Evolution can both add and remove junk DNA. Humans are descended from bacteria.
More particularly, the equilibrium size of the DNA is very roughly inversely correlated with population size. A larger population size is better at filtering out disadvantagous traits. It’s not linear—there are discontinuities as decreasing population size eliminates natural selection’s ability to select against different things. And those things sometimes can even go on to be selected for for other reasons—there are genomic structures that are important for eukaryotes that could probably never have evolved in a bacterium because to get to them you need to go through various local minima of fitness.
Soil bacteria can have trillions of individuals per cubic meter of dirt and they actually experience direct evolution towards lower genome size—more DNA means more sites at which something could mutate and become problematic and they actually feel this force. Eukaryotes go up in volume by a factor of ~1000 and go down in population by at least as much, and lose much of the ability to select against introns and middling amounts of intergenic DNA and expanding repeat-based centromere elements.
Multicellular creatures with piddlingly tiny population sizes compared to microbes lose much of the ability to select against selfish transposon DNA elements, gigantic introns and gene deserts, and their promoter elements get fragmented into pieces strewn across many kilobases rather than one compact transcriptional regulation element of a few dozen to a few hundred base pairs (granted, we’ve also been able to make good use of some of these things for interesting purposes from our adaptive immune system to the concerted regulation of our hox gene clusters that regulate our body plans). They also become very sensitive to the particular character of the transposons or DNA repair machinery of their particular lineage and wind up random-walking like crazy up and down an order of magnitude or two in genome size as a result.
Thanks! I was hoping you’d show up, it’s always nice to get a lesson :-)
Going back to the original question, are there any “general purpose adaptations” that never disappear once they show up? Does evolution act like a ratchet in any way at all?
Closest thing I can think of from what I know without going through literature is the building up of chains of dependencies. Once you have created a complex system that needs every bit to function, it has a tendency to stay as a unit or completely leave.
You can see that in a couple contexts. One is ‘subfunctionalization’. Gene duplications are fairly common across evolution—one gene gets duplicated into two identical genes and they are free to evolve separately. You usually hear about that in the context of one getting a new function, but that’s actually comparatively rare. Much more likely is both copies breaking slightly differently until now both of them are necessary. A major component of the ATP-generating apparatus in fungi went through this: a subunit that is elsewhere composed of a ring of identical proteins now has to be composed of a ring of two alternating almost identical proteins neither of which can do the job on its own. Ray-finned fish recently went through a whole-genome duplication, and a number of their developmental transcription factors are now subfunctionalized such that, say, one does the job in the head end and the other does its job in the tail end.
Another context is the organism I work in, yeast. I like to call yeast “a fungus that is trying its damndest to become a bacterium”. It lives in a context much like many bacteria and it has shrunk its genome down to maybe 2.5x that of an E. coli and its generation time down to 90 minutes. But it still has 40 introns hanging out in less than 1% of its genes so it needs a fully functional spliceosome complex to be able to process those transcripts lest those 40 genes utterly fail all at once, and it has most of the hallmarks of eukaryotic genome structure and regulation (in a neat, smaller, more research-friendly package). That being said it has lost a few big eukaryotic systems, like nonsense-mediated RNA decay and RNA interference, and they left relatively little trace behind.
More particularly, the equilibrium size of the DNA is very roughly inversely correlated with population size. A larger population size is better at filtering out disadvantagous traits. It’s not linear—there are discontinuities as decreasing population size eliminates natural selection’s ability to select against different things. And those things sometimes can even go on to be selected for for other reasons—there are genomic structures that are important for eukaryotes that could probably never have evolved in a bacterium because to get to them you need to go through various local minima of fitness.
Soil bacteria can have trillions of individuals per cubic meter of dirt and they actually experience direct evolution towards lower genome size—more DNA means more sites at which something could mutate and become problematic and they actually feel this force. Eukaryotes go up in volume by a factor of ~1000 and go down in population by at least as much, and lose much of the ability to select against introns and middling amounts of intergenic DNA and expanding repeat-based centromere elements.
Multicellular creatures with piddlingly tiny population sizes compared to microbes lose much of the ability to select against selfish transposon DNA elements, gigantic introns and gene deserts, and their promoter elements get fragmented into pieces strewn across many kilobases rather than one compact transcriptional regulation element of a few dozen to a few hundred base pairs (granted, we’ve also been able to make good use of some of these things for interesting purposes from our adaptive immune system to the concerted regulation of our hox gene clusters that regulate our body plans). They also become very sensitive to the particular character of the transposons or DNA repair machinery of their particular lineage and wind up random-walking like crazy up and down an order of magnitude or two in genome size as a result.
Thanks! I was hoping you’d show up, it’s always nice to get a lesson :-)
Going back to the original question, are there any “general purpose adaptations” that never disappear once they show up? Does evolution act like a ratchet in any way at all?
Closest thing I can think of from what I know without going through literature is the building up of chains of dependencies. Once you have created a complex system that needs every bit to function, it has a tendency to stay as a unit or completely leave.
You can see that in a couple contexts. One is ‘subfunctionalization’. Gene duplications are fairly common across evolution—one gene gets duplicated into two identical genes and they are free to evolve separately. You usually hear about that in the context of one getting a new function, but that’s actually comparatively rare. Much more likely is both copies breaking slightly differently until now both of them are necessary. A major component of the ATP-generating apparatus in fungi went through this: a subunit that is elsewhere composed of a ring of identical proteins now has to be composed of a ring of two alternating almost identical proteins neither of which can do the job on its own. Ray-finned fish recently went through a whole-genome duplication, and a number of their developmental transcription factors are now subfunctionalized such that, say, one does the job in the head end and the other does its job in the tail end.
Another context is the organism I work in, yeast. I like to call yeast “a fungus that is trying its damndest to become a bacterium”. It lives in a context much like many bacteria and it has shrunk its genome down to maybe 2.5x that of an E. coli and its generation time down to 90 minutes. But it still has 40 introns hanging out in less than 1% of its genes so it needs a fully functional spliceosome complex to be able to process those transcripts lest those 40 genes utterly fail all at once, and it has most of the hallmarks of eukaryotic genome structure and regulation (in a neat, smaller, more research-friendly package). That being said it has lost a few big eukaryotic systems, like nonsense-mediated RNA decay and RNA interference, and they left relatively little trace behind.