How do you tell HGT from Synapomorphy?

[jasonhernandez74]

This question is inspired by the thread in General on whether generic analysis will replace morphology in determining taxonomy. One commentator said that acquired characteristics are not inherited. Well, if they were acquired by Horizontal Gene Transfer (HGT), they can be. As it turns out, Lamarckian evolution is occurring concurrently with Darwinian evolution.

So when doing phylogenetic analyses, and you find the same sequence, how do you tell if it is a synapomorphy (inherited from a shared common ancestor), or was acquired through HGT?

[sedgequeen]

In general, you recognize Horizontal Gene Transfer (HGT) when most of the genes in species X and Y are as different as expected, but then one is very similar. It’s easiest to recognize when the transfer is from a really distantly related organism.

[cthawley]

Smaller point, but HGT wouldn’t qualify as Lamarckian evolution, which is the inheritance of physical characteristics an organism might gain (or lose) during its life (bigger muscles, a tan, lost limb, whatever) through use or disuse. HGT entails genetic characteristics and doesn’t rely on use (or not).

[pfau_tarleton]

@cthawley is correct (although I think it’s a major point)…HGT is not an acquired (Lamarckian) character. Lamarckian evolution isn’t occurring in the sense that Lamarck was proposing. The closest thing to Lamarckian evolution that I know of is epigenetic inheritance. This occurs when the environment causes a molecular tag to be added to the DNA. The DNA sequence itself isn’t changed, but the tag changes how the DNA sequence is interpreted by the cells machinery–thus altering the trait. These tags can be passed on to kids or grandkids (but not much further). So it’s not even permanent inheritance as the tag is removed (and the associated trait disappears) after a generation or two at most.

I’m not totally understanding your question…because I think you’re confusing a couple of different concepts.

For example, some aphids have carotenoid pigments which most aphids and other insects lack. So where’d it come from? Horizontal gene transfer from fungi. How do we know? The aphid gene coding for the carotenoid pigments has a DNA sequence most similar to the gene in fungi which codes for carotenoid pigments.

Moving from there to synapomorphy. The fungi gene in the group of aphids that posses it is a synapomorpy for that group of aphids. All the aphids share that trait, and the most parsimonious explanation is that they inherited it from the aphid ancestor that acquired the gene via HGT. In science, we always go with the more likely explanation until mounting evidence suggests otherwise (there would be fewer conspiracies propagated if we take that approach in other aspects of our lives also!).

When you say “and you find the same sequence”, what do you mean? That’s the part that confuses me. Same sequence as what? The same sequence in multiple organisms? A synapomorphy is something shared by a group of organisms that is NOT shared by other organisms. So in the aphid example, the carotenoid sequence is shared by some aphids, but absent from other aphids and insects. The character acquired by HGT is a synapomorphy. How do we know that each aphid didn’t acquire it independently (a non-synapomorphy) rather than inheriting it from a single ancestor? Other options include the sequence being acquired independently from the same fungus by all those aphids that have it, or the sequence is the same in all the aphids because of chance mutations that happened upon the same sequence independently. Either of those is less likely than it being acquired by one aphid which passed it to its descendants. A close examination of details of the DNA sequence can help differentiate amongst those scenarios, also.

[trickman]

@pfau_tarleton

(there would be fewer conspiracies propagated if we take that approach in other aspects of our lives also!).

Very true. And i must say, reading this thread and other threads on the Forum, and the many posts within, is something of a mental restorative, a welcome respite, given what’s been in the news and the delusions of conspiracy theories and theorists. Thank you all for sharing what you know and causing me to look up and learn a bit about such things as synapomorphy.

[jasonhernandez74]

@pfau_tarleton

Same sequence as what? The same sequence in multiple organisms?

Yes, that. If you find the same sequence in multiple organisms, how do you tell whether it indicates that they shared a common ancestor with that sequence, or whether they acquired it separately through HGT? I see that after asking me this question, you began to answer my intended question.

The reason I asked is because I just read The Tangled Tree, by David Quammen, and some things in it confused me. Namely, bacteria that have many sequences acquired through HGT from archaea, and archaea that have many sequences acquired from bacteria. I did not understand how this was determined to be the result of HGT, rather than sequences held over from the common ancestor of bacteria and archaea.

[langlands]

I think is a lot simpler to differentiate HGT from vertical inheritance in multicellular organisms, for example in the way wrote by @pfau_tarleton, if only because the chances of HGT to the reproductive cells are much smaller than with unicellular organisms. Another barrier to HGT is the nucleus, so archaea and bacteria are more likely to have events of HGT than unicellular eukarya. I don’t know much about the phylogenies inside archae and bacteria but my impression is that they are very messy precisely because is hard to tell between HGT and vertical inheritance, and the concept of species and taxa are a lot more fluid in those organisms.

[kmagnacca]

Bacteria and archaea are quite different from eukaryotes in terms of HGT. HGT does occur in eukaryotes, as in the aphid example above, but like in that example it tends to be between totally unrelated organisms so it’s relatively easy to recognize. Bacteria on the other hand will readily exchange DNA between each other, which makes things a lot more difficult. Hence phylogenies are based on genes that are shared among all organisms, like rRNA and cytochrome oxidase.

For other things, the common ancestor between bacteria and archaea was somewhere around 3 billion years ago IIRC, so things that are more similar than expected based on that have a good chance of being acquired through HGT. In many cases though, those are also relatively easy to recognize because they are simply different enzymes, which aren’t present in related taxa. For example, if nearly all archaea have the gene for ribulose synthetase (as a completely fabricated example) – while only alphaproteobacteria have it and their sequences fall out phylogenetically within the thermophile archaeans’ sequences – you can infer that at some point an ancestral alphaproteobacteria acquired the ribulose synthetase gene via HGT from a thermophile archaea.

[cthawley]

Echoing other posters: yes, figuring this out is much more complex in bacteria and archaea than eukaryotes.

A short answer is: a common way to answer these questions is by using different types of algorithms that assess the likelihood/probability of various ancestry scenarios (evolutionary trees). In this case, HGT would be a horizontal branch cutting across the pattern of common descent. Probably the simplest principle to understand is that of parsimony: all things being equal, the simplest evolutionary scenario that requires the fewest changes/gene transfers would be favored as the most likely.

For instance, let’s say you have a group A in which all its members had a gene (A1), but it’s sister (most related) group, B, does not. You might ask: does the presence of gene (A1) in group A derive from ancestry or gene transfer? You would then want to look and see if the most recent common ancestor of groups A and B also possessed (A1) or gene (almostA1). If so, you would likely assume that A1 was inherited or that a small mutation led to almostA1->A1 in group A, as this would be most parsimonious. However, if the most recent ancestor does not have gene A1 or anything like it, you might assume HGT is a potential source for gene A1 in group A.

Current phylogenetic methods use pretty complex programs to search through “tree space” (the billions and billions of possible ways that organisms are related) and then assess which relationships are more or less likely. These programs will incorporate models of how evolution occurs based on knowledge from other systems (what types of changes are more or less likely, etc.). You could also incorporate a priori knowledge (we see this gene being transferred via HGT in other organisms as well…seems somewhat common), etc.

In the end, when talking about deep time evolutionary changes, there will generally be a favored, but not definitive, tree (hypothesis). Usually the best we could say is: given what we know, a certain scenario is most likely. But all of these scenarios are really just hypotheses and open to modification with new knowledge in the future.