@thoughtful asked me in the “Dating the Noachian Deluge” thread to share the genetic evidence which convinced me about common ancestry, so I’ll summarize it here for her. There are many converging lines of genetic evidence for common ancestry, but I’ll just include the three that convinced me the most.
- Ancestral sequence convergence
Using phylogenetic techniques, it’s possible to determine the ancestral sequence of a group of organisms with high accuracy. The accuracy of ancestral sequence reconstruction (ASR) techniques has been confirmed by many studies.
For example, an early study used ASR to determine the ancestral sequence of 111 modern HIV sequences, and the resulting predicted sequence was found to be very close to a preserved 1958 HIV sequence from Africa (Zhu et al. 1998). More recently, another study induced rapid mutagenesis in a red fluorescent protein to produce 19 different strains. They then predicted the ancestral sequence using five different ASR techniques, with accuracies between 97.88 and 98.17% (Randall et al. 2016). So we know that ASR is very accurate.
Now, using ASR, it’s possible to test a strong prediction of common ancestry (CA). Since CA states that two given groups of organisms shares common ancestry, it predicts that the ancestral sequences for those groups of organisms should be closer to one another than the extant (modern) sequences of such organisms. In contrast, the separate ancestry (SA) hypothesis states that such groups of organisms began at different points and diversified from there.
(Taken from Testing a Strong Prediction of Universal Common Ancestry – EvoGrad)
This prediction was finally tested in 2013 by White, Zhong, and Penny. Using a statistical test involving ASR, they calculated the probability (p-value) for SA for eight different sixteen different clades. Here are their results:
Table 2 from White, Zhong, and Penny (2013). P-values are in column “p (Χ^2)”.
As you should be able to see in the above table, they found ancestral sequence convergence at progressively deeper levels on the “tree of life.” The absolute maximum p-value was 1.05E-6 (for Vertebrata+Urochordata and Echinoderms+Hemichords), which is just infinitesimal. In statistics, usually a p-value of 0.01 or less is enough to reject the null hypothesis with high confidence – all of the p-values for the null hypothesis (SA) in this study were orders of magnitude lower than 0.01. So this shows, with extremely high confidence, that (at least) all plants and all animals, respectively, share common ancestry.
This evidence for common ancestry isn’t susceptible to any of the usual creationist objections. For example, ancestral sequence convergence can’t have been due to a “common designer” – unless that designer was being duplicitous. And there’s no bias in the statistical tests; they didn’t presuppose common ancestry between the groups tested, nor did they even presuppose common ancestry within the groups.
The only possible way this could have been happened on creationism is by chance. But the chance that none of the groups tested are related is 2.59E-132, basically impossible. It can really only have been due to common ancestry.
- Shared endogenous retroviruses
When an organism is infected by an RNA retrovirus, the virus inserts its genome into that organism’s cells, which basically turns their cells into a virus factory that allows the retrovirus to reproduce. If this happens in the germline of an organism, then the genetic material from the virus becomes part of that organism’s offspring, and is passed on from generation to generation. The genetic material is now known as an endogenous retrovirus (ERV).
This is where common ancestry comes in. According to CA (at least, human CA) humans should share at least some of our ERVs with other great apes, since it’s very unlikely that every ERV in the human genome came after the human-chimp split. In contrast, SA predicts that there should be no ERVs shared between humans and other great apes, since it’s extremely unlikely for a retrovirus to insert in exactly the same place in two different lineages.
This prediction was tested in 2018 by Grandi et al. According to their research, out of 211 human ERVs that were examined, there are 205 that chimps have in the exact same location. Likewise, we share 207 ERVs with gorillas, 205 with orangutans, 190 with gibbons, and 131 with rhesus monkeys.
Now, based on a study by Wang et al. (2007), it’s been calculated that there are about 10 million different locations for retroviruses to insert in the human genome (see here). Using binomial distribution, it’s possible to calculate the chance that we share 205 out of 211 ERVs with chimps by random chance (as would be necessary if SA is true) – this chance is 8.954E-1424, or in other words, 1 in 112 followed by 1421 zeroes.
Obviously, this chance is so infinitesimal it renders separate ancestry for humans and chimps effectively impossible. For this reason, creationists have chosen to argue that ERVs weren’t actually inserted by retroviruses, but were created in place as functional elements of the genome.
However, this is also impossible unless God was intentionally being duplicitous. There is actually a huge body of evidence showing that ERVs are the result of retrovirus insertion. For one, there are genetic ‘scars’ surrounding ERVs, consisting of “Long Terminal Repeats” and small DNA duplications on either side of the ERV (e.g., Mamedov et al. 2004), which are only produced by the enzymes used in retrovirus insertion. Furthermore, we have actually observed the process of endogenization (e.g., Crittenden et al. 1989), and there are many ERVs which are currently being fixed in human (Belshaw et al. 2005), chicken (Lee et al. 2017), and koala genomes (Stoye 2006). In light of all of this evidence, it’s clear that ERVs must have been produced by retroviruses.
Some creationists have argued that since ERVs are functional and contain ‘information,’ they must have been created. But that’s not true. First of all, only a few ERVs have function, and we still share many non-functional ERVs with chimps.
Second, the type of ‘function’ that creationists point to is gene regulatory function. But one recent study showed that no less than 1 in 10 random DNA sequences 100 nucleotides in length can act as gene regulators, with no modification (Yona et al. 2018). So this type of function evidently does not require a creator, it can appear totally randomly. In light of this, it’s not at all surprising that some ERVs were co-opted as gene regulators.
Third, we’ve actually observed an ERV that we know to have been inserted by a retrovirus confer function to its host. There are a few ERVs which can confer a special “dilute coat color” allele to a mouse when they insert in the correct location, and this has been known for decades (Jenkins et al. 1981; Hutchison et al. 1984; Tanave and Koide 2020). Creating an entirely new coat color is certainly a biochemical function, especially by creationist definitions of “function” (by which some 80% of the genome is “functional”). So this definitively demonstrates that ERVs can have a function without being created in place.
In summary, we share 205 out of 211 ERVs with chimps, and >130 out of 211 with even distantly related primates like rhesus monkeys. The probability of this occurring if we don’t share common ancestry is infinitesimal. All of the evidence shows that ERVs are the result of viral insertion, even those which confer function to their host, so God could not have created them in place unless He was being duplicitous.
- Shared silent mutations
As you probably already know, DNA codes for proteins. Specifically, each amino acid is coded for by different three-nucleotide DNA codons. However, there is functional redundancy in the DNA code, so the same amino acid can be coded for by different codons – for example, the amino acid serine is coded for by the UCU, UCC, UCA, and UCG codons. Because of this, there are some sites in the genome where single-nucleotide mutations do not affect the output protein. Such mutations are effectively neutral, and the sites where they occur are referred to as “silent sites.”
Now, CA (human CA, that is) predicts that such silent mutations should consistently produce the same nested hierarchical pattern between humans and other great apes, since we share common ancestry. In contrast, SA predicts that they would not produce a consistent nested hierarchy, because a “common designer” would only create genetic differences where they make a functional difference. This is true according to creationists themselves: AiG tells us that “the Creator God… use[d] similar design plans for his creatures when best suited for particular functions.”
This prediction was tested in 2016 by Bontrager et al. What they found is that silent sites do indeed produce a consistent phylogenetic signal between humans and great apes. Statistically, the p-value for the null hypothesis of separate ancestry was between 3E-9 and 1E-12, based on the phylogenetic tree agreement. Again, in statistics, usually a p-value of 0.01 or lower is enough to reject the null hypothesis, and this is many orders of magnitude lower than that. Therefore, we can (yet again) confidently reject separate ancestry for humans and other great apes, and conclude that we do share common ancestry with all the other primates.
I suppose the only ‘out’ for a creationist is to suppose that silent mutations do make a functional difference. One recent study suggests that silent mutations in yeast are strongly deleterious (Shen et al. 2022), and creationists have subsequently jumped on this bandwagon (Carter 2022).
However, as other authors have pointed out, this would overturn decades of evidence to the contrary, and there are significant methodological problems with Shen et al.'s study (Kruglyak et al. 2022). It seems safe to say that silent mutations do not have a fitness effect, or at least that if they do, it’s certainly not enough to explain the extremely strong phylogenetic signal of silent sites between humans and other primates.
That was a lot, but it doesn’t even scratch the surface of all of the evidence that I considered before realizing that universal common ancestry is true. Those are just the three things that convinced me the most. Those are also the only quantitative tests of common ancestry that have been done (that I know of), and I’m more of a numbers guy, so I guess that explains why I found them convincing.
Hopefully that helped you understand why I concluded that common ancestry is true, @thoughtful!
