Sunday 13 October 2019

Looking back on the eDNA results




It has now been just over a month since Professor Neil Gemmell announced the results of his environmental DNA studies of Loch Ness to the world. I thought I would wait for the media frenzy to abate before I digested what data was available to the general public as well as asking Professor Gemmell to clarify some points for me.

So, as a believer in the Loch Ness Monster, what can I conclude from these results? In some sense, the survey follows on from two large scale searches of the loch over the last five decades and they feed into one another. First, we had the extensive surface watches of the Loch Ness Investigation Bureau in the 1960s. This was followed by the sonar surveys typified by the large Operation Deepscan in 1987. Thirty years later, science has progressed to the point where actual animal material in microscopic quantities can be extracted, sequenced and matched to known animals.

Unlike the previous two searches, the eDNA survey was focused on a study of the flora and fauna of the loch, the other two were concerned with finding evidence of the Loch Ness Monster. Nevertheless, there was the hope to many that the creature would intersect with the study in some way.

THE DATA

But before I compare and contrast these searches, what can be said about the results of the DNA survey? At the time of writing, a series of results have been published by Otago University at their Loch Ness Hunters website. These results can be searched by species or location and it is the species-oriented results that have got the most attention. If you did not know by now, here is the pie chart of species found.



I base my comments on the assumption this is a complete record of vertebrate matches. As I understand it, Arctic Char, Sea Trout and Brown Trout are not explicitly mentioned as they are likely included under "Salmon" as members of the salmonidae family alongside Atlantic Salmon. Perch are not explicitly mentioned either, but will come under the family name of percidae (which suggests an exact species match was not achieved). Some species appear to have been missed, namely otters, newt, carp and roach. The last two are actually unconfirmed by "official" sources, but people claim they are there.  So does their absence from the DNA record dismiss their existence? That depends if you believe people's anecdotes about them!

No reptile DNA was found though reptiles do live by the loch such as adders. lizards and slow worms. They can enter the water, but it is assumed that such ventures are too rare to leave any traceable DNA. The same could go for the amphibian newts. However, we know otters live by the loch and enter the waters, but they have been missed by the sampling regime. This will simply be down to the fact that sampling did not occur near places of otter activity.

Some results were surprising such as sample "Ness 10" in the middle of the loch being identified as 100% pheasant DNA! It was proposed by Professor Gemmell that this was likely due to some birds defecating into the loch at that point.

You will note there is no mention of plant life or microscopic life, one assumes they were not included in the public results. The main point here is that most but not all species were detected and that was down to the element of uncertainty in choosing the best sampling sites. In total, about 250 samples were taken at the loch at depths from 0.5 to 200 metres. However, if one looks at the public data, only 56 samples are listed.

That perhaps should give me pause for thought if not all the data is available. Professor Gemmell told me all the data would come in the scientific paper he intends to publish around the end of the year. But with that limitation in mind, I will proceed.

I also note that some of the sample results are not complete. For example, if one looks at sample location "Ness 2", there were three samples taken at 0.5m, 100m and 200m. The results are stated as 321 for humans and 1 for toads, but it does not state which applies to what depths. Clearly, the human result would be for the surface (perhaps human waste from a cruise boat), but at what depth was the toad DNA retrieved?



This brings to mind a headline from 2007 when a deep water survey team found a toad in Loch Ness at a depth of 98 metres (above). The depth of the loch at the point of sample "Ness 2", north of Inverfarigaig, was about 220 metres, so the team must have sampled the water at best 20 metres above the surface. One wonders how common this amphibian is at these depths? But until I see the depth data, the toad DNA could have been retrieved at the surface.

Looking at the public database, 11 of the 56 samples were taken at depths of 100-200 metres. I am not sure if this is a proportionate representation, in which case there were about 50 deep water samples taken. If not, we have 11 to work with and it is my guess, having eliminated terrestrial and pelagic creatures that next to no vertebrate matches were made at these depths which we call the Profundal Zone.


DEEP WATER MONSTERS

However, it may be that any data for these 11 samples are simply missing or too scarce because it has been established that fish do inhabit this zone as per the capture of a potentially benthic form of Arctic Char at 200m by the Loch Ness Project. Now the reason I am most interested in this depth data is because I believe the creature spends most of its time at these depths, generally not moving around, with occasional forays up the sides of the loch walls.

This can be established from the witness database. If we filter out the spike years of 1933-1934, we are averaging about 10 sightings per year since then - and that is before one decides what proportion of these are misidentifications and hoaxes. Clearly, this is a creature which does not surface very often which leads to the conclusion that it is not a creature that spends much time in the shallower pelagic zone.

The surface watches of the 1960s confirmed this and the more penetrating sonar surveys, though they do produce occasional sonar hits of the creatures, it is clear that it is in the deepest depths that these creatures must be sought. This is not so easy for sonar due to beam attenuation and widening, but this has been my belief since 2012 that any searches in the pelagic zone will be generally fruitless. 

But if only 11 deep water samples were taken, would much be picked up? The public data suggests nothing, but I await further information as surely some known lifeforms were detected. I would point out a further potential problem with eDNA surveys at these depths. The relatively inert nature of the abyssal plain does not lend to distribution and scattering of DNA due to the higher water pressure at those depths and the lack of disruptive water movements such as the higher thermocline. As Adrian Shine says:

In contrast to the turbulence and variety of physical conditions among the stones of the shoreline, the fine and relatively rich silts of the abyssal regions offer remarkable stability. In an environment of great hydrostatic pressure, constant darkness, and a scarcely changing low temperature of 5.6C, high oxygen levels (over 80% saturation), permit surprising variety in the profundal community of the 200m deep basin floors.

I am not sure how one gets around this more difficult sampling region. I had suggested prior to the team's arrival that they actually sample the silt itself which may preserve more DNA, but that did not happen. Note higher oxygen levels are a boon to the survival of bottom dwelling creatures. So the jury is out for me on what was detected and what was detectable at these extreme depths and I await Professor Gemmell's scientific paper.


THE UNIDENTIFIED DNA

Which brings us to the data that was certainly not in the data. It was stated that 25% of the DNA was not amenable to identification. When I asked Professor Gemmell about this his answer was that unexplained DNA sequences were generally short DNA sequences that can not be accurately attributed to any specific species or taxonomic group with statistical certainty. Most metabarcoding and eDNA studies have portions of these sequences so he did not see any significance in that data.

The more relevant piece of data in regard to this was the study conducted at the nearby lochs of Cluanie, Oich, Duntelchaig and Ashie. When I asked how much unidentified DNA was present in those loch samples, he said it was largely the same. In other words, we should not look for monsters in that unprocessed set of data.

It also has to be said that there was another indeterminate region in which low samples of DNA, though processable, were too small to produce enough confidence and hence were discarded. In other words, anything that came up with fewer sequences than was detected for any species in the negative control were discarded. 

As an aside, it had been mentioned in pre-trip publicity that Loch Morar would form part of the "control" lochs. Professor Gemmell informed me that the loch in the end did not get sampled, which was a pity given its monster tradition.


PLESIOSAURS AND GIANT EELS

As said before, no reptilian DNA was detected and that would eliminate extinct animals such as plesiosaurs right away. But if reptile DNA was detected, how could one zero in on a plesiosaur identification? Professor Gemmell's approach was to use a rough DNA composite somewhere between crocodiles and birds. Some have suggested plesiosaurs lie closer to turtles by relation and this was conceded by Neil, though it is a moot point given the absence of reptilian DNA.

The matter of giant eels was the main takeaway from the conference given by Professor Gemmell. However, the truth of the matter is that the eDNA survey had only failed to eliminate giant eels as a monster candidate as giant eels could have the same DNA sequence as smaller ones. Indeed, it could never eliminate giant eels in the same way it could not eliminate giant salmon, giant dogs or giant toads! I suspect that conclusion was more a sop to the worried Highland tourism industry. 

My own take is that giant eels are not the main explanation for Loch Ness Monster sightings. They could not possibly account for long necks, land sightings, semi spherical humps or sustained surfacings. This would only be possible if these features are explained by other non-eel causes. I do concede the historical possibility of large eels in the loch, perhaps of the order of two or even three metres long. Whether these have played a part in surface sightings is indeterminate, but certainly not the corpus of accounts.

My own question to Professor Gemmell was how the eels had been identified in the loch as some identifications from DNA had only been accurate to the family level and not the species level. His confirmation was that the species anguilla anguilla had indeed been matched and that is where I think I will leave that theory.


CONCLUSIONS

In the broader scheme of things, Professor Gemmell's eDNA survey did not produce anything unusual from a cryptozoological point of view. He did mention some "surprising" results, but one must assume those surprises were confined to the microscopic level. I was not expecting anything from the majority half meter samples unless he struck lucky and a benthic monster had passed by that way in the last few weeks. Indeed, one may have passed that way close to June 2018 according to Gary Campbell's sightings register:

28 May - Morag Connor and her friend were driving north out of Drumnadrochit between 11 and 11.30 am. They saw a creature with a long neck with some humps behind it sticking about 7-8 feet out of the water and about 50 m from the shore. The creature had an all dark body but with no discernible head. They were unable to stop as they were driving and there was no place to pull over.

One suspects that if this was genuine, the creature's DNA had degraded by the time Professor Gemmell's team had started, even if he had intersected with its widening DNA dispersion trail back into the abyss. Be that as it may, we know that not all creatures were identified and that was purely down to the coverage of the loch not being complete and no one is blaming anyone else over that herculean task.

The Loch Ness Monster is a non-abundant species, just as I suspect the missing otters, newt, carp and roach are. It likewise did not intersect with the survey and that's just the way it statistically falls out,  especially if this species spends most of its time in the inert silt 200 meters or more below. But I will defer final judgement until I see the complete data when Professor Gemmell's paper comes out.


The author can be contacted at lochnesskelpie@gmail.com







36 comments:

  1. Excellent summary GB.

    Regarding the lack of reptilian DNA or other missing life (Otters etc.), they did say the DNA was temporal and would degrade. Isn't it possible they just missed each other, so to speak. Wit that in mind, can reptilian life be totally ruled out?

    I was a little disappointed that they suggested very strongly that Eels or a giant Eel sightings are responsible, when clearly a lot of the sightings (including the video we see Prof Gemmell watching on the actual documentary) wouldn't match Eels, as you mentioned with the Morag Connor sighting.

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  2. Okay...

    There are many problems with eDNA detecting species. Or should I say how scientists interpret those eDNA results.

    This can be found by simply typing into Google the question "What is the error rate for eDNA testing?" To make something statistically meaningful it has to have results greater than 95% certainty. That means having 25% to 28% of the eDNA detection stuff unreadable or unidentifiable moots the whole claim of knowing the total types of creatures there are can be detected via eDNA testing in the Loch.

    As with any tests that involve biologicals, there are error rates. And eDNA is not immune to these errors.

    eDNA testing is also affected by seasonal changes--of how creatures operate in their environment, as well as the quality of the effluent at different times of the year, and so on.

    I don't want to get too pedantic here, but for eDNA testing to detect creatures properly there would have to be such testing throughout Loch Ness on a quarterly basis over probably at least two years, and probably have close to 350 to 450 sampling points--and doing this at least at five or six different consistent depths. I think that Roland correctly pointed out that nothing was taken way down deep, and there probably should have been. Also, eDNA actually lasts much, much longer in soils than in water. So taking samples off the Loch bottom might be a fruitful endeavor.

    Here are some URL links to papers that I think are decently germane. The scientists were trying to grapple with whether eDNA can actually detect endangered or rare species. The tests were in ponds, and not super huge bodies of water like Loch Ness. Another paper finds high rates of misidentification of species in eDNA, although these were looking at land-based creatures.

    Here are some URL links to what I am talking about.

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117544/
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798829/
    https://link.springer.com/article/10.1007/s10344-019-1264-8
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165273

    I would also direct your attention to Appendix B ("Cautions about the use of eDNA sampling") of the following paper at this URL link:
    https://www.fs.fed.us/rm/pubs/rmrs_gtr355.pdf

    So even though eDNA was tested at Loch Ness, the results are very far from definitive. It was a nice first foray, but more forays are needed.

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    1. Well nothing's perfect, it seems they managed to identify the majority of species bar the ones mentioned.

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  3. No otters proves that if they didn't go to certain areas wer certain creatures are they wudnt get dna of everything in the loch. I've always felt any monsters in the loch wud reside in the side walls and very bottom of the water so wud be intrestin to see how many samples wer taken deep down near the side walls? And I'm not sure how Mr gemmell can dismiss the 25% so easily.. That is a big amount of the tests to be unidentified and what if there was an unknown species living in the loch their dna wud have to come up as unknown or unidentified ! This test is far from conclusive in my humble!!... Cheers

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    1. So Roy, how is 25% unidentified from Loch Ness compared with a similar amount of unidentified from Loch Cluanie?

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  4. Roy, professor gemmell had to dismiss the unidentified 25% 'so easily' because for him the whole point of the exercise was to make a name for himself as The Expert on eDNA, he couldn't have the news headlines reporting the fact that he was only 75% successful, and that therefore any number of Nessie's could reside in the remaining 25%, that's why even at his own press conference that small detail did not get mentioned until the very last question from the audience, and even then he couldn't quite bring himself to say "25% remains unidentified", instead he merely mumbled "...20%." ever since that day I have been driving that detail home with any media outlet that I can, and have even managed to get a few of them to actually report that major fact.

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    1. Did they even sample the deepest parts of the loch (700ft +?) I would think that if a Nessie is a deep dweller and spends most of it's time in the deep, that would be where to sample. And mind you, a Nessie may be a creature that can withstand such high pressures and not necessarily a reptile. You ever see videos of creatures found thousands of ft in the deep ocean? If per chance a Nessie is an itinerant to the loch, it is a deep dweller in the ocean as well. We are dealing with something truly strange here. It ain't over till the fat lady... er fat Nessie sings.

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    2. My understanding is that DNA degrades by breaking into fragments. With a sufficiently small fragment it will be impossible to say what species is from (humans share about 60% of their DNA with fruit flies). Therefore any study that includes degraded DNA will fail to identify some.

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  5. Totally agree with u Steve Feltham and if any unknown creatures wer in the loch they wud come under the 25%! So Mr gemmell shudnt dismiss it so easily! I get the hint that he was just out to proove nessie wasn't a plesiosaur or that type of creature.. yet most of us have dismissed this theory many years ago! You could tell by the way the results kept getting put back and back until they came out just nicely in time for his tv programme that Mr gemmell wanted to make a name for himself! Keep up the good work of reminding the media of the 25% dna unknown... In my humble its very significant! Mr gemmell in my opinion hasn't prooved anything and as u rightly said before... We still have a mystery.. Cheers

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    1. I can assure you Roy, that 25% isn't a plesiosaur and to be fair to Prof Gemmell, he did not set out to find a long lost dinosaur. 6% or less according to the pie chart of eels, or maybe I'm color blind. Is that all? I thought the report said gizzzilions of eels

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    2. Still trying to get my goat "john"? LOL

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    3. JA, I did ask Prof Gemmell if the various amounts of DNA could give an estimate of biomass, he said it couldn't. That was an absolute number, could the DNA numbers give relative population indicators (e.g. more eels than char)? Possibly, but that would suggest the sampling was equally proportionate for all species.

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  6. John alvarado u don't need to assure me that 25% is not a plesiosaur.. I didn't say that! And I disagree with u.. Im not saying gemmell set out 'solely' to say nessie wasn't a plesiosaur but he cudnt wait to announce it...why else wud he mention it! I don't see any of the monster Hunters or anyone who has an interest in the mystery saying its a plesiosaur.. Bit old hat that!.... What I'm saying is that if an unknown or unidentified creatures dna was picked up in the loch it wudnt be coded therefore wud come under the unknown or unidentified dna!... Cheers

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    1. Quite right Roy. Hard to get away from the "Plesiosaur" model. You mention Loch Ness Monster in conversation and most people think plesiosaur. LOL

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    2. Years ago ..not so much now.. some things cam resemble a plesiosaur without bin one !!

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    3. Roy, can you stop saying HUMBLE? I know somebody had a dig at your writing methods but from my point of you are great 4 this blog and the loch ness monster. You know your stuff indeed. So if it makes you feel better i will buy some tennants, buy Ted Holiday's book and look up the Tullimonstrum and maybe write like you now and again....ok....??? LOL only joking Roy, i have 2 admit i agree with most things you say.Keep it coming.

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  7. I didnt mean gemmell shudnt dismiss 25% as a plesiosaur I meant he shudnt dismiss getting 25% unknown dna as nothing to get excited about.. . Or along them Lines. He tried to say its normal and means nothing but the point Im making is if there is anything new to science or unknown or even a hybrid then u wudnt get a complete match therefore it wud come under the 'unknown'.. So for me plus the missing otters it all adds to us still having a mystery...to be honest I think humble me cud of told Mr gemmell that there was no plesiosaurs in Loch Ness and there is eels!!!!! Lol . . Cheers.

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  8. I agree, most interviews with Prof Gemmell he always mentioned a plesiosaur.It was like he was saying No plesiosaur no monster.

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  9. Way back before this eDNA study I stated there were too many variables at Loch Ness. I knew it. Inconclusive results and now many unanswered questions. A 25% window of non usable data, this study should be a model for practicing eDNA methods.

    Every water sample depth/location must have been recorded. Am I missing those records? After all the decades of searching that Loch it's clear by now that room for error should be minimalized as much as humanly possible. It just seems every effort of search always contains grey areas.

    One thing those results indicate to me is that Nessie has more on the menu than just fish. She ( they ) may be large enough to eat duck, birds, rodents, possibly young otters.

    Still need a proper photo or video though.

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  10. Still.....it would be awesome to find a plesiosaur in Loch Ness :-D

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  11. Question: Are there no turtles in Loch Ness?

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    1. From what I've read there are no native turtles in the UK, just North American and European ones that have been introduced to some bodies of water (probably released pets), and it is not clear if these can reproduce. Found nothing about turtles in Loch Ness...

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  12. There's absolutely no viable reason why plesiosaurs can't be inhabiting Scottish lochs.Karl Shukers makes a great argument for this in his excellent book "In Search of Prehistoric Survivors".I've always been firmly in the Plesiosaur camp on this one & always will be.The evidence is just too compelling.

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    1. Triumph100rider there is little chance of any plesiosaur surviving the cold of Loch Ness for longer than a few weeks. Unless they became amphibious and have survived the ages no plesiosaur would survive a winter in Loch Ness. The Loch is too cold for reptiles

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    2. There is evidence that the plesiosaur family did live in cold water...
      https://www.foxnews.com/science/how-did-giant-reptilian-dinosaurs-stay-warm-in-frigid-oceans

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  13. Yeah u wud think so Jordan.. but then again u woudnt of thought terrapins wud survive in British lakes in cold winters but they have for over 20 years! Remarkable... Cheers

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  14. So it looks like the eDNA results have decimated this page it's like a funeral wake over here. A few years ago I still held up some hope of a small herd of large animals living in the Loch but you can't deny that evidence is pretty thin on the ground these days and this blog has many times highlighted the obvious fakes and mistakes despite the rampant followers ready to believe the slightest splash or long distance blur is strong evidence of something unusual in Loch Ness. You staunch believers are getting trapped into a lonely narrowing corridor with all this benthic rubbish. it's a shame and it's a great old story but I think you will still be inventing make believe animals ten years from now with no more positive results and probably a lot more negative evidence.

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    1. Well, if you had read the article properly, it was stated that this "benthic rubbish" was concluded long before any eDNA tests. I can quite understand why they could not sample that region enough, but I do not have the full results, which probably doesn't help much either.


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    2. So are you saying that you used to be as dumb as the rest of us seem to be?

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  15. Jordan, for the record it's becoming increasingly recognized by the paleontologists that at least some plesiosaurs were a lot more cold tolerant than previously thought. Fossils have been found in environments that had an antartic climate at the time the animals were alive.

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  16. Its amazing how animals can adapt. I remember having this argument with Tony Harmsworth, but it would not sink in with him. He thought hee knew it all.

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  17. I will post three URL links here. What this data tells me is that things relating as to when plesiosaurs/elasmosaurs died off is quite murky. There are fossil finds pointing to plesiosaur materials into the Cenozoic/Paleocene era. But it is controversial, and these claims have been identified as finds that are "re-worked" deposits, but strangely enough, the "re-working" would have to have the fossils migrate "upwards" rather than "downwards"....

    And of course, the Alvin sighting from 1965, near the tail end of its very first month of operations....checking out the ARTEMIS array on the sea floor about 5,000 feet down. This indicates that sea reptiles of the Mesozoic could dive really deep down.

    https://pinebarrensinstitute.com/cryptids/2018/8/18/cryptid-profile-the-dsrv-alvin-plesiosaur

    https://www.academia.edu/23213363/Plesiosaur_Questions_and_Answers_by_Scott_Mardis

    https://www.academia.edu/7557849/Perspectives_on_the_Living_Plesiosaur_Controversy

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  18. paddy, okay perhaps plesiosaurs could live in cold waters and could survive Loch Ness. The loch was solid ice up until 10,000 years ago. It's possible sea creatures may have come in from the sea and became trapped as the land rose. Slim odds though of plesiosaurs ever making it in - no evidence they survived until now.
    Being air breathers they would be observed often and would have been photographed regularly. They would appear as actual creatures and not dark blotches from a distance. It would be like whale watching, tour boats would know the best spots to view them.
    Visit Loch Ness and you will notice locals are not fixed on the Loch, they are not glued to the surface with a camera in hand or binoculars. Plesiosaurs are not living in the Loch, sorry to break it to you. Look at the lack of evidence, no dinosaurs. No clear photo's or videos. No bones or tissue samples. No hydrophone recordings. No sonar recordings that are clear.
    Let it sink in and stop wanting dinosaurs to be living in Loch Ness. The ocean possibly.

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  19. Jordan, I was not arguing that there are plesiosaurs in Loch Ness, only pointing out that they were more cold tolerant than previously thought. As for the LNM I'm more or less a fence-sitter.

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  20. A Canadian lake monster theorized by some to be a giant eel. Note that divers there recently reported being attacked by eels as thick as a man's thigh!
    https://www.cbc.ca/news/canada/newfoundland-labrador/water-monster-cressie-1.5340888

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