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A synopsis of a 2005 paper in PlosBiology by Yohn et al. states that:

Searching the genomes of a subset of apes and monkeys revealed that the retrovirus had integrated into the germline of African great apes and Old World monkeys—but did not infect humans and Asian apes (orangutan, siamang, and gibbon). This undermines the notion that an ancient infection invaded an ancestral primate lineage, since great apes (including humans) share a common ancestor with Old World monkeys.

Also, Micheal Lynch writes :

"Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes," Lynch said. "This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor."

Since shared ERVs in humans and chimps is touted as one of the proofs of humans and chimps sharing ancestry (like by Ken Miller here), does the above paper (and quote) undermine this line of reasoning?

Is there any good (recent) source which discusses proof of common descent using ERVs?

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  • $\begingroup$ I have changed the first sentence of the question so as to provide a reference to the actual paper, rather than just the synopsis. I have changed the title so that it indicates the area of biology the question is about and spells out endogenous retroviral for general comprehensibility and indexing. In relation to the original title ("Does this paper show…") would point out that it is scientific facts established by observation or analysis that may or may not show something, not the papers. $\endgroup$ – David Dec 31 '17 at 16:50
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The Yohn et. al. (2005) paper (from Evan Eichler's lab) is describing a single type of endogenous retroviral element (loosely think of it as a 'species'), called PTERV1. They show that there were multiple independent infection events that resulted in permanent integrations in the ancestors of modern species (~3-4 MYA in the ancestors of gorillas and chimps, ~1.5 MYA in the ancestors of baboons and macaques). This in no way contradicts the notion of common ancestors among the apes/monkeys; indeed, they state this as a given in their analysis (emphasis mine):

A total of 275 of the insertion sites mapped unambiguously to non-orthologous locations (Table 2), indicating that the vast majority of elements were lineage-specific (i.e., they emerged after the divergence of gorilla/chimpanzee and macaque/baboon from their common ancestor).

The presence of an ERV (or intron, or any general genomic synteny), can be used as evidence to support a particular model of common decent. Changes in genomic architecture are stochastic processes, and the work you cite by Li et. al. (Lynch lab) is showing us that ERV placement can occur at a similar, or nearly identical, location at a much higher rate than previously thought. We therefore need to take this into account then calculating how strongly a shared ERV increases our confidence in a given phylogenetic model.

The video you linked to uses a completely random (i.e., very simple) model of ERV integration, setting the chance of an insertion at a given location at 3.3e-10. The findings by Li tell us that this is incorrect. In daphnia, at least, ‘hotspots’ may account for nearly 25% of new intron gain. The video also failed to include all of the instances of ERVs that are not shared between humans and chimp (back-of-napkin, this could account for differences of ~0.3% between their genomes, see Mun et al. 2014). This will increase the probability of an exact match occurring by chance (e.g., put two people in a room, what’s the chance of them having the same birthday? Put 100 people in a room, what’s the chance of any of them having the same birthday?).

So, let’s be extremely conservative and say that the chance of the same insertion at a given location in both chimps and humans is one in one thousand (1e-3, seven orders of magnitude more probable than in the original model). Sixteen shared ERVs are identified in the video; if each is considered an independent event because of no shared decent, we are still looking at odds around 1e-48 (1e-3 ^ 16). An alternative could be that they are derived from insertions that predate the split from a common ancestor. Given Li et. al., maybe each event should be given a probability of only 0.75 instead of 1.0 (as per the video) because up to 25% of them could be from hotspots. In this scenario, the probability is 0.01 (0.75 ^ 16). Therefore, the second hypothesis is 46 orders of magnitude more probable than the first. In my mind, this is extremely compelling evidence that humans and chimps share a common ancestor, using only ERV data.

I want to be clear, I am fudging these numbers extensively towards not supporting common descent. The real odds will be much higher in favour of common descent.

For further reading, Welkin Johnson wrote a comprehensive review on ERVs in 2015 (paywalled, so you may need to search for Alexandra Elbakyan's scientific literature retrieval method if you don't have institutional access).


References

Johnson WE. (2015). Endogenous Retroviruses in the Genomics Era. Ann. Rev. Virology. doi: 10.1146/annurev-virology-100114-054945

Li W. et al. (2009) Extensive, Recent Intron Gains in Daphnia Populations. Science. doi: 10.1126/science.1179302

Mun S. et at. (2014) Chimpanzee-Specific Endogenous Retrovirus Generates Genomic Variations in the Chimpanzee Genome. PLoS One. doi: 10.1371/journal.pone.0101195

Yohn et. al. (2005). Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans. PLoS Biol. doi: 10.1371/journal.pbio.0030110

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  • $\begingroup$ I wasn't saying that these quotes contradict common descent. I was asking if, in the light of the quotes I mentioned above, ERVs can be presented as evidence of common descent of man and chimp (as many, like Ken Miller, have done). $\endgroup$ – Daud Dec 27 '17 at 5:26
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    $\begingroup$ Yes, they absolutely can be used as evidence. This is just one class of ERV, and the authors clearly explain why this class presents as non-orthologous copies in different taxa. $\endgroup$ – Steve Bond Dec 27 '17 at 23:13
  • $\begingroup$ Ok. I got that this paper was talking of only one type of ERVs, but Michael Lynch's statement above says that even if we find ERVs (or generally, introns) at the same site in multiple lineages, it doesn't serve as proofs of common descent. If this is the case, then how can ERVs be used to prove common descent (especially, human/ape common descent)? $\endgroup$ – Daud Dec 28 '17 at 8:05
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    $\begingroup$ I've modified my answer to better address our discussion. $\endgroup$ – Steve Bond Dec 29 '17 at 17:18
  • $\begingroup$ @Bond....SteveBond You have a cool name. And on top of that you write good answers +1. Good to have you active on Biology.SE! $\endgroup$ – Remi.b Dec 31 '17 at 16:46

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