[HN Gopher] Evidence of long-term directionality in origination ...
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Evidence of long-term directionality in origination of human
mutation: study
Author : gmays
Score : 38 points
Date : 2022-02-02 01:06 UTC (1 days ago)
(HTM) web link (phys.org)
(TXT) w3m dump (phys.org)
| culi wrote:
| The biggest thing in ecology right now is niche construction
| theory. It's the realization that organisms don't just respond to
| their environment, but also shape it and reproduce it
|
| I think it's high time for the equivalent perspective to reach
| evolutionary molecular biology and realize that organisms aren't
| just gonna sit idly by and wait for the random process of
| mutation to let them adapt. As shown by the recent studies on the
| prevalence of genes being shared across animals,[0] there's
| clearly many mechanisms of action missing from our molecular
| analysis toolbox. One recent finding was the discovery of
| epigenetic inheritance. If epigenetics allows organisms to adapt
| to environments in their lifetimes and these adaptations can, in
| some capacity, be passed down. In addition, we've already shown a
| number of factors to increase the rates of mutation. Given these
| findings, I don't think it's far-fetched to imagine some level of
| "~~niche~~[gene] construction" happening at the molecular level
|
| [0] https://www.quantamagazine.org/dna-jumps-between-animal-
| spec...
| [deleted]
| culi wrote:
| Some species of mycorrhizal fungi have been observed to have a
| fascinating stress response to being exposed to a new
| soil/environment. The mycellium will somehow ramp up it's rate of
| HGT (horizontal gene transfer) and therefore borrow genes from
| other soil organisms in that soil. These genes are borrowed
| across phylums from even bacteria or microalgae.
|
| Essentially, it's a natural mechanism to rapidly increase its
| rate of evolution.
| biorach wrote:
| Source?
| culi wrote:
| - Elevated rates of HGT in the industrialized human
| microbiome. Transferred gene functionality reflect the
| lifestyle of their hosts[0]
|
| - HGT from bacteria and plants to mycorrhizal fungi. These
| genes are functional[1]
|
| - More about fungi sharing genes[2][3]
|
| - Lab experiment showing HGT can act as a directional
| evolutionary force in bacteria adapting to antibiotics[4]
|
| - A species of fungi used HGT (mostly from bacteria and some
| from eukaryotes) in order to adapt to colonize apple trees[5]
|
| - A call for a replacement of neo-Darwinism with a new
| evolutionary synthesis that takes into account the role of
| HGT (among other things)[6]
|
| Ok, so I didn't save the actual paper I was paraphrasing. I
| thought I'd read it in Annual Reviews, but I can't seem to
| find it. However, I hope I provided enough sources to show
| that: (1) fungi often share genes across phylums, (2) we have
| clear examples of elevated rates of HGT in microbiota faced
| with a new environment, and (3) HGT can play a critical role
| in adaptation
|
| [0] https://www.sciencedirect.com/science/article/pii/S009286
| 742...
|
| [1] https://www.frontiersin.org/articles/10.3389/fpls.2018.00
| 701...
|
| [2] https://massivesci.com/articles/fungi-gene-plants-
| mutualism/
|
| [3] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643240/
|
| [4] https://www.pnas.org/content/117/43/26868
|
| [5] https://www.nature.com/articles/srep33129
|
| [6] https://royalsocietypublishing.org/doi/10.1098/rspb.2009.
| 167...
| alsaaro wrote:
| The article states that mutations arise randomly (de novo
| mutations), but the rate of of these mutations differ based on
| populations experiencing differing environmental pressures.
|
| The naive hypothesis would be to expect that de novo mutations,
| being random, should arise in differing populations -- even in
| different environments -- at the same rate; apparently this isn't
| the case.
|
| The article doesn't explain the underlying mechanism, so I assume
| this is just premilitary observational science? The authors say
| this challenges neo-Darwinism, how?
|
| One explanation is that environmentally selected genes (meta
| genes?) that promote mutation of de novo genes in regions of the
| genome under environmental pressure. These meta genes dispersed
| in a population would prime that population for the synthesis of
| new adaptations.
| AlotOfReading wrote:
| The underlying paper lists 3 different hypotheses that could
| explain the results.
|
| 1. Unrelated fragility of this particular sequence in Africans
|
| 2. Modifier theory
|
| 3. Having mutations makes future generations more susceptible
| to nearby mutations. This what the authors are suggesting.
|
| There's a sort of soft-assumption in modern biology that
| mutations are approximately random, which underlies things like
| the molecular clock. It's well-known to be wrong, but at scale
| the experimental evidence suggests that it still holds in many
| useful situations.
|
| Combine a paper pointing out a limitation of that assumption
| with popsci press and you get the breathless headline above.
| jon_richards wrote:
| > One explanation is that environmentally selected genes (meta
| genes?) that promote mutation of de novo genes in regions of
| the genome under environmental pressure.
|
| This has been studied. They're DNA repair pathways. Put a bunch
| of E. coli in a bioreactor and trace the lineages. As soon as
| one lineage loses a DNA repair pathway, new mutations explode
| and out-compete the old lineages (and each other).
|
| Besides cancer and viability concerns, highly stable DNA is
| mainly beneficial in cyclical conditions (as adaptive memory).
| In the stable--but highly competitive--environment of a
| bioreactor, sacrificing DNA stability for adaptive pace is a
| very beneficial mutation.
| gameswithgo wrote:
| If anyone is here who works in the field of evolutionary biology
| can answer this: The article seems to be saying this result goes
| against the mainstream thinking that mutations are entirely
| random. But is that really the mainstream thinking of modern
| evolutionary scientists? Or just the simple high-school
| explanation which is devoid of a lot of known nuance?
| culi wrote:
| I don't work in evolutionary biology, but I found this paper
| calling for a replacement of neo-Darwinism to be a really
| helpful overview (it also sites many similar works)
|
| https://royalsocietypublishing.org/doi/10.1098/rspb.2009.167...
| ravar wrote:
| I know with some bacteria (which I work with for evolutionary
| biology) they can intentionally mutate at higher rates when
| under stress.
| guga42k wrote:
| Is that survivorship bias here? surely people in Africa should
| have higher rate of the mutation. because people who didn't have
| it died from malaria.
| vagabund wrote:
| This study measures the rate of de novo (not inherited) HbS
| mutation, and finds it occurs at significantly greater than
| random chance in populations where malaria is prevalent. So
| there is a survivorship bias, but not just for the inheritance
| of the specific downstream adaptively relevant mutation, but
| also for some meta-process that controls the rate at which that
| mutation appears anew without inheritance. They're able to
| observe this through a new method that can measure the rate of
| de novo mutations in specific areas of interest in the genome,
| as opposed to prior methods which were constrained to measuring
| the rate of mutations in general across the whole genome.
| moonshinefe wrote:
| Thanks for explaining that. The article just jumps right into
| using "de novo" all over the place with minimal explanation,
| but the link they highlight it with is broken.
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