatic and human change.

Modelling an Elusive Landscape

The first step was to investigate the geomorphology and hydrology of the lake basin using digital mapping tools such as QGIS. I set out to model how water flows into and through the basin — but quickly ran into two key problems.

First, the elevation differences across the basin are extremely subtle. Small variations in the digital elevation model (DEM) caused the drainage network to fragment, making it difficult to produce a coherent flow model.

Second, modern infrastructure — the road and railway that cross the valley — introduced a more fundamental distortion. Both are built on raised causeways, which appear in the model as solid barriers, interrupting natural drainage pathways. In reality, culverts allow water to pass beneath them, but this is not captured in the elevation data.

The result? A broken and unrealistic model that did not reflect how water actually moves through the landscape.

Drainage to the West?

However, when I adjusted the model parameters — allowing more tolerance for subtle elevation changes — a surprising pattern emerged. The drainage system began to cohere, but it flowed westward, rather than east through the gorge as it does today.

This modelled flow crossed the present watershed, which lies only a metre or two above the basin and just a few hundred metres from the western lake.

Could the basin once have drained westward?

This possibility gains weight when considering the gorge at Clashnacrona, the present eastern outlet. Both the road and railway appear to have required substantial rock cutting here, suggesting that the gorge may not be entirely natural.

Clues in the Historical Maps

Historical mapping offers further support. I had examined early Ordnance Survey maps many times without finding anything conclusive. That changed when I came across late eighteenth-century route maps.

These maps show the principal routes between towns in Ireland. In the south west, the main route from Cork to Bantry — via Dunmanway — is shown on the 1777 Taylor and Skinner map. Crucially, it does not pass through the Three Lakes valley.

Instead, it follows a higher route: from Dunmanway along the Kilbarry road and across the north side of the Ruagagh valley, through Drimoleague and Castle Donovan.

Part of the Taylor & Skinner route map of 1777 showing the main route between Dunmanway and Drimoleague

Parts of this route still exist today, though some sections have been absorbed into private land or have reverted to overgrown farm tracks.

By the time of the first edition Ordnance Survey in the 1830s, the modern road appears — running through the gorge and across a causeway in the wetland. By 1880, the railway is also in place.

Engineering the Landscape

This suggests that the route through the gorge was constructed sometime after 1777 and likely required substantial engineering.

It is possible that this work formed part of wider strategic improvements in the late eighteenth century, perhaps linked to the threat of French-supported rebellion in the 1790s. If so, this route may have been developed as a matter of urgency.

The construction would have involved blasting through rock at the gorge and building a causeway across the wetland. It may also have required partial drainage of the lake system.

These works appear to have significantly altered the landscape — possibly even dividing a once larger lake into the three smaller lakes we see today.

A Lake Shaped by Ice and Engineering?

Could the Three Lakes valley once have held a much larger body of water — perhaps a proglacial lake formed at the edge of a retreating glacier?

It is certainly plausible. The gorge may once have been blocked by bedrock or moraine, directing water westward. The glaciofluvial sediment mounds in the Ruagagh valley may support this idea. They catch my attention every time I pass — and I hope one day to survey them in detail.

Further clues may lie in the peatlands near the road. If lake sediments are found beneath the peat, this would suggest that water once extended far beyond the present lake margins.

In this way, palaeoecology and geomorphology can work together to reconstruct the hidden shape of past landscapes.

What’s Next?

The next step is to improve the resolution of the elevation data. A planned drone survey will provide high-resolution topographic information.

This will allow us to remove modern features such as roads and railways from the digital model and reconstruct a more natural drainage system.

In doing so, we hope to understand how the Three Lakes basin has evolved — how water shaped it, how ice left its mark, and why this place has remained, against the odds, a quiet and undisturbed sanctuary for thousands of years.

May 2025 - Soil Fertility, Biodiversity, and the Arc of Collapse and Recovery

For the past 15 years, I’ve been gardening a small piece of land in the south-west of Ireland, in West Cork, and trying to coax life from a soil that just does not want to yield. The field and the garden I inherited had been treated the same way for decades: ploughed, planted, and served with synthetic fertiliser. In the field, animals had been kept pretty constantly — some donkeys, a pony or two, or some bullocks — but there was no rotation, no deliberate manuring, no return to the land of what was taken out. In the garden, there had been no animals at all. It had been worked and reworked, stripped bare and fed only chemical nutrients. A lot of the farm rubbish was buried there — I still dig up fertiliser sacks, bits of car, silage sheet, and pieces of farm machinery.

When I arrived, the pasture was poor. We kept sheep and pigs, but after ten years the sheep had destroyed the fences and the pigs had soured their ground. So the pasture is now planted as open woodland and allowed to revert, with some management. We have lizards and frogs, flowers, trees, and berries. But for the garden areas, even after five years of composting, mulching, and attempting to regenerate the land, many vegetables still do not grow well. Onions, peas, and beetroot will grow if given compost. Everything else either does not germinate, fails to thrive, succumbs to pests, or is hit with disease. Carrots and parsnips get carrot fly. Brassicas (apart from Brussels sprouts) fall to cabbage root fly. Potatoes are blighted and chewed by wasps. Slugs are rampant and leave their mark constantly on everything. The fruit trees — apple, pear, gooseberry, plum — are cankered and will not fruit. Some do not even flower. The only produce we get is blackcurrants and raspberries.

From Personal Experience to Research Question

This personal experience has become one of the entry points into my PhD study, which focuses on long-term ecological change and biodiversity, particularly through the use of sedimentary ancient DNA (sedaDNA) and microbial population analysis. But in addition to the stated objective of understanding how Ireland’s biodiversity has built up and responded to environmental change since the last glaciation, I realise now that a useful adjunct to this story is that of Ireland’s soil fertility.

By combining observations of contemporary soil degradation with the reconstruction of post-glacial ecosystems, I hope to understand not just what constitutes a healthy soil, but how soil forms, collapses, and regenerates through time.

Soil Had to Begin Again

After the last glaciation, when Ireland was covered entirely by ice as much as 1.2 kilometres thick, even as far out as the edge of the continental shelf, this land was scraped clean. Soil had to start again from nothing. Life returned slowly to the glacial gravels, sticky heavy boulder clay, and deep alluvial silts: lichens, mosses, microbial crusts. Then plants. Then fungi and insects. Over millennia, soil became rich and diverse.

Now, we appear to be reversing that trend at extraordinary speed.

And so the central question arises: if we understand how soil first formed, and what makes it functionally alive today, can we reverse the current collapse in soil fertility?

A Broken Soil

My investigations of my own soil, using microscopy and basic lab tests, revealed disturbing signs: very few fungal hyphae, almost no visible protozoa or nematodes, poor soil structure, compaction layers below the surface, sour smells, waterlogging in winter, and dry, cracked conditions in summer.

Even the no-dig method failed after a promising start. I mulched with cardboard and compost, and for two years the beds were productive. Then couch grass, buttercup, bindweed, and nettles broke through. The weeds became stronger. The crops weaker. I found that not disturbing the soil allowed the perennials to colonise with a vengeance.

The revelation came slowly, but I finally realised: this soil is broken. Not in the superficial sense, but at a functional level. Its structure, its biology, its nutrient cycling — all disrupted. And the cause? Long-term negative management. Never before have I inherited a garden that had been managed like this. Fertiliser instead of manure. Overgrazing by animals without rotation. No return of organic matter. No time for recovery. Even well-intentioned interventions like mulching with compost were not enough to reverse it without deeper, systemic repair.

The Easy Fix — and Why I Rejected It

I might well have fixed the problem, temporarily anyway, with fertiliser, pesticide, herbicide, and fungicide. But that would just be propagating the problem. Did I want immediate results in vegetables grown with the aid of chemicals and made to produce in spite of the natural order? Or did I want to fix the problem and see that natural order return, allowing billions of years of natural evolution and symbiotic partnerships to manage it for me?

What is truly sobering is this: my garden and field are not the exception. They are the rule.

All across Ireland, and especially here in West Cork where we farm on siliceous bedrock — naturally low in calcium and high in iron — soils have been treated as inert, chemical-dependent substrates. Fertilisers have masked the decline, but the biology is gone. The structure is gone. The humus is gone. And so, quietly, the fertility is gone too.

Two Fields, Two Futures

Yet examples of regeneration do exist. Our neighbour, a dairy farmer, has taken a strikingly different path. He has focused on improving his herd through careful breeding and keeps his stocking rate low, lower than the optimum. He applies very little bagged fertiliser. Two years ago, he reseeded his poorest field — once conventionally managed for beef with fertiliser, heavy silage cuts, and poor drainage — with a diverse pasture mix: many species of grass, red and white clovers, hawkweeds, chickweeds, and a generous proportion of chicory.

Now that field is transformed. The pasture is thick, varied, verdant, and visibly alive. He notes that when the cows graze there, milk yield rises noticeably.

Next door is another field, managed conventionally, owned by a different farmer. It is ryegrass only. Mown three times already this year, after the latest cut it was quickly spread with slurry, and will soon receive bagged fertiliser. The grass looks stemmy and lifeless. No dandelions, no clover, not even docks. No biomass accumulating at the base. Just grass stems growing from bare soil.

What is the ryegrass feeding on? Slurry and fertiliser. But what is feeding the soil? Nothing. There are no deep-rooted plants to bring up minerals, no dying back to return organic matter. The system is linear and extractive.

Compare this to the chicory-clover pasture: tap-rooted plants cycle nutrients from depth. Leaves, stems, and flowers fall and decompose in place. Organic matter accumulates. The soil improves, year on year. One method gives back to the land. The other takes, and props up with chemistry.

If we ask which of these two management styles will impoverish the land, and which will improve it, the answer is obvious. And if we recognise that the ryegrass model dominates the national dairy system, the conclusion is deeply troubling.

Not Just a Farming Problem

This is not just my problem. It is not even just a farming problem. It is an international ecological crisis in slow motion.

A soil that cannot grow food without chemicals is a soil on life support. A nation that cannot farm without inputs is a nation without resilience. And in a world of rising input costs, extreme weather, and biodiversity collapse, this is not sustainable. It is an existential threat.

Signs of a Different Direction

A blog titled How diverse is the soil life across Europe? A first continent-wide DNA analysis sheds light on the biodiversity below our feet was published a year ago on the GSBI website. This is another excellent blog from the Global Soil Biodiversity Initiative (GSBI) that is pointing in a very interesting direction. Even more so since the launch of the First Local Soil Biodiversity Network: The Irish Soil Biodiversity Research Network (ISBRN).

How Soil Heals

The soil can be healed. It starts with awareness. Then with action. With compost, yes — but also with biology, with roots, with fungi, with time. It is essential to realise that fertility is not something to buy, but something to grow.

If we can successfully determine how to achieve good and sustainable fertility, then the power to restore the land is within reach. We need to understand that soil fertility is about biodiversity in the soil, as well as on it. The microbiota that do so much to release nutrients, enable gas exchange, ensure good soil structure at the micro level, and more than we even yet know about — that is what we need to focus on and learn about. There is so much we do not yet know, so much more to it than a bag of fertiliser and a dose of slurry.

The Heart of the Research

And perhaps by understanding the great cycles of collapse and regeneration that shaped Ireland’s soils over the last 12,000 years, we can learn how to restore them again — not just chemically, but biologically and systemically.

This, ultimately, is the heart of my research: to understand how natural systems dealt with deep systemic changes in the environment, and to learn how we can use that knowledge to mimic natural processes; to uncover how soils live, die, and might live again; and, hopefully, to halt the degradation that will otherwise eventually lead to ruin.

June 2025 - Tromsø - A Trip to the Arctic Circle

The second meeting of the sedaDNA Scientific Society was held at the Arctic University of Norway from June 24th–25th, 2025, in Tromsø. Pre-conference workshops took place at the University Museum on June 23rd, and two post-conference excursions were held on June 26th.

We arrived on the 21st — Midsummer’s Day — along with many entrants from all over the world who were taking part in the Midnight Sun Marathon.

Tromsø is situated at 69° North, about 350 km north of the Arctic Circle. The city is built on an island that lies sheltered behind the larger island of Kvaløya, in the strait of Tromsøysundet — a looping branch of the Arctic Sea that winds behind the islands of Senja, Kvaløya, Ringvassøya, and Reinøya. The Norwegian coastline is deeply cut by fjords and scattered with an incredible 320,000 islands, giving the country a long and rugged edge.

The City

Tromsø itself is a modern city, reached from both east and west by wide, high-spanning bridges. The old Cathedral of Our Lady, built in the mid-nineteenth century, lies in the centre of the island — a wooden church of great character. In contrast, the modern triangular Arctic Cathedral stands across the bridge to the east in Tromsdalen.

We had sunshine every day — and every night — with few exceptions, and used our first two days as an opportunity to explore the city. The most striking thing was the expense of everything, largely due to the need to import goods, but also reflecting high taxation policies.

One afternoon we took a boat trip up the strait and into one of the long inlets — not strictly fjords, but still deep-water channels between forested, mountainous hills. It was sunny, warm, peaceful, clear, and clean, and when the breeze came off the land it carried an icy chill and the smell of snow. Ice still lingered on the hilltops, later than usual after a late snowfall in the spring.

The Conference

The presentations and workshops were generally interesting, though often at or beyond the limits of my understanding. Bioinformatics occupied the morning of the 23rd — the processing of data produced from DNA analysis — followed by nanopore sequencing in the afternoon.

Nanopore sequencing is not directly relevant to my project, as it relies on long strands of DNA. Sedimentary ancient DNA (sedaDNA) tends to be very short — often only a couple of hundred bases long — whereas nanopore methods are better suited to much longer strands, sometimes thousands or even millions of bases in length. The method works by passing DNA strands through a detector, so length is critical to obtaining a readable signal.

Even so, it was fascinating. One clear theme throughout the conference was that boundaries are constantly being pushed back — new ground is continually being broken, new methods developed, tested, refined, and adopted. Sedimentary DNA analysis is a rapidly advancing field.

That evening there was an icebreaker at the museum, with plenty of food and drink. Afterwards we walked down to the beach through bright green, fresh birch woodland and brilliant sunshine. It was 10pm.

Key Presentations

On the 24th, I attended sessions on lacustrine sedaDNA and DNA taphonomy in the morning.

The afternoon began with a plenary by Eske Willerslev, which for me was the highlight of the conference. Willerslev, an evolutionary geneticist from the University of Copenhagen, focused on how ancient environmental DNA can be used to reconstruct past ecosystems and track how plants, animals, and microbes responded to climate change over long timescales.

His argument went further: these records may not just describe the past, but could help design future agricultural systems that are more climate-resilient, productive, and biodiversity-friendly. He made a strong point about the existential crisis facing humans with food insecurity, reliance on global transport and failure to manage the environment sustainably.

He also highlighted how sedimentary DNA has reshaped debates on megafaunal extinction, human migration, and ecosystem change by revealing entire communities from soil and sediment, even where fossils are scarce.

Some examples were striking — including work on the timing and sequence of human movement from Siberia into North America, and studies in Iceland showing that biodiversity actually increased following human settlement, due to the introduction of agriculture, animals, manure, and cropping.

This plenary was followed by further lacustrine DNA presentations, particularly relevant to my own project at Three Lakes.

The conference dinner that evening, held in the dockland area of Tromsø, was well attended, with excellent food, drink, and companionable conversation, ending with a long stroll home through sunlit streets at midnight.

The following day focused on computational and molecular methods, finishing with a third lacustrine sedaDNA session.

The Excursion

Thursday 26th June was excursion day. There were two options: a gentle walk to an alpine meadow (which my wife chose), and a longer, more strenuous hike to the Steindalsbreen glacier — which I was very keen to undertake.

We have excellent glacial deposits and erosion features in south-west Ireland, so I was eager to see a glacier in action. My only previous experience had been the Cook Glacier in New Zealand.

Both excursions involved a 90-minute drive south onto the mainland. The coaches split near the end of the journey.

The Glacier Hike

The hike to Steindalsbreen (69.4°N, 19.9°E) began in a wooded V-shaped valley, surrounded by steep hillsides, with a milky-blue river flowing energetically below. The woodland consisted of birch and alder, with high light levels allowing rich ground vegetation.

The track climbed steadily along the northern side of the valley. Along the way we saw a wide range of plant life: low-growing Cornus with creamy white flowers and dark centres, juniper bushes, and abundant berry plants — crowberry, blueberry, and cranberry. Cow-wheat, heather, brambles, ferns, and grasses formed the main ground cover.

As we climbed, the valley widened, revealing exposed rockfaces and formations shaped by recent glacial activity. We crossed several ridges marking former moraine positions.

About two-thirds of the way up, the trees disappeared, replaced by open grassy slopes. The valley broadened into a classic U-shape, with smooth slopes rising to rocky outcrops and boulder fields.

The final third of the hike was fully exposed, with sparse vegetation: stunted willow, grasses, stonecrops, and small heather. We crossed exposed rock and old ice before reaching newly exposed ground of gravel, silt, and rock.

Here we could clearly see striations on exposed rock surfaces — scratches left by the grinding passage of the glacier.

The Landscape in Motion

Looking down the valley, the river could be seen flowing across flats of sand and gravel, dividing, subdividing, and then converging and coalescing — forming a classic braided (anastomosing) system. This occurs where large volumes of water flow across mobile sediment, constantly reshaping the channels.

Classic.

To the north, with the sun breaking through, we could see the glacier itself — an icefall descending like a frozen river down the mountainside.

We still had some distance to go, crossing old ice, but our guides informed us that we could go no further. The late snowfall meant that crevasses were hidden beneath snow, and the lake ahead was covered by fragile ice. It was simply too dangerous.

So we gathered at the highest safe point, taking photographs and absorbing the scene — the environment, the scale, and the pristine, untouched beauty.

The Return

The walk back was steady, with fewer pauses, though the return journey offered new perspectives on the landscape. Eventually we reached the final descent to the car park and the welcome comfort of the bus.

In total, the hike gained about 450 metres in elevation, and the 10–12 km journey took us from around 10 am to 4 pm.

Final Thoughts

A great day out — and one that alone would have made the entire trip to the Arctic Circle worthwhile.

June 2025 - Tromsø - A Summary of the Presentations

• Stoltenberg region: Multi-proxy sediment and DNA analyses reveal continuous sedimentation, ecological shifts, and vegetation changes despite limited archaeological evidence.
• Siberia winter ecology: Sedimentary DNA shows distinct winter microbial communities, highlighting seasonal ecosystem dynamics under ice.
• Lake proxy reconstruction: Geochemical and molecular proxies reconstruct past vegetation, climate, and human impact in a Himalayan lake over millennia.
• Tibetan lake (Nam Co): Genetic and fossil proxies track lake-level, salinity, and climate-driven ecological shifts over the last ~2,000 years.
• Ecological networks study: Changing species interactions over time increased ecosystem fragmentation and reduced connectivity.
• Beaver ecosystem engineering: Sedimentary DNA reconstructs long-term beaver presence and shows their strong influence on vegetation and biodiversity.
• Udymanis paleoecology: Ancient DNA reveals long-term vegetation succession and megafauna dynamics, with gradual environmental change rather than abrupt shifts.
• Sweden sediment genome: High-quality ancient DNA from sediments reveals unexpected brown bear ancestry and dispersal patterns.
• Ancient proteins: Proteins can extend molecular analysis beyond DNA limits, though extraction and contamination remain major challenges.
• Global sedaDNA databases (Neotoma): Building large, standardized, open databases enables global-scale biodiversity and climate-change research.
• Ecological niche modelling with sedaDNA: Process-based models improve predictions of vegetation change by incorporating species interactions and environmental factors.
• Pipeline benchmarking (marine/shotgun DNA): Database choice and pipeline design strongly affect taxonomic accuracy and sensitivity in metagenomic analyses.
• Data filtering & database effects: Species detection and richness estimates depend heavily on filtering strategies and reference databases.
• Automated DNA lab workflows: High-throughput, automated systems increase consistency and scale but reduce flexibility and require major infrastructure.
• Capture probe design (genome targeting): New methods improve DNA capture efficiency for both single-species and biodiversity studies.
• Metabarcoding vs shotgun comparison: Different sequencing approaches recover different biodiversity signals, highlighting trade-offs in detection.
• Ancient biomolecules & biotech: Reconstructing ancient genes and metabolites opens applications in medicine, agriculture, and climate resilience.
• Climate-vegetation modelling (Norway): Including competition, herbivory, and temperature improves predictions of vegetation responses to climate change.
• Molecular dating of DNA: A new computational method estimates the age of ancient DNA directly from sequence data, accounting for damage and fragmentation.

July 2025 - Bioinformatics

The trip to Tromsø was both interesting and overwhelming. I was plunged into the depths of sedimentary ancient DNA analysis, processing, and all the different aspects in and around that, along with all the jargon. I learned a lot, but unfortunately not in any proportion to the knowledge that surrounded me. A lot of the papers presented were clearly breaking new ground, and likewise some of the procedures employed in the processing of both the sediments and the data resulting from analysis. Some of the most highly regarded studies were referred to time and again.

In 2022 an article was published in Nature which has been highly influential in its groundbreaking use of sedimentary ancient DNA (sedaDNA). The title of the article was "A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA" and amongst the authors was Mikkel Winther Pedersen from the University of Copenhagen. Mikkel introduced, and also presented at, the bioinformatics workshop at the sedaDNA Scientific Society conference in Tromsø in June 2025.

Now there are lots of things about sedaDNA that are confusing, principally whole concepts and processes that are encompassed by single words and phrases.

Bioinformatics is one of them.

Bioinformatics is the way that data is handled and manipulated during, before, and after the extraction of sedimentary ancient DNA from a sample of sediment.

So I decided to translate some parts of the paper in question because it shows just how much work is done at the computing and information technology end of DNA analysis.

Abstract of the Paper

First though, here is the abstract, which details what the paper is all about.

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago had climates resembling those forecasted under future warming. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare. Here we report an ancient environmental DNA (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

So let’s skip straight to the DNA extraction and processing. If you want to read the whole paper — and it is worth reading — it is here: A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA.

Some Background Points

A couple of things to bear in mind. The sedaDNA they were hoping to find was going to be old — very old — around 2 million years, and hopefully preserved in sediment. It was therefore likely to have been severely fragmented, because DNA normally exists as long-chain molecules, but over time it degrades and breaks up into short lengths.

Also, the DNA that is present in the environment can come from various sources, depending on the organism. The three main types of DNA are:

• Nuclear DNA – from the nucleus of a cell
• Mitochondrial DNA – from the mitochondria of a cell
• Plastid DNA – from structures such as chloroplasts

Not all organisms have all these, and the different types of DNA have very different properties. So there is not just one kind of DNA per organism.

Another thing to know is that DNA has different properties at the two ends of the strand — one end is called the 5′ end, the other the 3′ end. Known as 5 prime and 3 prime, these refer to specific carbon atoms in the sugar molecule (deoxyribose) that make up the DNA backbone. The 5′ carbon is where the phosphate group is attached, and the 3′ carbon has a hydroxyl group (-OH), which is important for adding new nucleotides. This is one way that strands can be marked for tracking. It is possible to process several different samples all together in one batch, which saves time and money. To do this, the different samples are processed so that each sample has a unique identifying sequence put on the 3′ end.

It is appropriate to mention here that sequences used in primers, although they only make use of the four bases, can also include what are called degenerate primers. These are primers that include mixed base positions. These make use of IUPAC nucleotide codes — so within these primers, as well as A, C, T and G, you might see R, Y, S, W, K, M, B, D, H, V and N. These act as wildcards. So for example:

• N means allow any one of A, C, T or G
• B means not A, so any of C, T or G

And so on.

I have simplified and translated into plain English, in the fifteen points below, the main tenor of the bioinformatics of this research.

1. Ancient DNA from Sediment Is Extremely Old and Very Damaged

The DNA the researchers hoped to find was 2 million years old. Over time DNA breaks into tiny fragments, so instead of long strands, ancient sediment DNA (sedaDNA) is usually just short, degraded pieces from many organisms.

2. DNA Can Come from Different Parts of a Cell

Organisms can contribute different types of DNA to sediments:

• Nuclear DNA (main genome, in the nucleus)
• Mitochondrial DNA (from mitochondria; abundant in animals)
• Plastid DNA (from chloroplasts; abundant in plants)

Each kind behaves differently and preserves differently, so scientists must consider all of them.

3. Samples Need Unique ID Tags for Tracking

To analyse many samples at once, each sample is given a unique DNA barcode — a short artificial DNA sequence added to one end of the fragments so the sequencer knows which sample each read came from.

4. Primers Can Include “Wildcard” Bases to Detect More Species

Primers are short DNA sequences used to match and amplify targets.

They sometimes include degenerate bases (like N, R, Y) which allow variation — helpful for catching many species that might differ slightly in sequence.

5. The Team Collected 41 Soil Samples and Created 65 DNA Libraries

A DNA library is a prepared batch of DNA fragments ready for sequencing, each with barcodes. Libraries are needed because ancient samples usually contain extremely little usable DNA.

6. They Checked Whether Plant DNA Was Present Using Droplet Digital PCR

They targeted a chloroplast gene called psbD, which nearly all plants have.

Droplet digital PCR splits the sample into tens of thousands of droplets and runs PCR in each tiny droplet. A droplet glows if the target sequence is present, allowing very sensitive detection even for fragments only about 39 bp long.

7. They Also Looked for Grass DNA Using Another Chloroplast Gene, psbA

By designing primers specific to Poaceae (the grass family), they could detect grass-related DNA even in tiny, degraded pieces.

8. To Find Mammal DNA, They Used an “Arctic PaleoChip” Enrichment Method

This uses known Arctic mammal DNA fragments as “bait” to pull out matching pieces from each library. It works even if the match is not perfect — ideal for ancient, degraded remains.

9. All Samples Were Then Sequenced on High-Throughput Machines

Sequencing machines like HiSeq and NovaSeq read millions or billions of DNA fragments.

Out of 16.8 billion raw reads, about 2.87 billion high-quality reads remained after cleaning, with very short, low-quality, or duplicate sequences removed.

10. The Cleaned DNA Was Scanned for Short Patterns (“k-mers”)

A k-mer is a short DNA “word”, usually 31 bases long.

Software such as Simka compares k-mers across samples to find shared patterns.

This does not assume any species beforehand, which makes it useful for discovering unexpected organisms.

11. Reads Were Identified Using HOLI and a Large Arctic Plant DNA Database

HOLI is a bioinformatics pipeline that tries to match each DNA read to the best-fitting species in a reference library of more than 1,500 Arctic and Boreal plants.

Because the ancient DNA might have mutated over 2 million years, they allowed a 95% similarity threshold — close enough to be meaningful, but not so strict that ancient changes would exclude matches.

12. Taxonomic Assignment Used the “Lowest Common Ancestor” Method (ngsLCA)

Sometimes a short read matches several species.

ngsLCA assigns it to the most specific group all matches belong to, for example “deer family” rather than one exact species.

This avoids overclaiming and is safer for short, damaged DNA.

13. Researchers Tested Whether DNA Was Truly Ancient, Not Contamination

They used a tool called metaDMG to check for chemical damage typical of ancient DNA:

• C → T changes at 5′ ends
• G → A changes at 3′ ends

These occur due to cytosine deamination after death.

They only trusted taxa showing strong, statistically robust ancient damage patterns.

14. Strict Filtering Removed Unreliable Taxa and Noisy Samples

To avoid false claims, they removed:

• species with too few matching reads
• samples with very low total DNA
• taxa not appearing in at least three samples

Finally, they converted counts into proportions, letting samples be compared fairly.

15. The Final Dataset Represents a Rigorously Verified Ancient Ecosystem

Only DNA fragments that were:

• frequently found
• matched known species at high confidence
• showed clear ancient damage
• appeared across multiple sediment samples

...were accepted as real evidence.

This produced a remarkably reliable reconstruction of a 2-million-year-old Arctic ecosystem that no longer exists today.

Final Thoughts

I’ll stop here. The purpose of this was to take the bioinformatics part of the paper apart, explain it in a fairly jargon-free way, and show how relatively straightforward it is in concept.

The rest of the paper is certainly worth reading, whether you are interested in sedaDNA extraction and analysis specifically and how it can be used, or in the science behind the whole palaeoecological investigation, or simply out of curiosity about a completely new type of ecological community — a community that does not exist any more, dating from just before the start of the series of ice ages.

November 2025 - Coring - at Last!

In our project timeline we had initially set May 2025 as the date for obtaining the crucial sediment core from the lakebed. For various reasons — though always because of other commitments on the part of other people — the date kept being put off. Summer holidays, of course, also intervened. For me, this being the big driving event, I would have made sure I was available to go coring at any time, but most especially while the weather was pleasant and conducive through the summer. October 17th — my birthday! — was finally settled on, but a back injury to a crucial member of the team postponed the date yet again.

It was November before the date was firmed up and it actually happened. The fear at this point, particularly after such a long dry and warm summer, was that by the 19th November the weather would have turned cold, wet, and stormy.

I know the lake so well. It is surrounded by a floating mat, and the most secure footing I had found for getting into the lake followed the course of the inflowing stream — there was plenty of sediment brought in by the stream. But with a single outlet stream to the north east, and with small, shallow, fairly choked channels between the lakes, water levels rise quite quickly with heavy rainfall and do not recede too fast.

Well, the weather had turned cold, wet, and stormy. But amazingly both the 19th and 20th November were clear, sunny, and calm days — absolutely perfect weather for working knee-deep in the lake margin, out on the lake, and flying a drone. This turned out to be an exceptional bonus. It was an incredible break in the weather; the day after coring, the rain and wind returned.

The Team Assembles

We had managed to gather what turned out to be an excellent crowd of people to work as a team — nine of us altogether. Aaron and Karen brought the raft and coring equipment down from Galway. Andy and Sarahjane came down from Dublin. Michelle, Amanda, and Cathal drove down from UCC. Myself and my son Oscar were local.

Cathal brought the drone — he was to fly it if the weather was good enough. I had gathered together a lot of consumables — bags, pens, scalpels, chemicals, boxes, bins, tape, phials — most of which, as it turned out, we did not need. I also used the old Land Rover to bring over half a dozen wooden pallets to provide firm footing and spread the load; without some sort of support, feet generally sink into the wet ground.

Preparing the Raft

We met at the lake at midday on Wednesday 19th. It was a clear blue sky with bright sunshine and autumnal warmth in the air. We spent the afternoon assembling the raft. After some trials we decided on an area of the floating mat where the distance both to open water and from the trailer was minimal.

We laid the pallets down and started assembling the raft. With only a couple of missed footings off the pallets — resulting in a soaking to the thigh — the afternoon went without a hitch, and by sundown the raft had been assembled, launched, and towed out.

That evening we met at the local pub in Drimoleague, where we had a meal, some fluid refreshment, and a most convivial gathering.

A Perfect Morning for Coring

The next morning dawned beautifully sunny, with well-frosted ground and a heavy local fog lying over the lakes. Cathal managed to get the drone up and took some stunning aerial photographs of the lake basin, looking north east over the eastern lake covered in fog, and south west over the big western lake.

Four of us went out to the raft to begin coring — myself, Aaron, Michelle, and Amanda. Oscar and Andy paddled about in the dinghy, ferrying people and cores to the shore, and Karen operated the extruder up by the vehicles. Several people moved from one team to the other as necessary.

The Coring Begins

The middle lake is shaped rather like a figure of eight, with two basins: the nearest almost circular, the further one much narrower. The raft was anchored by four ropes in a position central within the larger of the two lake basins, and the corer was directed down a tube that hung from the raft to the surface of the sediment. Thus we could be sure that every drive of the corer went down the same hole. It pulled out 2 metres of sediment in each drive. The water where we anchored was 3.6 metres deep.

In previous coring of this lake, we had tried near the centre of this basin and found only 3.5 metres of sediment before hitting stones. A second attempt near the edge of the floating mat gave 6.5 metres of sediment, but the top 2 metres were so fluid that we were not able to save them. Aaron and Karen’s experience assured us that the centre of the basin would give a good firm surface to the sediment, and we hoped for more than 3.5 metres depth.

The first two metres (0 to 1 and 1 to 2) came out, and when extruded we could see a consistent black-brown gyttja.

The next two metres (2 to 3 and 3 to 4) — would we strike bottom? We didn’t — were also of a consistent dark organic colour, but with an interesting pale band at one point.

We drove the corer down for a third drive (4 to 5 and 5 to 6). At the bottom there was quite strong resistance, so we attached the “spokes” and two of us - the heaviest - jumped up and down on them to drive the corer down. This suggested to us that we had possibly found heavier sediment.

I accompanied this core back to where Karen would extrude it. As the extruder was ratcheted along, the bottom metre was extruded first. The first sight we had was of blue-grey clay, quite light in colour, and beginning to ooze away slightly. The top end of this metre — in reality about 60 cm — was dark organic gyttja, and slicing it in half exposed some beautiful layering.

The Big Moment

The top metre of this core was the big one. We needed a good strong section that would show the Nahanagan Stadial (or Younger Dryas) termination. The whole metre was extruded and nothing was visible, but the sides of the core were smeared. Karen ran the wire through the middle of the metre while two of us held each side.

The suspense was hovering in the air around us.

We opened the core — and there was a most glorious sequence of coloured lines indicating sediment changes, including the main transition, at about 465 cm depth, from dark organic gyttja above to blue-grey clay below.

The Nahanagan Stadial termination.

Michelle and Aaron had stayed on the raft in preparation for sending down another drive if necessary, or even worse, moving the raft and starting again. They were given the thumbs up, and so dismantling of the anchoring ropes, corer, tripod, and raft began.

One Regret

Only later did I regret this hurried dismantling. Potentially there was another metre or two — or more — of Late Glacial lacustrine clay further down. We would probably have had to use a smaller-bore corer, and it may have required a lot of force to get it down, but if we had retrieved another one, two, or even three metres, this may well have displayed varves or some other rhythmites.

I will explore what use this could have been to us in a later blog, but the fact is that there are few varved sediments recorded from lakes in Ireland. We are breaking new ground here with our exploration of a lowland lake, with Late Glacial sediments continuous into the Holocene and up to the present, and in the south west corner of Ireland.

So what has been found — or not found — in Ireland to date will not necessarily be a good indication of what we are going to find here. which makes this project particularly exciting.

November 2025 (2) - An Aerial Survey of Three Lakes

I have already explored the landscape history of the Three Lakes site in an earlier blog. But, as is often the case with this kind of investigation, new evidence has emerged that allows the story to be taken further.

Before doing so, it is worth briefly revisiting what we were trying to understand — and what we already knew.

From Coarse Models to Fine Detail

In April 2025 – Tracing Hidden Waters, I examined the drainage of the basin using a Digital Elevation Model (DEM) derived from Ordnance Survey Ireland data at a 10 m resolution.

This dataset is highly accurate in terms of elevation, but not particularly precise at the scale of a small lake basin. With one elevation point every 10 metres, subtle but important features of the landscape are easily missed. For modelling drainage — where differences of less than a metre can determine flow direction — this becomes a serious limitation.

The effect of resolution can be seen clearly by comparing models generated from different datasets:

• 25 m resolution model
• 25 cm resolution model

The difference is striking. Features that are completely invisible at 25 m resolution emerge clearly at finer scales.

A Drone Survey Opportunity

As described in November 2025 – Coring – at Last!, we were fortunate to have near-perfect weather during the coring campaign — clear, calm, and bright. This allowed us to carry out a drone survey of the site.

The result was a very high-resolution dataset, with a ground resolution of approximately 5 cm.

This survey used photogrammetry, a technique that reconstructs the three-dimensional shape of the landscape from overlapping photographs.

How Photogrammetry Works

The principle is straightforward. The drone captures many overlapping images of the ground from slightly different positions. When the same point appears in multiple images, its position shifts slightly — an effect known as parallax.

The amount of this shift depends on elevation:

• Higher points shift more between images
• Lower points shift less

Using the known position and orientation of the camera, software calculates the exact three-dimensional location of each point. Millions of these points are combined into a point cloud, which is then converted into a Digital Elevation Model.

The Cost of Resolution

Such detail comes at a computational cost.

At a 10 m resolution, a square kilometre contains around 10,000 elevation points — easily handled by modern computers.

At 5 cm resolution, however, the number of points increases dramatically — by a factor of 40,000 — resulting in roughly 400 million points per square kilometre.

Processing datasets of this size is time-consuming, even on modern machines, and requires careful data management.

What the Drone Can — and Cannot — See

Photogrammetry captures the visible surface — effectively what the eye sees from above. This introduces an important limitation.

It does not measure the ground where the ground is hidden.

Instead, it records:

• the tops of vegetation
• tree canopies
• hedges and shrubs
• buildings and walls
• road surfaces

In areas of woodland or dense vegetation, the “ground surface” in the model may actually be several metres above the true ground level.

A second limitation arises from how drones must be flown. To comply with regulations and privacy requirements, flights must avoid buildings, gardens, and restricted airspace. As a result, the dataset inevitably contains gaps.

Even with excellent flying conditions, the survey is therefore partial rather than complete.

Lidar — The Ideal, but Expensive, Solution

The most effective method for capturing true ground elevation beneath vegetation is Lidar (Light Detection and Ranging).

Lidar works by emitting pulses of laser light and measuring the time it takes for them to return. Crucially, some of these pulses pass through gaps in vegetation and reach the ground.

This produces multiple returns:

• early returns from leaves and branches
• later returns from the ground surface

By selecting the lowest returns, it is possible to reconstruct a highly accurate ground surface, even in wooded areas.

The drawback is cost. High-resolution Lidar surveys are expensive and not always available for small, localised study sites.

Working with the Data in QGIS

Despite these limitations, the drone-derived dataset is extremely powerful when used within GIS software such as QGIS.

The density of the point cloud allows the creation of detailed terrain models and derived visualisations, including:

• hillshade models
• slope and aspect maps
• local relief models
• flow accumulation and drainage patterns

These visualisations can reveal subtle features that are otherwise invisible — slight ridges, shallow channels, or low-relief mounds that may reflect past hydrological or glacial processes.

At this scale, the landscape begins to resolve itself.

Where This Leads

Each survey method has its strengths and its limitations:

• Coarse DEMs — broad coverage, but miss fine detail
• Photogrammetry — extremely detailed, but surface-limited
• Lidar — highly accurate ground data, but expensive

The challenge is to combine these approaches to build the most reliable interpretation of the landscape.

In the case of Three Lakes, the new high-resolution data is already revealing features that were completely invisible in earlier models — and these, in turn, raise new questions about how the basin formed, how it drained, and how it has evolved over time.

The story, it seems, is far from complete.

December 2025 - Rewriting the Landscape: When One Lake Became Three

In earlier posts, I explored the possibility that the drainage of the Three Lakes basin may once have been very different from what we see today. Digital modelling hinted at an alternative past, while field observations raised questions about the role of the gorge at Clashnacrona.

Since then, new evidence has come to light — and it strengthens the case that the present landscape is not entirely natural, but has been significantly shaped by human engineering.

A Map That Changes the Picture

The first piece of evidence comes from the Cork Grand Jury map of 1810. This map shows the road running through Clashnacrona Gorge between Dunmanway and Drimoleague — clearly established by this date.

More striking, however, is how the lake itself is depicted.

Instead of three lakes, the map shows a single large body of water: O’Mahony’s Lake.

This is a critical observation. By 1810, the road exists — but the lake system has not yet taken on its modern form.

The Mail Coach Road

Further historical references help place this development in context.

In Lewis’s Topographical Dictionary of Ireland, the entry for Bantry describes the “new mail coach road” approaching the town from the south and following the coastline. This aligns with the known route of the improved road network in the early nineteenth century.

Richard S. Harrison, in Four Hundred Years of Drimoleague, also refers to the construction of this mail road.

Taken together, these sources suggest that the road through the Three Lakes valley was part of a major infrastructural project around the early 1800s, likely completed around 1810.

Engineering the Gorge

Physical evidence on the ground supports this interpretation.

At the eastern end of the lakes, where the road enters Clashnacrona Gorge, there are bare, steep rock faces rising sharply beside the road. These are not gentle, weathered slopes, but abrupt cuts — strongly suggesting that a substantial volume of rock was removed.

Given the period, this would almost certainly have involved the use of explosives.

The question then arises: where did all that material go?

The most likely answer lies immediately to the west — in the low-lying, waterlogged ground now occupied by the Three Lakes. The construction of a road across this terrain would have required a stable base, almost certainly in the form of a causeway built from imported fill.

It is highly plausible that the excavated rock from the gorge was used to construct this causeway.

From One Lake to Three?

If this interpretation is correct, the implications are significant.

The construction of the road and causeway may have:

• lowered the effective water level within the basin
• altered the natural drainage pathway
• and physically divided a single lake into multiple smaller basins

In other words, O’Mahony’s Lake may have been transformed into the Three Lakes we see today.

What remains unclear is how this change was managed hydrologically. Lowering a lake level would normally result in increased downstream flow — yet there is, so far, no clear historical record of flooding or increased discharge through Dunmanway.

Was the outflow controlled during construction? Was the transition gradual rather than sudden? At present, we do not know.

Evidence in the Sediments

This is where palaeoecology becomes crucial.

If the lake level changed significantly in the early nineteenth century, that change should be recorded in the sediments.

Previous coring has already revealed an intriguing clue: a layer of diatomite — indicative of open water conditions — located approximately two metres above the current level of Middle Lake, in sediments between the lake and the road.

This suggests that, at some point in the past, the water level in the basin was substantially higher than it is today.

The key question is whether this higher water level persisted into the historical period — and whether its reduction can be linked to the construction of the road and causeway.

Bringing the Evidence Together

We now have three independent lines of evidence:

• Cartographic — the 1810 map showing a single large lake
• Historical — records of a major road-building project around the same time
• Physical — rock-cutting in the gorge and a causeway across the basin

To these we can add a fourth:

• Stratigraphic — sediment evidence indicating a previously higher lake level

Taken together, these strongly suggest that the modern landscape is, at least in part, the result of early nineteenth-century engineering.

Where This Leads

The next step is to test this hypothesis more rigorously.

High-resolution elevation data from the drone survey will allow the causeway and surrounding terrain to be mapped in detail. Further sediment analysis may reveal whether a distinct change in lake level occurred at the time the road was constructed.

If confirmed, this would mean that the Three Lakes are not simply a natural post-glacial feature, but a landscape shaped at a critical moment in recent history — where geology, hydrology, and human engineering intersect.

The landscape, it seems, is not just ancient — it is also surprisingly modern.

January 2026 - The Next Six Months

One of the useful things about a four-year PhD project is the rhythm it imposes. Every six months there is a project team meeting, a chance to stop, take stock, and ask two simple questions: what have we achieved? and what comes next?

Research rarely moves forward in a straight line. Some parts take longer than expected. Some methods prove less useful than hoped. New opportunities appear unexpectedly. What matters is that, step by step, the project continues to move forward — and that is very much where we are now.

Looking Back on the First Year

Overall, the project is moving ahead well. Although there has been a certain amount of juggling of timescales to fit around other people’s schedules and the realities of laboratory and fieldwork, the major goals of the first year have been achieved.

The two biggest tasks were:

• the scoping review
• the recovery of the main sediment core

Both of these turned out to be larger undertakings than originally expected, but both are now well advanced or completed.

The Scoping Review Grew into Something Bigger

The scoping review began as an attempt to assess the use of six biological proxies across Ireland:

• sedimentary ancient DNA
• pollen
• chironomids
• cladocera
• testate amoebae
• diatoms

The aim was not to analyse the results of those studies in detail, but to examine their metadata — where work had been done, what time periods had been studied, and where clear geographical or chronological gaps remained.

During the year, this work expanded significantly when I came into contact with similar research being carried out by Nick Scroxton. By combining datasets, what had begun as a focused scoping review became part of the development of the Danu database, a much larger and more useful resource for Irish palaeoecology.

This broadened the scope of the work and lengthened the timescale, but it also made the final result far more valuable. A second draft of the review has now been completed and handed on to Michelle and Aaron.

Some Things Worked Better Than Others

Not every line of investigation progressed as hoped. Early in the project I worked on extracting and identifying testate amoebae from older sediment cores collected in 2018 and 2021. Unfortunately, whether through storage conditions or the nature of the sediments themselves, very few usable tests were found, and none at all in the deeper layers.

That was disappointing, but not disastrous. Since the project is centred mainly on lake sediments and sedimentary ancient DNA, it does not stop the broader work from moving forward.

Alongside this, I also completed postgraduate training modules in statistics and data analysis and spatial ecology and GIS, both of which have already proved useful to the project.

Building the Surface Record

As part of the groundwork for the main analysis, we collected surface sediment cores from three locations:

• Glandart Lake — a small, higher-elevation lake at about 350 m, with relatively little human influence
• Three Lakes, Middle Lake margin
• Three Lakes, Middle Lake basin centre

These surface cores are important because they give us a modern or near-modern reference point. One of the useful questions emerging from the meeting was how the biological signal from a relatively undisturbed upland lake compares with that from the main project site at Three Lakes.

This comparison may itself become a paper in due course.

The Core — At Last

The biggest fieldwork achievement of the year was the successful recovery of the main sediment core from Middle Lake at Three Lakes in November.

After several postponements, the core was finally recovered over two days of remarkably good weather. In total, we obtained a sequence of about 5.5 metres of sediment, with visible changes in colour and texture strongly suggesting that the record spans from the Late Glacial through the Younger Dryas and into the Holocene.

This is the backbone of the project.

Very soon after the core was recovered, around 100 small subsamples were taken, especially at points where visible sediment changes occurred. These have now been stored safely at -80°C for future sedimentary ancient DNA analysis.

A Bonus from the Fieldwork: The Drone Survey

At the same time as the coring, we were also able to carry out an aerial drone survey of the lake basin.

This was a major bonus. The drone data will help refine our understanding of:

• the catchment draining into the basin
• the present drainage channels and hydrology
• the geomorphology of the basin
• the possibility that the site was once a single larger lake

This work links directly to my interest in the landscape history of the site, and should allow much more detailed GIS modelling than had previously been possible.

So What Comes Next?

The next six months are not simply about “doing more work.” They are about targeting.

The most expensive part of the project is the sedimentary ancient DNA analysis. That means we need to use the next phase wisely: gathering enough supporting evidence from other methods to decide exactly which parts of the core are most informative and worth sequencing.

Several tasks now come into focus.

1. Chironomid Analysis

The first major strand of work is chironomid analysis. I have already made good progress with the surface sediments and improved greatly in both extraction and slide preparation. The next step is to continue with the surface samples and then move into targeted sampling of the main core.

The chironomids should help identify major environmental shifts, especially cooling and warming phases, and may be particularly useful in refining the interpretation of the Late Glacial and early Holocene parts of the sequence.

2. Loss on Ignition and Particle Size Analysis

We will also begin loss on ignition (LOI) and particle size analysis. These will help distinguish between more organic and more minerogenic layers, clarify the sediment structure, and help identify the most important transitions in the core.

This is the kind of background work that is not always visible from the outside, but it is essential. These methods help turn a long sequence of sediment into a readable environmental history.

3. Tephra and Other Chronological Markers

Another line of investigation now moving to the fore is tephra — microscopic volcanic ash layers that may provide valuable chronological control.

If tephra can be identified in the core, it may allow us to tie parts of the sequence to known volcanic events, reducing the need for some radiocarbon dates and helping refine the age model.

There was also discussion of using XRF and other scanning approaches to help identify unusual layers before committing to more detailed analysis.

4. Radiocarbon Dating

Radiocarbon dating will also be important, but the meeting made it clear that dates need to be chosen carefully. The goal is not simply to date as much as possible, but to date the most informative points in the core.

That means using the sedimentology, the chironomids, and any tephra evidence first, so that the dates can be placed where they are most useful.

5. Choosing the sedaDNA Samples

Perhaps the most important decision over the coming months will be deciding which samples should be prioritised for sedaDNA extraction and sequencing.

The discussion strongly suggested that the lowest metre to metre and a half of the core may be the most scientifically valuable part. This section appears to cover the Late Glacial, the Younger Dryas transition, and the beginning of the Holocene — a period of major environmental change, and one that is still poorly studied in Ireland.

At the same time, there was also agreement that a small number of carefully chosen samples from further up the core may be worthwhile, so that the record does not focus exclusively on the earliest part of the sequence.

Step by Step

What came through most clearly in the meeting was that this phase of the project is about building a chain of reasoning.

We cannot sensibly choose the most important DNA samples until we know more about the structure of the core.

We cannot build a strong age model until we know where the key transitions are.

And we cannot answer the bigger ecological questions until these smaller, careful steps have been taken.

That is how a project like this moves forward: not in one dramatic leap, but by linking one piece of evidence to the next.

The Bigger Picture

The first year was about groundwork: learning methods, building collaborations, collecting material, and establishing the main record. The next six months will be about refining that record and deciding where to focus effort, time, and funding.

If all goes well, by the end of this next phase we should be in a much stronger position to decide:

• which parts of the core deserve detailed sedaDNA analysis
• where dates should be placed
• how the major environmental changes are structured through time

In other words, the first year was about gathering the evidence. The next six months will be about finding where, within that evidence, the most important story lies.

February 2026 - Radiocarbon Dating and Bryozoa

One of the tasks identified in last month’s blog, 'The Next Six Months', was to determine the levels to be dated and send those samples off.

I had already identified the levels to sample for dating, and I then spent three weeks, far longer than I expected, examining these levels to find terrestrial plant macrofossils suitable for radiocarbon dating.

How Radiocarbon Dating Works

Radiocarbon dating is based on the principle that the ratios of different isotopes of carbon in the atmosphere—embedded in CO₂—can be used to determine the age of organic material.

The key isotope is carbon-14 (¹⁴C), an unstable form of carbon created in the upper atmosphere when solar radiation converts nitrogen atoms into carbon. Once formed, this isotope begins to decay, with a half-life of about 5,700 years.

Because carbon dioxide is used in photosynthesis, this radioactive carbon becomes incorporated into plant tissue, along with the stable isotopes ¹²C and ¹³C. Once inside the plant, the ¹⁴C begins to decay, gradually altering the ratio between these isotopes. Measuring this ratio allows us to estimate how long the carbon has been decaying, and therefore the age of the material.

Why Terrestrial Plant Material Matters

We aim to use terrestrial plant material because plants take their carbon directly from the atmosphere. This avoids complications that arise when carbon is sourced from elsewhere.

Aquatic plants, for example, may absorb carbon dissolved in water, which can include “old” carbon that has been stored for long periods. This forms what is known as a carbon reservoir, and can produce misleading radiocarbon dates.

To avoid this, we try to ensure that the material we date comes directly from the atmosphere, and has not been influenced by older carbon sources.

Extracting Plant Macrofossils

Finding suitable terrestrial plant macrofossils in sediment that is 10,000–12,000 years old is not straightforward.

The process involves:

• Disaggregating the sediment – breaking down clumps of organic-rich material (gyttja)
• Gentle sieving – using water and sieves of ~250 µm and ~90 µm
• Microscopic examination – identifying fragments under a stereomicroscope
• Selection – isolating material that can confidently be identified as terrestrial plant remains

For radiocarbon dating, we need between 3 and 10 mg of suitable material.

What I Found (and Didn’t Find)

I found a large amount of plant fibres—mostly long, ribbon-like, parallel-sided structures that appear to be stem material. However, I could not determine whether these came from terrestrial, aquatic, or emergent plants.

Only terrestrial material is suitable for dating, so this presented a problem.

I did find one promising specimen: a large seed from 526 cm depth (pre-Younger Dryas, probably ~13,000 years old). It was about 5 mm long, black, ridged, with a flattened peak at one end and tapering at the other.

Despite extensive effort—including consulting this excellent macrofossil reference material from the University of Minnesota—I was unable to identify it with confidence.

Given the cost of radiocarbon dating (around €300 per sample), we were wondering whether to proceed with bulk sediment dating, which is not unusual for material of this age. But the uncertainty of the resulting date makes this an undesireable option. More time needs to be spent on seasrching for, finding and identifying plant macrofossils.

The week was not wasted, however.

Late Glacial Observations

Once into the Late Glacial sediments (below the Younger Dryas), two things became very apparent.

1. Absence of Sphagnum

I found no sphagnum moss remains in these levels.

Sphagnum has very distinctive cell structures, including large hyaline cells that resemble stretched “S” or “Z” shapes. Above the Younger Dryas termination (~11,700 BP), sphagnum fragments were abundant. But below this level, they were completely absent.

This suggests that environmental conditions were not suitable for sphagnum growth during the Late Glacial period. It may reflect:

• insufficient water availability
• slow establishment of plant communities
• the possibility that sphagnum is not an early coloniser

2. Abundance of Cristatella mucedo Statoblasts

I observed relatively large numbers of Cristatella mucedo statoblasts.

Cristatella mucedo is a freshwater bryozoan. Statoblasts are its reproductive units—effectively “seeds”—and are quite distinctive and often beautifully preserved.

Bryozoans are soft-bodied, colony-forming organisms, somewhat similar in structure to coral polyps. Each individual extends tentacles into the water to capture food particles, and colonies grow through budding.

An interesting detail: statoblasts are classified as:

• floatoblasts – capable of floating
• sessoblasts – which remain attached

The latter term derives from Greek: statós (“placed”) and blastós (“bud”).

Why these are more abundant in Late Glacial sediments remains an open question. Possible factors include:

• water temperature
• nutrient availability
• light conditions
• predation pressure
• lake size and depth

At that time, the site likely formed a single, larger lake—significantly bigger than the present Middle Lake.

A curious note: unlike most bryozoans, Cristatella mucedo colonies are capable of movement—up to about 1 cm per day—reminiscent of slime mould behaviour.

3. Chara Oospores

A third notable observation was the presence of large numbers of Chara oospores.

Chara (stonewort) is a large alga that resembles a plant. It often becomes encrusted with calcium carbonate. The oospores are:

• oval in shape
• yellow to pale brown
• characterised by a distinctive spiral ridge

These are also known as gyrospores, and may or may not be coated in calcium carbonate.

This raises an interesting geological question. West Cork is predominantly siliciclastic, with very little calcareous bedrock. So:

• Are these oospores calcified?
• If so, where is the calcium coming from?

And again: why are they more abundant in pre-Younger Dryas sediments?

Looking Ahead

These observations raise many new questions. As I continue working through the full core, I will be recording these patterns carefully.

Even if they are not directly related to the primary research questions, they contribute to the broader goal:

to understand what was living here at different times—and why.

Further reading:
Mundy, S. P. – A Key to the British and European Freshwater Bryozoans (Freshwater Biological Association, 1980)

And the other is....

March 2026 - Lateglacial Life and Sediments

Hidden Life in the Sediment: When the Record Misleads Us

In my search for terrestrial plant macrofossils, I came across something unexpected. In the lowest dark organic layer of the core, there were clear signs of biological material. I have not yet examined the fraction retained by the 90 µm filter (that’s 90 thousandths of a millimetre), but I expect it will contain sponge spicules, diatoms, and other traces of aquatic life.

At first glance, this seems straightforward. Darker sediments usually indicate more organic matter, and therefore more life. Lighter, blue-grey sediments are typically taken to represent the opposite: low organic content, and a less productive environment.

But the reality may not be so simple.

What Sediment Colour Is Supposed to Tell Us

In palaeoecology, we often use sediment colour as a quick guide to past conditions.

• Dark brown or black sediment → high organic content → more biological activity
• Blue-grey sediment → low organic content → fewer organisms

This fits neatly with the standard model of post-glacial environmental change. As the climate warms after the ice retreats, landscapes gradually become more hospitable. Life returns, ecosystems develop, and organic material accumulates in lake sediments. In this view, the transition from blue-grey clay to dark organic sediment marks the recovery of life.

In this core, that transition happens gradually over about 10 cm.

So far, so good.

But Nature Is Not That Simple

The problem is that environments are not uniform, especially in the period just after the last glaciation.

Even if winters were harsh, summers could still support significant plant and animal life. At the same time, spring thaw would have produced large volumes of meltwater, carrying fine glacial sediment into lakes.

This creates an important possibility:

The sediment may be hiding the evidence of life, rather than showing that life was absent.

In other words, the blue-grey clay may not indicate a lifeless environment. Instead, it may reflect a situation where large amounts of mineral sediment were being deposited so rapidly that any organic material was diluted and effectively masked.

Why This Matters

This has serious implications for how we interpret the core.

We usually rely on radiocarbon dating of organic material—ideally terrestrial plant remains—to establish a timeline. But in these minerogenic (mineral-rich) layers, there may not be enough organic material to date reliably.

That creates a second problem: we cannot easily determine how fast the sediment was deposited.

And that rate may vary dramatically.

• In a typical temperate lake:
  ~1 cm of sediment might represent 25–30 years
• In a meltwater-dominated environment:
  1 cm might represent as little as 5 years

This means that two identical thicknesses of sediment in the core could represent completely different spans of time. Simply comparing centimetres is no longer meaningful.

A Closer Look at the Core

This issue becomes particularly clear in the lower part of the sequence.

The lowest dark organic layer occurs at 531 cm depth. I examined the ten centimetres below this, down to 541 cm, taking 1 cc samples from each slice.

As I went deeper, I found fewer and fewer signs of life.

But what does that actually mean?

• Was there genuinely less life present at the time?
• Or was I sampling sediments that represent shorter time periods, with a higher proportion of mineral material and less visible organic content?

At this stage, it is not possible to say for certain.

Rethinking a Standard Interpretation

Traditionally, the transition from blue-grey clay to dark organic gyttja in Late-glacial lake sediments is taken as evidence of a shift from a cold, sparsely vegetated environment to a warmer, more biologically productive one.

This interpretation is supported by many studies, including work on Irish lake records, where highly minerogenic sediments are associated with early post-glacial conditions and limited vegetation.

However, the visual properties of sediment—especially its colour—do not necessarily provide a direct measure of biological productivity.

In glacial and post-glacial lakes, large volumes of fine sediment can be delivered into the basin, often in seasonal pulses. If sedimentation is rapid enough, organic material can be diluted to the point where it becomes difficult to detect, even if ecosystems are already developing.

How Can We Untangle This?

To move beyond this uncertainty, we need to look beyond sediment colour alone.

1. Rhythmites and Varves

One approach is to identify rhythmites (or varves)—layers deposited in a regular, often seasonal pattern.

If present, these can:

• reveal annual or seasonal cycles
• allow us to estimate sedimentation rates
• help determine whether rapid deposition is masking organic signals

2. Sedimentary Ancient DNA (sedaDNA)

Another powerful tool is sedimentary ancient DNA.

DNA can bind to mineral particles, especially clays, which helps preserve it even in sediments that appear biologically poor. This means that even where visible fossils are scarce, DNA may still reveal what organisms were present.

While sedaDNA does not directly measure abundance, it can confirm the presence and composition of past biological communities.

A More Nuanced View

Taken together, these observations suggest that the conventional interpretation is not necessarily wrong—but it may be incomplete.

The blue-grey minerogenic layer may reflect:

• cold climatic conditions
• and high rates of sediment input

These two factors do not have to occur at exactly the same time, or at the same rate as biological recovery.

The key challenge is to distinguish between:

• a genuinely low-productivity environment
• and one where biological signals are present but hidden by rapid sediment deposition

Looking Ahead

Resolving this question will require combining multiple lines of evidence—sediment structure, dating, and biological proxies, including sedaDNA.

For now, the important point is this:

The absence of visible evidence in the sediment does not necessarily mean the absence of life.

Sometimes, the story is there—but buried a little deeper than we expect.