The fuzzy network of life
April 13, 2022 2:57 PM Subscribe
Classic evolutionary theory holds that species separate over time. But it’s fuzzier than that – now we know they also merge. Bonus: If our closest relatives are chimps, why is some human DNA more like gorilla DNA?
Roving genes have been found in every branch of the tree of life where geneticists have looked. Today, the technical terms for the process of genes moving between populations are introgression or admixture.
Introgression occurs in plants such as maize and tomatoes. In mosquitoes, the entire genome except for the X chromosome can be swapped with other species. In a tropical genus of butterfly called Heliconius, gene jumping has been found to cause critical changes in the patterns of their colourful wings. Introgression has been documented in finches, in frogs, in rabbits, in wolves and coyotes, in swine, in yaks and cows, in brown bears and polar bears. And in us.
Self-grafting, or inosculation is very common in trees, mostly between trees of the same species, but also occasionally within a single tree.
posted by jamjam at 5:53 PM on April 13, 2022 [2 favorites]
posted by jamjam at 5:53 PM on April 13, 2022 [2 favorites]
Crowdsourcing hybrids in order to find resilient gene lines that can survive catastrophic man made climate disaster puts the "Best" into "bestiality"
posted by otherchaz at 7:39 PM on April 13, 2022 [7 favorites]
posted by otherchaz at 7:39 PM on April 13, 2022 [7 favorites]
I'm... going to favorite that, but remember that favorites don't always mean endorsement.
posted by biogeo at 7:52 PM on April 13, 2022 [8 favorites]
posted by biogeo at 7:52 PM on April 13, 2022 [8 favorites]
The mosquito article points out that the two processes talked about in the two above-the-fold articles are different but extremely hard to disentangle when comparing DNA:
Recently diverged species often have incomplete reproductive barriers, hence, may hybridize in sympatry. However, another feature of rapid radiations is that ancestral polymorphism predating lineage splitting may be sorted stochastically among descendant lineages in a process known as incomplete lineage sorting (ILS). Alleles shared through ILS can be difficult to distinguish from those shared through secondary contact and introgression. Newly developed methods can differentiate these two processes but only if the correct species branching order is known.posted by clawsoon at 4:24 AM on April 14, 2022
biogeo: Turns out the tree of life should have been the DAG of life.
I recently learned about ancestral recombination graphs (ARG), which are used to separately trace the history of each snippet of genome. How much to ARGs and DAGs have in common?
posted by clawsoon at 4:31 AM on April 14, 2022
I recently learned about ancestral recombination graphs (ARG), which are used to separately trace the history of each snippet of genome. How much to ARGs and DAGs have in common?
posted by clawsoon at 4:31 AM on April 14, 2022
Oh, one more DAG question: If a grandchild had offspring with their grandparent - maybe pollen from some old tree landing on an even older tree that happens to be its grandparent - would that introduce a cycle to the graph, breaking the acyclic requirement?
posted by clawsoon at 6:03 AM on April 14, 2022
posted by clawsoon at 6:03 AM on April 14, 2022
Well I admit I've never heard of ancestral recombination graphs (not an evolutionary geneticist, at least not in this timeline), but according to Biowiki, "The ancestral recombination graph is a DAG". DAGs are pretty general and can be used for modeling lots of things.
The example you give wouldn't introduce a cycle so could still be modeled with a DAG. It would look something like this:
where A is the grandparent, C is the grandchild, and D is their offspring. The graph has no cycles because you can't move "backwards" against an arrow.
posted by biogeo at 8:09 AM on April 14, 2022 [1 favorite]
The example you give wouldn't introduce a cycle so could still be modeled with a DAG. It would look something like this:
(A) --> (B) --> (C)
\ ↘
\--------------> (D)
where A is the grandparent, C is the grandchild, and D is their offspring. The graph has no cycles because you can't move "backwards" against an arrow.
posted by biogeo at 8:09 AM on April 14, 2022 [1 favorite]
> Turns out the tree of life should have been the DAG of life.
I spent several months skiving off from what I should have been doing and working on this issue in grad school. What I arrived at is that you define chain-complete partial orders of individuals by descent, but defining things like species becomes really difficult. Which it is. The long arguments of systematics in microbiology ended in exhaustion, not solution. And then you get into the question of bacterial communities and obligate symbiotes. And ring species.
At this point my use of "species" is a shorthand for "the possible individuals that are collected by a sampling procedure in a given environment that selects individuals which a reasonable practitioner can make inferences beyond the individual about." Is that extremely vague? Yes. But the error modes of sampling from bacterial communities in isolated caves are really different than those of sampling from a ring species overlap.
posted by madhadron at 11:19 AM on April 14, 2022 [3 favorites]
I spent several months skiving off from what I should have been doing and working on this issue in grad school. What I arrived at is that you define chain-complete partial orders of individuals by descent, but defining things like species becomes really difficult. Which it is. The long arguments of systematics in microbiology ended in exhaustion, not solution. And then you get into the question of bacterial communities and obligate symbiotes. And ring species.
At this point my use of "species" is a shorthand for "the possible individuals that are collected by a sampling procedure in a given environment that selects individuals which a reasonable practitioner can make inferences beyond the individual about." Is that extremely vague? Yes. But the error modes of sampling from bacterial communities in isolated caves are really different than those of sampling from a ring species overlap.
posted by madhadron at 11:19 AM on April 14, 2022 [3 favorites]
The example you give wouldn't introduce a cycle so could still be modeled with a DAG.
Now I'm trying to envision an actual cycle. Hmm. I guess it would have to be novel DNA generated in offspring and then transmitted and integrated into the parent's genome. Maybe some sort of plasmid transmission?
At this point my use of "species" is a shorthand for...
My take is "an often useful hack for understanding the world, but a hack."
posted by clawsoon at 12:50 PM on April 14, 2022
Now I'm trying to envision an actual cycle. Hmm. I guess it would have to be novel DNA generated in offspring and then transmitted and integrated into the parent's genome. Maybe some sort of plasmid transmission?
At this point my use of "species" is a shorthand for...
My take is "an often useful hack for understanding the world, but a hack."
posted by clawsoon at 12:50 PM on April 14, 2022
Well, one of the nice things about DAGs is that when they don't work, you can usually adjust your model in very sensible ways to make them work. So I think you could plausibly construct a cyclic graph describing your bacterial transformation example with plasmid gene transfer from offspring to parent. But you could also quite reasonably argue that after the transformation event, the parent is qualitatively no longer the same as it was prior to it, and if we make our graph time dependent (i.e., parent at t(before) and parent at t(after) are different nodes in the graph), that removes the cycle and makes it a DAG once again.
clawsoon, I think you might get a kick out of Richard McElreath's online course "Statistical Rethinking". His lectures are all freely available on YouTube.
posted by biogeo at 2:25 PM on April 14, 2022 [2 favorites]
clawsoon, I think you might get a kick out of Richard McElreath's online course "Statistical Rethinking". His lectures are all freely available on YouTube.
posted by biogeo at 2:25 PM on April 14, 2022 [2 favorites]
Many, many years ago, when I was twenty-three, I may or may not have introduced a cycle into the graph
posted by fantabulous timewaster at 5:32 PM on April 14, 2022 [1 favorite]
posted by fantabulous timewaster at 5:32 PM on April 14, 2022 [1 favorite]
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(Alternative for the computer scientists:)
Turns out the tree of life should have been the DAG of life.
posted by biogeo at 5:35 PM on April 13, 2022 [2 favorites]