New Italian Vipera

[Ruggero M.]

https://www.researchgate.net/publicatio ... NA_markers


Abstract
The review considers the current problems of molecular phylogenetics based on mitochondrial and chromosomal DNA sequences. The emphasis is placed on mtDNA markers, which are widely employed in reconstructing molecular evolution, but often without a critical analysis of the physiological and biochemical features of mitochondria that affect the adequacy and reliability of the results. In addition to the factors that make mtDNA-based phylogenies difficult to interpret (unrecognized hybridization and introgression events, ancestral polymorphism, and nuclear paralogs of mtDNA sequences), attention is paid to the nonneutrality and unequal mutation rates of mtDNA genes and their fragments, violations of uniparental inheritance of mitochondria, recombination events, natural heteroplasmy, and mtDNA haplotypic diversity. These factors may influence the congruence of phylogenetic inferences and trees constructed for the same organisms with different mtDNA markers or with mitochondrial and nuclear markers. The review supports the viewpoint that mitochondrial genes and their fragments fail to provide reliable evolutionary markers when considered without a thorough study of the environmental conditions and life of the taxa.

[Jeroen Speybroeck]

https://www.researchgate.net/publication/257842569_The_problems_of_molecular_phylogenetics_on_the_example_of_squamata_reptiles_Mitochondrial_DNA_markers


Abstract
The review considers the current problems of molecular phylogenetics based on mitochondrial and chromosomal DNA sequences. The emphasis is placed on mtDNA markers, which are widely employed in reconstructing molecular evolution, but often without a critical analysis of the physiological and biochemical features of mitochondria that affect the adequacy and reliability of the results. In addition to the factors that make mtDNA-based phylogenies difficult to interpret (unrecognized hybridization and introgression events, ancestral polymorphism, and nuclear paralogs of mtDNA sequences), attention is paid to the nonneutrality and unequal mutation rates of mtDNA genes and their fragments, violations of uniparental inheritance of mitochondria, recombination events, natural heteroplasmy, and mtDNA haplotypic diversity. These factors may influence the congruence of phylogenetic inferences and trees constructed for the same organisms with different mtDNA markers or with mitochondrial and nuclear markers. The review supports the viewpoint that mitochondrial genes and their fragments fail to provide reliable evolutionary markers when considered without a thorough study of the environmental conditions and life of the taxa.

Useful link, thanks! Yet, (1) uniparental inheritance (and some other problems listed) is still rare (2) the walser case was not based solely on mtDNA and (3) the signal their mtDNA data gives is just too strong.

[Ruggero M.]

Useful link, thanks! Yet, (1) uniparental inheritance (and some other problems listed) is still rare (2) the walser case was not based solely on mtDNA and (3) the signal their mtDNA data gives is just too strong.

Thanks Jeroen!
I think you make the question too easy in only 3 lines!

Point 1) You have written the concept wrongly, but I won't use this fact in my favor!
Uniparental inheritance of mithochondria "should" be the norm: you should have written: " VIOLATIONS of uniparental inheritance of mitochondria " is still rare.
It does not seem to be so rare indeed, and, if you sum this problem with the many others present (high frequency of mutations in mtDNA -this is well known-, possibility of hybridization, introgression events, recombination events, and so on...) you can argue the heavy probability that mtDNA studies could mean, in our case, almost nothing. Especially if you consider that hybridization (with aspis? the discussion started from this interesting concept!) could be happened not hundreds years ago, but maybe thousands years ago...

Point 2) You write: "the walser case was not based solely on mtDNA".
Fortunately not. But of nuclear DNA we have only one sample, taken from an old preserved specimen, compared with one sample each of 3 other species...
I would like to compare the sequences of this DNA with the ones taken from a second specimen of walser: maybe (but not totally surprisingly) could be that the two samples are totally different each from the other!
In the abstract I've linked you can read: "The review supports the viewpoint that mitochondrial genes and their fragments FAIL to provide reliable evolutionary markers when considered without a thorough study of the environmental conditions and life of the taxa."
Ok: what does tell us the analysis of mtDNA? "Walser" is closely related to kaznakovii...
What does tell us the study of the environmental conditions and life of the taxa?
It says us that the taxa lives 3000 km (maybe less, maybe more...not important) far from the Turkey, where the kaznakovii lives: it's impossible that they are closely related, and of the two evidences, the mtDNA one is necessarily the wrong one!
Besides this, the study of the environmental conditions and life of the taxa tell us (you were there) that the "walser" is an isolated viper population inside the areal distribution of berus, which live in strict contact with many specimens of aspis viper. And the observation tell us also that the slight external differences between "walser" and typical berus are all in the direction of an "aspis morph viper": fragmentation of head scales and discontinuity of the dorsum markings.
And I remember what Gregoire Meier thought when he met a walser viper for his first time: something like "it was strange, and I was not sure if it was a berus or an aspis..."


Point 3) Very simple answer. Are you really sure the mtDNA proof is "too" strong in our case?

[Ruggero M.]

Paper says:

The genetic differentiation between V. walser and V. berus, both on mitochondrial and nuclear DNA,
is beyond known values between well-established species within the same subgenus.

Don't know what more the slow readers seem to need.

Nothing more, indeed, if one believes in this "verdict" - and why shouldn't one, after all? That's the most
important issue (regarding the publication). All the rest is just conjecturing, showing-off knowledge and
alike... But I certainly wouldn't discourage anyone to "think aloud". Mario said he would not - for the time
being - and I sided with him, but that's just a private decision, not a recommendation to anyone.

I take this phrase of our herp friend Bero (if one believes in this "verdict") as a starting point for other in my opinion interesting and maybe not so obvious considerations.

Another interesting aspect of our problem is that DNA analysis statements require always (as Bero correctly wrote) from the side of the "readers" a grade of “belief”.
I will explain this.
This is a well known problem also in legal medicine: in these days is on the Italian news the fact that a guy is condemned for homicide only or almost only from the base of DNA analysis.
And the legal doctor wrote he had many difficulties to explain to all the laymen how reliable the DNA test is.
The problem is actually not so easy:
1) At first the test MUST be really 100% reliable (and in the case of our mtDNA it’s not!);
2) Second problem: people must understand not perfectly but at least rather well why it’s so reliable (we all don’t know much about DNA sequences, differences of nuclear DNA and mtDNA, and so on: me included, as I’ve already pointed out!);
3) People must ANYWAY trust 100% the person (legal doctor, geneticist, scientist…) who materially took the samples and made the test: not only must be that person in totally good faith, but he/she must be very well prepared and experienced (which DNA sequences could be similar, which could be often different, which sequences must be examined, which not and so on) and have a good practical and manual “technique”;
4) I'm always for the double blind studies. And the studies of DNA sequences are normally not double blind ones. The researcher, on the contrary, knows perfectly what he's working for, and which are the samples he/she is analyzing.

As regards the case of homicide in Italy, for instance, I cannot be 100% sure of the guilt of the condemned: too many variables are present, and the percentage of faith/belief required is too high for me.
I cannot say nothing: I hope only that who made the DNA test was a honest and well trained doctor, and that the test was actually 100% reliable.

To summarize my concept.
If I show you a new species and all the people can clearly see the markings/colors differences, the morphology of the animals, their distribution... the acceptance of this new species is automatic: not a “faith” but a "fact".

If a species is determined almost exclusively by DNA studies (which, in our case, are NOT 100% reliable), the acceptance of this new species is only (for most of us, except obviously for the authors of the study!) more or less a “belief” thing.

[Ilian Velikov]

I've been following this thread with interest. I'm not a scientist and I only have a basic knowledge regarding DNA and almost none regarding how it is tested and so on. So as Berislav and Ruggero pointed out I have to believe what the scientist say. However, this whole separation of species based on DNA analysis seems very abstract to me. As it is well known for considerable time the old accepted definition of "species" is incorrect. So for me anything following that cannot be regarded as a fact and it makes me cautious with putting my trust in what scientist say regarding those "new species". How can scientists divide species into new species when they don't even know what "species" is? And how can people trust them in this case? I think before this question is answered it's all a bit "too much noise for nothing".

[Jeroen Speybroeck]

If I show you a new species and all the people can clearly see the markings/colors differences, the morphology of the animals, their distribution... the acceptance of this new species is automatic: not a “faith” but a "fact".
If a species is determined almost exclusively by DNA studies (which, in our case, are NOT 100% reliable), the acceptance of this new species is only (for most of us, except obviously for the authors of the study!) more or less a “belief” thing.

OK, I will start writing a paper about Vipera atra, a black species that lives together with Vipera aspis populations in the Alps. All the people will see the difference and say “fact”.
You keep saying “NOT 100% reliable” but that strikes me as a subjective notion. There IS morphological data and we can always cry out that we want more evidence, but then nothing ever gets resolved. Personally, I myself call for more evidence if restricted gene flow is likely and not looked into. While I am very curious about the existence of natural (sterile) walser x aspis hybrids, I don’t think much else is or has been going on.

I think you make the question too easy in only 3 lines!

While I do appreciate this (after all, I asked for it, practically), I want to try to write a forum post, not an essay (although it’s hard to be brief, I admit, and I am certainly not very good at it).

I’ll try to be brief again. Probably will fail, though.

I am also mainly fascinated rather than fully up to speed with this, so I won’t bet my life on the validity of any species. But still..

1) The support of the branches that set it apart from aspis and berus is strong and the entire tree is in line with the evolutionary relationships between all involved species as understood today. Both your alleged hybrid parent species are far away from their alleged walser child and I cannot believe that a mixture of them would produce a Frankenstein that would pop up within an entirely different group.
2) If the nuclear markers are properly chosen, one animal per species can be enough.
3) There are plenty of sister taxa that are very far apart (even across oceans) and imho kaznakovi and walser ecology are fairly similar.
4) So what if walser lives together with aspis? The same goes for ursinii/aspis (France), ursinii/ammodytes (Greece), ursinii/bosniensis (Montenegro), ammodytes/xanthina (Greece), despite the text book cliché of niche segregation.
5) So what if walser has aspis-like traits? Look at the Vipera graeca example (and the understandable Tomovic response that Bero described). The entire Vipera berus “Alpine clade” also looks like aspis. Is that due to introgression? Is bosniensis flooded with aspis genes? Don’t let morphology and the limitations of our eye and urge to see what we know fool you…
6) Finally, I know it’s a lame argument which I have criticized myself in the past too, but I would have a hard time imagining Sylvain Ursenbacher authoring a piece that would omit such a radically different possibility. If only he, or maybe WW, could share their wisdom with us. In fact, I might ask Sylvain “can you rule out a hybrid origin?”…

I am usually fairly skeptical about poorly substantiated splits (no Emys trinacris, Bufotes variabilis, Salamandra longirostris, Stellagama, Hierophis carbonarius, Darevskia pontica, Zootoca carniolica for me (yet)), but this is just too strange not to be true, to put it bluntly. My understanding of the details is limited, but for now, I see absolutely no reason to reject it, I think the evidence suffices.

Voila! Not much more to add, I think, from my part. Or rather, already too much

[Grégoire Meier]

Discussion very interesting and I agree with the relativity of genetic analysis ... or rather I believe we still understand very little of genetics.

Of course, in areas at low altitude Vipera walser lives with Vipera aspis atra (I doubt genetics, so atra). We must explore the habitat of higher share and understand if aspis them live, or if it happens what happens in other areas, that such aspis gives way to berus.


Then I see an animal like this .... and this is really thinking

. by Greg, auf Flickr
Vipera berus by Greg, auf Flickr

https://www.flickr.com/photos/31371458@N06/28128834115/in/dateposted-public/

sorry, my english is bad and I'm not able to put photos right here ... sorry!

edit by Mario (admin): for Flickr pictures with NO *.jpg, etc in the link. Use the share link (between favorite and download link - BBcode (choose size and copy this link shown. insert here

[Jeroen Speybroeck]

I sent these questions and will let you know the answers, if I get any.

1) Can we, with what is available in terms of data, rule out that walser stems from an ancient ‘hybrid’ origin?
2) Is one specimen per species enough for the applied nuclear analysis, or are these markers just highly conservative (within each species)?
3) How would you interprete the berus-like morphology of walser? Often, people would shout “convergence”, but I don’t really see what the evolutionary drivers would be to force this taxon into the looks of an equally useful design.
4) Is there any hybridisation with aspis documented? If not, how likely would you consider it to be.

[Grégoire Meier]

I agree with Jeroen, Sylvain is one of the leading specialists and I do not think he would have a light weight and does not take into account the different hypotheses.
I think the species is valid ... the nature reserve us many surprises.


I am still interested to read the answers you receive.

[Jeroen Speybroeck]

There's also what I would like to call the Mind-Clouding Effect of the Search Effort. People who make a special effort to find an animal want it to be at least a different species. So, I'm all for walser.