Woolly mammoths and Neanderthals may have shared genetic traits: Findings...

You are what you eat?

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I guess this is one better explained by a dependency graph concept than common descent models…
.Did you read this part of the article-

“Neanderthals and mammoths lived together in Europe during the Ice Age. The evidence suggests that Neanderthals hunted and ate mammoths for tens of thousands of years and were actually physically dependent on calories extracted from mammoths for their successful adaptation,” says Prof. Barkai. "Neanderthals depended on mammoths for their very existence.

"They say you are what you eat. This was especially true of Neanderthals; they ate mammoths but were apparently also genetically similar to mammoths.

Better be careful what you eat… Eat too much chicken and we might end up as flightless birds!

No it is not better explained by dependency graph. Why would you think this?

The similarity is not due to common descent… so a pattern of descent should not explain it .
Whereas the similarity is genes and function, could be better explained by a dependency graph.
Basic idea being that molecular convergences are better explained by dependency graphs.

@Ashwin_s you don’t understand dependency graphs, it seems. Look again, read up. You are just flat out wrong here.

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How would you go about explaining this similarity in a tree like structure in a common descent model?

The way I see it is that, a common descent model explaining this phenomenon would be far less parsimonious that a dependency graph.

It seems this could easily be explained as an example of convergent evolution.

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The paper is available in a pre-print version here.

Neanderthal and Woolly Mammoth molecular resemblance: Genetic similarities might underlie cold adaptation suite

The authors do indeed conclude convergent evolution at the molecular level is the cause. They also surmise mammalian adaptations to extreme cold environments may be quite limited in number and variety which is why different species hit upon the same solutions to the cold weather problems. Several other examples of cold weather molecular convergent evolution are given (i.e. Siberian horses) besides the ones listed in the OP article.

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Indeed. I found Ashwin’s statement baffling. Then I recalled an Evolution News & Views article and looked it up:

https://evolutionnews.org/2018/08/of-species-and-software-what-is-a-dependency-graph/

@Ashwin, had you by any chance read this article by Cornelius Hunter?

I am not seeing any reference to the same exact mutation occurring in multiple species. Rather, an increased rate of evolution is occurring in the same genes. This would mean different mutations in the same gene leading to adaptations for cold climates. This is the textbook definition of convergent evolution.

As to Ewert’s model, all of the species in question share the same gene, so I don’t think this fits well with his model, if I am understanding it correctly.

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His model ignores mutations and focuses on presence or absence of a gene. He has to do it this way, because as soon as he starts using mutations it won’t work any more.

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Don’t remember. But I might have.
What I was thinking was that, if the gene appeared in both the woolly mammoth and neanderthals, then on a species tree, you will have several incidents of this gene appearing and disappearing along lineages.

The paper does the analysis for three types of genes/set of genes which are supposed to facilitate Adaptation to extreme cold. Out of these, they find “molecular similarity” for LEPR genes, and don’t have enough data to conclude on the rest. Though they seem to anticipate finding more instances of molecular similarity based on adaptation.

If the kind of scenario the paper envisions turns out true… I.e Sets of genes which give an adaptive advantage appearing in diverse organisms which are not closely related, while not being present in other closer organisms (in this example, humans for neanderthals and elephants for mammoths). It should be easier to explain through a dependency graph.

The paper talks about LEPR being present in both neanderthals and woolly mammoths. It claoms that the genes show “molecular similarity”…

The paper isn’t talking about genes “appearing” in particular species. LEPR isn’t only present in neanderthals and woolly mammoths, it’s a gene found in all jawed vertebrates. The allele of this gene in neanderthals and woolly mammoths (and no doubt other cold-adapted gnathostomes) is adapted to promote cold-tolerance.

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Thanks for the clarification…
Would it change the argument?
This particular variant of LEPR, would have to appear and disappear several times in a tree correct?

They’re nothing to suggest that neanderthals and mammoths share precisely the same variant of LEPR. The paper just says that both are probably cold-adapted. The specific mutations might be completely different for all we know.

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That could be possible… except the authors keep talking about “molecular resemblance”…

For example they say about similarities between the yukatan horse and Siberian human beings (quoted below) -
I guess further research will clarify the levels of resemblance of any.

Furthermore, in that same study Librado and colleagues compared adapted genes from
the Yakutian horse to those of other ‘well-known’ cold-adapted mammals, such as the woolly
mammoth and modern-day Siberian human populations. They detected a shared appearance of
the BARX2 gene (involved in skin and hair regulation) in Yakutian horses and the woolly
mammoth, and a shared appearance of the PRKG1 gene (involved in constriction of blood
vessels to minimize heat loss) between Yakutian horse and Siberian human populations (Librado
et al., 2015). We see these remarkable finds as a supporting evidence for the contention
regarding the nature of convergent evolution through molecular resemblance – in which the
similarities in genetic adaptation between adapted species are present, offering a significant topic
for future research.

I just skimmed through the preprint. It’s a review that does not present any new data whatsoever. It doesn’t even have figures. Here is the entirety of the section on LEPR:

The First Case Study: Leptin Receptors (LEPR Gene).

Sazzini et al. (2014) discuss cold adaptations among different human populations, hypothesizing that cold adaptation processes, and more specifically changes in the metabolic system and modulation of non-shivering thermogenesis,2are associated with a unique activity of brown adipose tissue. These researchers conducted a number of experiments and found an allele of the gene LEPR which presents strong adaptive behavior to cold and is found among the Neanderthal and Denisovan genome sequences.The LEPR gene encodes for the leptin receptor. Among other things, this protein is associated with the activity of adipose tissues and the regulation of body heat (Villanueva et al., 2008). This gene was also identified during the mapping of the woolly mammoth genome; it is noted under the category of ‘Genes associated with insulin signaling, lipid metabolism and adipose biology’. The LEPR gene is described as responsible for the creation and regulation of brown adipose tissue cells (Lynch et al., 2015). As noted, fat deposits take part in several cold adaptation processes, such as contributing to insulation, and may also serve as a stored energy source for times of need (Churchill, 2014; Garstang, 2015; Lynch et al., 2015).

This is not exactly earth-shattering stuff.

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I agree… do you think it will clear peer review?

I’ve just checked. Lynch et al (2015) identified a missense mutation specific to mammoths that changed amino acid 319 of the LEPR protein from an N to a K:
https://usegalaxy.org/u/webb/d/bbd44e69cb8906b5da669214049c29b0
https://www.uniprot.org/uniprot/G3SSQ3

Meanwhile, Sazzini et al (2014) identified 3 human polymorphisms potentially associated with cold-tolerance: rs6413506, rs1137100, and rs1137101. Only the latter is observed in neanderthals. These mutations change amino acids as positions 109 and 223, and represent a synonymous mutation in the codon that specifies amino acid 1008 (not in that order).

In other words, the mutations that might have adapted the neanderthal and mammoth LEPR genes to become cold-tolerant were completely different.

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