Climate change affects the genetic diversity of a species

“When I use a word,’ Humpty Dumpty said in rather a scornful tone, ‘it means just what I choose it to mean — neither more nor less.’
’The question is,’ said Alice, ‘whether you can make words mean so many different things.’
’The question is,’ said Humpty Dumpty, ‘which is to be master — that’s all.”

An analysis of the alpine marmot’s genome

Charité – Universitätsmedizin Berlin

IMAGE: Playing marmots. Credit: Carole and Denis Favre-Bonvin
IMAGE: Playing marmots. Credit: Carole and Denis Favre-Bonvin

What effects does climate change have on the genetic diversity of living organisms? In a study led by Charité – Universitätsmedizin Berlin, an international team of researchers studied the genome of the alpine marmot, an ice-age remnant that now lives in large numbers in the high altitude Alpine meadow. Results were unexpected: the species was found to be the least genetically diverse of any wild mammal studied to date. An explanation was found in the marmots genetic past. The alpine marmot has lost its genetic diversity during ice-age related climate events and been unable to recover its diversity since. Results from this study have been published in the journal Current Biology*.

A large rodent from the squirrel family, the alpine marmot lives in the high-altitude mountainous terrain found beyond the tree line. An international team of researchers has now successfully deciphered the animal’s genome and found the individual animals tested to be genetically very similar. In fact, the animal’s genetic diversity is lower than that of any other wild mammal whose genome has been genetically sequenced. “We were very surprised by this finding. Low genetic diversity is primarily found among highly endangered species such as, for instance, the mountain gorilla. Population numbers for the alpine marmot, however, are in the hundreds of thousands, which is why the species is not considered to be at risk,” explains Prof. Dr. Markus Ralser, the Director of Charité’s Institute of Biochemistry and the investigator with overall responsibility for the study, which was co-led by the Francis Crick Institute.

As the alpine marmot’s low genetic diversity could not be explained by the animal’s current living and breeding habits, the researchers used computer-based analysis to reconstruct the marmot’s genetic past. After combining the results of comprehensive genetic analyses with data from fossil records, the researchers came to the conclusion that the alpine marmot lost its genetic diversity as a result of multiple climate-related adaptations during the last ice age. One of these adaptations occurred during the animal’s colonization of the Pleistocene steppe at the beginning of the last ice age (between 110,000 and 115,000 years ago). A second occurred when the Pleistocene steppe disappeared again towards the end of the ice age (between 10,000 and 15,000 years ago). Since then, marmots have inhabited the high-altitude grasslands of the Alps, where temperatures are similar to those of the Pleistocene steppe habitat. The researchers found evidence to suggest that the marmot’s adaptation to the colder temperatures of the Pleistocene steppe resulted in longer generation time and a decrease in the rate of genetic mutations. These developments meant that the animals were unable to effectively regenerate their genetic diversity. Overall results suggest that the rate of genome evolution is exceptionally low in alpine marmots.

Commenting on the significance of their results, Prof. Ralser says: “Our study shows that climate change can have extremely long-term effects on the genetic diversity of a species. This had not previously been shown in such clear detail. When a species displays very little genetic diversity, this can be due to climate events which occurred many thousands of years ago,” He adds: “It is remarkable that the alpine marmot managed to survive for thousands of years despite its low genetic diversity.” After all, a lack of genetic variation can mean a reduced ability to adapt to change, rendering the affected species more susceptible to both diseases and altered environmental conditions – including changes in the local climate.”

Summarizing the study’s findings, Prof. Ralser explains: “We should take the results of the study seriously, as we can see similar warnings from the past. In the 19th century, the passenger pigeon was one of the most abundant species of land birds in the Northern Hemisphere, yet, it was completely wiped out within just a few years. It is possible that low genetic diversity played a role in this.” Outlining his plans for further research, he adds: “An important next step would be to study other animals more closely which, like the alpine marmot, managed to survive the ice age. These animals might be trapped in a similar state of low genetic diversity. Currently, estimates of a particular species’ extinction risk are primarily based on the number of animals capable of breeding. We ought to reconsider whether this should be the only criterion we use.”

###

Information on this study

Prof. Dr. Markus Ralser was appointed Einstein Professor for Biochemistry at Charité in May 2018. An expert in metabolism, Prof. Ralser came to Charité after spending time at the Francis Crick Institute in London and the University of Cambridge, where he led teams involved in this study. Other researchers involved in the research hailed from the University of Sheffield, Bielefeld University, the Max Planck Institute for Molecular Genetics and other institutions. The researchers originally set out to study the alpine marmot’s genome in order to gain a better understanding of the animal’s lipid metabolism.

* Gossmann et al., Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity, Current Biology. 2019 May 20;(29): 1-9. doi: 10.1016/j.cub.2019.04.020

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Hartog van den Berg
May 26, 2019 10:10 pm

Somebody should call Darwin?

Sheri
Reply to  Hartog van den Berg
May 27, 2019 5:58 am

Somebody in climate change research should read Darwin. I am always amazed how climate scientists deny and disparage Darwin. It’s as if ignoring or destroying Darwin somehow makes their case so much better. So much for “following the science”. Or was Darwin now declared “unscientific” and I missed it?

R Shearer
Reply to  Sheri
May 27, 2019 7:55 am

Climate change in this study clearly means natural climate change, that which involved glacial cycles. This is not the “climate change” being bandied about by most “climate change” researchers.

Over time, science should lead to more precise and accurate terminology. Modern “climate science” instead obscures such definitions. Therefore, it is not very good science.

Keith Rowe
Reply to  R Shearer
May 27, 2019 6:06 pm

Confused. Usually this low level of genetic diversity is from dwindling to a low population and rebounding. Like … after the last ice age. Not sure how this obviousness got past the peer review process. OH wait, it was climate change per review….anything gets a pass if it says the right thing.

tobyglyn
May 26, 2019 10:18 pm

Give us more money!

Moderately Cross of East Anglia
Reply to  tobyglyn
May 27, 2019 12:33 am

No, give the Marmots the money and tell them to go out more on the razz and meet new friends.

Or maybe who cares?

Jeff Alberts
May 26, 2019 10:35 pm

They used a lot of words to say, animals adapt. Next!

Mike
May 26, 2019 10:56 pm

”Climate change affects the genetic diversity of a species”

Yeah it’s called evolution dude

May 26, 2019 11:16 pm

1. Researcher studies Marmots because being in the mountains is fun.
2. Genetic diversity in isolated mountainous populations of marmots tells us “stuff” about changes in climate as ecosystems connect and disconnect over deep time.
3. Throw in “climate change” for changing climate as “stuff” is figured out.
4. Grant renewal.

– So Can ya’ blame a guy wanting OPM to fund his fun “stuff” in the mountains?

Reply to  Joel O'Bryan
May 27, 2019 12:20 am

The skiing is fantastic, there, Joel. I’m sure that they are also studying the snow bunnies (aka “rich young unmarried females”).

R Shearer
Reply to  Writing Observer
May 27, 2019 7:22 am

One has to take a lot of trips in the winter to get a glimpse, especially when flying down the hills at high speed.

tty
Reply to  Joel O'Bryan
May 27, 2019 3:35 am

Unfortunately the marmots are hibernating while snow bunnies are around.

MarkW
Reply to  tty
May 27, 2019 7:13 am

More time to spend on the snow bunnies.

Louis Hunt
May 26, 2019 11:24 pm

“The alpine marmot has lost its genetic diversity during ice-age related climate events and been unable to recover its diversity since.”

I guess we had better put more CO2 into the atmosphere to help stave off another ice-age that might cause the marmot to go extinct. Is that the take-away?

Reply to  Louis Hunt
May 27, 2019 12:53 am

I think you have it reversed. The Alpine Marmot is adapted to being buried in ice and snow for long periods. Therefore it range should be vastly expanded by the return of the ice age. That lack of diversity might supply genetic material for all humans in the coming centuries.

Alex
May 26, 2019 11:36 pm

Perhaps they are so well adapted that they don’t need to change.

Susan
Reply to  Alex
May 27, 2019 12:38 am

They’ve found a formula that works – if it ain’t bust, don’t fix it!
Surely it is stable climate that leads to one genetic variety predominating?

Samuel C Cogar
Reply to  Alex
May 27, 2019 7:54 am

Perhaps they are so well adapted that they don’t need to change.

EXACTLY ….. what I surmised.

A large rodent from the squirrel family, the alpine marmot lives in the high-altitude mountainous terrain found beyond the tree line. An international team of researchers has now successfully deciphered the animal’s genome and found the individual animals tested to be genetically very similar. In fact, the animal’s genetic diversity is lower than that of any other wild mammal whose genome has been genetically sequenced.

As the alpine marmot’s low genetic diversity could not be explained by the animal’s current living and breeding habits, ………………..

“DUH”, …….. is not the alpine marmot’s past and present “unchanging” environment (Alpine meadows in high-altitude mountainous terrain) ……. not reason enough to explain their “lower than normal” genetic diversity throughout their populations?

Gene mutations are either neutral, harmful or helpful, …… but to be denoted as “helpful”, said gene must make the offspring(s) better adapted to its changing environment, which increases its survival chances, …… and with greater survival chances means that “helpful” mutation will …… result in genetic diversity throughout the population.

But when one’s environment (Alpine meadows in high-altitude mountainous terrain) ……. has not changed much in thousands of years, …… then I would think that all gene mutations would be either “neutral or harmful”.

ray boorman
May 26, 2019 11:53 pm

No matter what they find, in any field of science related to climate, it’s always “worse than we thought”, and “give us more money to research this important finding”.

Now it’s an animal, very common in it’s home range, that could, maybe, if the ducks line up, be actually endangered, despite everything previously thought.

Boring.

ScienceABC123
May 27, 2019 12:28 am

Quoting Alice in Wonderland in a discussion about climate change, how appropriate.

paul courtney
Reply to  ScienceABC123
May 27, 2019 4:14 pm

Science A: I enjoyed that, too. “Squirrel (and Moose?) adapts to mountain top, other squirrels get snobby”, and they blame climate change? What next, “climate change causes snow, cold”? Oh, wait….

lee
May 27, 2019 12:35 am

“When a species displays very little genetic diversity, this can be due to climate events which occurred many thousands of years ago,” He adds: “It is remarkable that the alpine marmot managed to survive for thousands of years despite its low genetic diversity.”

So Climate events CAN alter genetic diversity. But DID it? And it survived thousands of years both warming and cooling. 😉

Reply to  lee
May 27, 2019 6:24 am

Or the populations simply moved upslope or downslope a few hundred metres to find the optimum
“climate” for genetic tolerance.

Jeff Alberts
Reply to  lee
May 27, 2019 8:29 am

What’s a “climate event”?

Dhémaïus
Reply to  Jeff Alberts
May 27, 2019 9:38 am

Is an interglacial period a climate event?

David Long
May 27, 2019 12:56 am

Apparently, with a little more genetic diversity, the passenger pigeon would have been more able to withstand bullets.

Tim.
Reply to  David Long
May 27, 2019 1:56 am

That response crossed my mind too.

ozspeaksup
Reply to  Tim.
May 27, 2019 3:16 am

ditto!

and seeing as the blood lipids was the supposed reason fro the marmot study they failed to mention a damn thing on that. whatever levels they have theyre doing just fine it would appear.

R Shearer
Reply to  ozspeaksup
May 27, 2019 7:20 am

The marmots in the Rocky Mountains appear to be stockier with fuller coats. In Colorado we have prairie dogs that are similar in appearance to those two animals in the picture. I wonder what this says about genetic diversity.

Randy
May 27, 2019 1:04 am

If those damn marmot get any less diverse they’re going to take over the world.

Javier
May 27, 2019 1:50 am

The scientific work is very good. The findings very interesting and significantly advance our knowledge. The comments, however, are very low level.

https://www.sciencedirect.com/science/article/pii/S096098221930418X

Highlights
•The Alpine marmot is among the least genomically diverse animal species
•Its diversity was lost during consecutive ice-age climate-related events
•An extreme lifestyle hampered the subsequent recovery of genetic variation
•Alpine marmots show why large populations can coexist with very low genetic variation

Low genetic variability translates into low capacity to adapt and evolve, and high susceptibility to diseases, resulting in a higher risk of extinction.

ozspeaksup
Reply to  Javier
May 27, 2019 3:20 am

yup and the tasmanian devil facial tumour problem is one good example small gene pool on an island most have the bad genes that keep the tumours growing and spreading. normally nature would take its course and the very few resistant ones would be left ..even smaller gene pool

tty
Reply to  Javier
May 27, 2019 3:47 am

It’s not that simple, since there are many species and populations that survive extremely well with low or even zero genetic diversity. Apomictic plants (e. g. dandelions) being an extreme example.

While it is true that all apomictic lineages must ultimately go extinct, this does not apply to sexually reproducing low-diversity lineages.

Javier
Reply to  tty
May 27, 2019 4:37 am

Plants are weird genomically. Apomixis is common in polyploids:
“Apomictic species or individual plants often have a hybrid origin, and are usually polyploid.[13]”
Therefore, as polyploids and often hybrids, they have an starting higher genetic variability.
The clonal reproduction appears to be a way of rapid mass production reducing the time to reproduce. This creates multiple lineages or microspecies that are a taxonomical nightmare.
“It appears unlikely that there are any truly completely apomictic plants, as low rates of sexual reproduction have been found in several species that were previously thought to be entirely apomictic.[11]”

So it is not a genetic impoverishment as in the case of the marmot. It is just that plants can do a lot more genomic things than animals. No nervous system though, so they don’t miss the lost sex.

Edwin
Reply to  Javier
May 27, 2019 9:47 am

Ok, now explain Indo-Pacific Geckos, one of the most successful and today widespread geckos in the world. They are parthenogenic. In other words they are all females and have been shown to be a very successful invasive species, found throughout the tropics and subtropics.

The author’s Passenger Pigeon example seems a bit off the wall. Passenger Pigeons are a good example showing that when humans set their mind to it they can drive even the most abundant species to extinction. Their extinction had damn little to do with genetic diversity.

tty
Reply to  Javier
May 27, 2019 10:13 am

You can forget about sexual reproduction in most dandelions. They don’t even produce any pollen. And parthenogenesis isn’t really that rare in animals either, though it apparently never occurs in mammals.

In the short run asexual reproduction is twice as efficient as sexual, since all individuals can produce offspring, but at the cost of forgoing genetic recombination.

Joel Heinrich
Reply to  tty
May 27, 2019 11:35 am

I don’t know when you last saw a dandelion, but the ones here are full of pollen. And busily visited by bees.

DaveW
Reply to  tty
May 28, 2019 12:56 am

I’m not sure that apomicts need go extinct any faster than sexual lineages, although it is probable that sexual lineages with very low genetic diversity are on a short tether. Many plant parthenogens are polyploid and extraordinarily robust (which is why many are weeds). Bdelloid rotifers seem to have been able to survive for at least 25 million years based on fossils. Thelytoky (all female parthenogenesis) and highly inbred haplo-diploid systems are very common in invertebrates and they seem to do just fine. A high degree of clonal diversity is often found in parthenogens and lineage sorting has given rise to morphological radiations, or so it seems. If you live in a fairly stable environment, then I’m not sure genetic diversity is all it is cranked up to be. And, of course, prokaryotes get by without sex and have done so for billions of years (although they do have interesting ways of assembling new genomes as that interesting review on plague that you linked in another discussion pointed out).

R Shearer
Reply to  Javier
May 27, 2019 7:34 am

I don’t think so, on admittedly a cursory examination. Populations of alpine marmots inhabit more than a dozen mountain ranges over several continents. A study on genetic diversity might have included some of these others.

tty
Reply to  R Shearer
May 27, 2019 10:45 am

Nope. The Alpine Marmot Marmota marmota only occurs in European mountains from the Pyrenees to the Carpathians. There are about ten other montane species in Asia and North America and also a few lowland species in steppe and woodland habitats (e. g. bobak marmot, woodchuck).

The only marmots I would consider as threatened or vulnerable are the Vancouver marmot and the Olympic marmot which are isolated and have small populations.

R Shearer
Reply to  tty
May 27, 2019 2:03 pm

You’re correct about the alpine marmot’s range and definition. I made an incorrect assumption probably because I see marmots often in the Colorado mountains.

There are however over a dozen other marmots that live within alpine habitats.

Javier
Reply to  R Shearer
May 27, 2019 3:11 pm

The article is about Alpine (Alps) marmots, not alpine (other mountain ranges) marmots.

Spain has a few cold adapted fauna that are remnants of the Pleistocene and some of they are having a very hard time surviving. The Pyrenees ibex, a subspecies of the Iberian ibex, went extinct in 2000 despite great efforts. They tried to clone it but it didn’t work. A lot of effort is going also into saving the Cantabricus subspecies of the Western capercaillie, but it doesn’t look good. There are very few left and last year a male died of stress while trying to sing its courtship song after being chased by excursionists trying to get a good shot with their mobile phones.

R Shearer
Reply to  Javier
May 27, 2019 6:54 pm

Yes, you are right. I wonder why “alpine” was not capitalized in modifying marmot but it was in modifying meadow. Seems backwards to me.

“Universitätsmedizin Berlin, an international team of researchers studied the genome of the alpine marmot, an ice-age remnant that now lives in large numbers in the high altitude Alpine meadow.”

flyfisher
Reply to  Javier
May 27, 2019 11:45 am

There are some lines of evidence that ‘source’ of this variability is cellular stress. This has been shown to increase the mutation rate in a few model organisms. If we are to completely accept the hypothesis that climate change is to blame for their lack of diversity, couldn’t we also accept the possibility that these rodents are completely comfortable in their environs – hence, no need to change?

Xenomoly
Reply to  Javier
May 27, 2019 1:08 pm

I don’t think that it follows that low genetic variabilities necessarily indicates and inability to adapt or evolve. The selection pressures they are under appear not to have changed because they can just alter their location in range on the slope of the mountain to acquire the same sorts of Flora and fauna through larger scale climate changes.

Mike Ozanne
May 27, 2019 2:49 am

” In the 19th century, the passenger pigeon was one of the most abundant species of land birds in the Northern Hemisphere, yet, it was completely wiped out within just a few years. It is possible that low genetic diversity played a role in this.”

So it lacked the genetic diversity to become immune to birdshot?? How long do you have to study to get this stupid?

Vicus
Reply to  Mike Ozanne
May 28, 2019 1:40 pm

I want to know what happened to the Rocky Mountain Locust. Largest movement of Life ever, just disappears.

Kurt Linton
May 27, 2019 3:05 am

“After all, a lack of genetic variation can mean a reduced ability to adapt to change” and also “the passenger pigeon was one of the most abundant species of land birds in the Northern Hemisphere, yet, it was completely wiped out within just a few years. It is possible that low genetic diversity played a role in this.” I see this everywhere. These are completely false statements uttered with utter confidence. Most of the people who call themselves scientists today don’t even understand their own disciplines, let alone science in general. As to the first quote above, even a genetics 101 student, properly educated, could point out that the “lack of genetic variation” meant that they DID possess the genetic diversity to survive—that is the very point (homo sapiens experienced genetic bottlenecks in the past and somehow manage to muddle through). These people literally have the cart before the horse. As to the second quote, I suppose one could argue that the failure of passenger pigeons to invent bullet-proof vests is somehow a failure of genetics…if one is an idiot, that is.

Garland Lowe
May 27, 2019 3:32 am

possibly, maybe, computer-based analysis to reconstruct the marmot’s genetic past. Bottom line, he knows no more now than when the study began, but his wallet is fatter.

tty
May 27, 2019 3:37 am

Two essentially nonsensical statements here:

“It is remarkable that the alpine marmot managed to survive for thousands of years despite its low genetic diversity”

Not really, there are lots of animals that have passed through extreme population bottlenecks and have virtually no genetic diversity, cheetahs for example, and many island forms.

“An important next step would be to study other animals more closely which, like the alpine marmot, managed to survive the ice age”

This includes all animals, since there are none around that didn’t survive the ice age, for obvious reasons. And ancient DNA studies have shown that bottlenecks and extinction of populations and re-colonizations is the rule rather than exceptions during glacial periods. By the way no animal is permanently “trapped” in a low diversity state, random mutations will ultimately restore diversity (of course a lot will die instead because most mutations are deleterious, but that is life).

HD Hoese
Reply to  tty
May 27, 2019 7:38 am

Haven’t seen this and whether they have anything on genetics, but it was quite a bottleneck. I recall some experts of the day predicting doom. Whooping cranes : Biology and Conservation by John B. French, Sarah J. Converse, Jane E. Austin, and Jack H. Delap (Eds). London, Academic Press, 2018.

Big animals don’t have a long history, but keep appearing. Some of these whoopers are getting spoiled.

Thomas Homer
Reply to  tty
May 28, 2019 7:22 am

tty: “random mutations will ultimately restore diversity ”

Seems you slipped a third ‘essentially nonsensical statement’ into your response.

tty
Reply to  Thomas Homer
May 31, 2019 9:59 am

Please elucidate. If you know of any other mechanism that can increase genetic diversity I would be extremely interested.

Sara
May 27, 2019 3:53 am

Marmots can have up to 9 offspring in a litter. That’s part of species survival, especially for rodents. They start breeding around age 2 and go up to 9 years. The males maintain harems, small groups of females to breed with. That alone reduces “genetic variability”.
There is nothing that says the father of a litter will not breed his own daughters. That should account for “lack of genetic diversity”. If that’s hard for a researcher to understand, he should find another job.

May 27, 2019 3:59 am

Thanks, CTM, for elevating one of my favorite memes, “which is to be master”?

May 27, 2019 4:04 am

Glow Bull Warning is extirpating all sorts of species, how come none of the ‘bad’ ones? Ticks, mosquitoes, flies, assassin bugs, et cetera? Lion fish, sharks, rats, mice, … Of course, who decides good and bad?

tty
May 27, 2019 4:07 am

As for the passenger pigeon it is true that it had a relatively low genetic diversity. It has been argued that this might be due to normal selection in an extreme ”boom and bust” species (which the Passenger Pigeon must always have been, since it was very dependent on the highly variable production of acorns):

https://science.sciencemag.org/content/358/6365/951

However it has also been hypothesized that the extreme numbers reported in the eighteenth-nineteenth centuries were very abnormal and due to exceptionally good foraging as young oak forests proliferated after the collapse of Mississippian agricultural societies and the extermination of buffaloes east of the Mississippi (yes, there were lots of buffaloes east of the Mississippi up to the early nineteenth century). In that case tight bottlenecks may have been a recurring event in the genetic history of the species.

commieBob
May 27, 2019 4:27 am

There are many kinds of marmots. My first question would be how the genetic diversity of alpine marmots compares with that of other marmot species.

Mother nature produces many genetic mutations. Most of them are not viable and die. In a harsh environment, it may be that very few mutations stand any chance of being viable. On the other hand, if the environment changes or if range expansion is possible, rapid microevolution may occur. link My guess is that the alpine marmot occupies a very specific ecological niche. Range expansion is probably not possible because neighboring ecological niches are well filled.

The lack of genetic diversity of alpine marmots may be explained by the maxim, “if it ain’t broke, don’t fix it.”

tty
May 27, 2019 4:54 am

The genomes used in the study were exclusively from the Central and Western Alps, with no animals from any other mountain chain, which is worrisome, particularly since these two populations apparently became isolated as recently as the Middle Ages.

The Alpine Marmot was hunted nearly to extinction in the nineteenth century, and from the data the effective population has been surprisingly low throughout this Interglacial, with a populaton in the low thousands during the Holocene optimum. The only previous bottleneck seems to have been during the Eemian Interglacial, which is hardly surprising, since this was significantly warmer than the present one.

Javier
Reply to  tty
May 27, 2019 5:24 am

That’s the point. The Pleistocene climatic madhouse has put a lot of stress on a lot of species causing genetic bottlenecks, loss of diversity, and extinctions. Temperate species survive in refuges the unfavorable times when they are very susceptible to extinction, and expand during the favorable times.

At the same time allopatric speciation at the isolated populations can create new subspecies and eventually species.

Pillage Idiot
Reply to  tty
May 27, 2019 7:49 am

tty’s comment was the first mention (in the article excerpt or the comments) that Alpine Marmots were heavily hunted.

I have no idea whether it is true. However, if it is true, then all of the conclusions drawn about environmental pressures on genetic diversity are immediately rendered suspect.

tty
Reply to  Pillage Idiot
May 27, 2019 10:25 am

Details here:

http://rcin.org.pl/Content/12600/BI002_2613_Cz-40-2_Acta-T40-Suppl3-87-100_o.pdf

Many current populations are the result of deliberate reintroductions, which are apparently often successful, even when comprising <10 animals.

MarkW
Reply to  tty
May 27, 2019 3:51 pm

<10 animals would result in a population with pretty low genetic variation.

That the authors missed the fact that the marmots were heavily hunted less than 100 years ago pretty much invalidates this research, and these researchers.

Javier
May 27, 2019 5:05 am

It is not surprising that climate change affects populations and entire species. The faunas of the Miocene and Pleistocene are very different and probably reflect very different climatic conditions over most of the planet.

Kenneth Richard reports on an article showing that an entire population of Southern elephant seals, genetically distinct from extant populations, that used to breed in Antarctica, 2000 km South of where it breeds now, was wiped out about 1000 years ago when Antarctica cooled so much and increased its sea ice so much that the seals could not survive.
https://notrickszone.com/2019/05/27/remote-sensing-data-indicate-a-2-44oc-summer-cooling-for-antarctica-sea-ice-regions-during-1982-2015/

May 27, 2019 5:29 am

Take a few samples, then extrapolate into infinity and pretend that the result apples to the globe.

“Results and Discussion
We sequenced, assembled, and annotated a reference genome for the Alpine marmot (Figure 1A) on the basis of a wild-living male selected from a typical, central Alpine habitat (Mauls region, North Italy;”

One male provided their reference genome.
Not considered is that the dominant male likely breeds with all available females that are in season.
Their attached spreadsheet shows that these researchers sampled a total of 12 Alpine marmots from a total of three sites:

“Sample collection
Four animals (two males, two females) each were obtained from three wild Alpine marmot populations in the Central Alps near Mauls (Italy, at 2367 m.a.s.l. at Mt Senges 46°52′40.55”N 11°34’56.12”E (including the reference individual), around St Martin, Gsies, (Italy) (at > 2,000 m.a.s.l, 46°49’44.2”N 12°12′15.5”E), and in the nature reserve of La Grande Sassière (at 2,340 m a.s.l., French Alps, 45°29’N, 65°90’E, “

The research authors rush to make quite a few claims based upon small samples sizes; while their conclusions appear to minimize differences found between sites.

“(C) Principal-component analysis (PCA) of whole-genome genetic diversity (SNPs, including singletons) of animals from Mauls, Gsies, and LGS. PC1 distinguishes the Mauls and Gsies populations from the LGS marmots, while only PC5 separates all three populations. Axes 2–4 mainly describe genetic diversity within the LGS population, which has comparable diversity to the combined sample.
comment image

The authors base many of their claims by comparing Alpine marmot genome against other mammal populations, including humans.
One wonders why the researchers failed to locate other isolated species; e.g. rats on small islands to provide similar family ancestry of animal populations in isolated locations?

Of course, much of the findings are based upon various models.

“Phylogenomic tree for rodent species
The Alpine marmot genome was aligned to whole genomes of 15 other rodent species and the human genome as outgroup. Genome assemblies were downloaded from the public NCBI assembly repository (as of January 2015). The genomes were aligned to the Alpine marmot genome using LAST [37]. The output was screened for ortholog matches using single_cov2 from the MultiZ package [42]. Pairwise alignments were combined into a multiple alignment using MultiZ. The multiple alignment file (MAF) was screened for blocks aligned in all species. All alignment blocks were concatenated into a multi fasta alignment (length 94 Mbp). We found that 500kbp fragments of the total alignment were sufficient to produce a stable tree topology using the FastTree [43] method with the GTR model of evolution. ”

“Gene model prediction
To avoid spurious matches to the genome, low-complexity repeat regions were masked from the genome assembly marMar2.1 using RepeatMasker. The paired-end RNASeq reads were aligned to marMar2.1 using TopHat v2.0.9 [44]. The transcripts were assembled using Cufflinks and merged with Cuffmerge [45]. The predicted proteomes of human, mouse, rat and thirteen-lined ground squirrel were obtained from Ensembl [46] and UniProt [47] and the protein sequences of naked mole-rat was obtained from NCBI [48] and UniProt respectively. The gene models were predicted with MAKER [34] genome annotation pipeline in three iterations (genome browser track: “Maker”). The predicted proteomes downloaded from UniProt [47] were used for the homology search ”

Are just a couple of the models used by the researchers.

Jerry Palmer
May 27, 2019 6:11 am

“A large rodent from the squirrel family”

So, they shared a common ancestor?
But they are distinct from each other now?
Can marmots breed with squirrels?
Sorry… what was your point?

bonbon
May 27, 2019 6:48 am

A delicacy in Switzerland – Murmeltierragout. Heck, I’ve even seen it as plat-du-jour in Geneva.
The varmint is probably protected today.

One thing seems odd – they like high altitudes , that means more ambient radiation, and show low genetic diversity? Something does not add up there….

MarkW
Reply to  bonbon
May 27, 2019 7:20 am

They spend a lot of time under rocks.

tty
Reply to  bonbon
May 27, 2019 10:28 am

They are not protected. Google “Murmeljagd”.

MarkW
May 27, 2019 7:11 am

All this study did is show that cold is bad. In this case for genetic diversity.

David Tallboys
May 27, 2019 8:43 am

Southampton University meekly admitted earlier this month that its three year study on bats vulnerability to climate change resulted in:

“New research led by the University of Southampton has shown that the threat of range losses for some species as a result of climate change could be overestimated because of the ability of certain animals to adapt to rising temperatures and aridity.”

Yes, the computer model needs to be changed. Again.

May 27, 2019 8:58 am

What does “recovering genetic diversity” even mean? From where would they recover it?

And, mountain gorillas? When they meet lowland gorillas they make lots of little gorillas. This claim that a species is separate from its identical cousins because the species lives in a different place, I find ridiculous.

May 27, 2019 9:07 am

I preferred the earlier article about how Global Warming is making Monster Marmots (July 21, 2010). This could be the basis of a really cute Horror Film. To ensure Marmot survival, perhaps the scientists involved in the present study could supply Marmot sized Viagra packets to the communities they study. On the other hand consider the danger posed by a Monster Marmot on Viagra.

tty
Reply to  nicholas tesdorf
May 27, 2019 10:33 am

Marmots are generally rather shy animals. The Groundhog is a lowland marmot species. Afraid of groundhog attacks?

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