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Fewer Mutations Means More Time

ape human mutations.jpg

Evolutionary theory incorporates several ideas: Adaptation to the environment, speciation, random mutations coupled with natural selection, and common ancestry. ID addresses the part of evolutionary theory that asserts mutations coupled with natural selection result in novel traits, and through this mechanism life, once it emerged, then formed the diverse biological structures that we see today. ID argues that biological structures are designed with an end in mind and cannot be the result of a random process. Common ancestry, the idea that all life is related by a common ancestor, may be compatible with intelligent design and need not have occurred via this bottom-up approach of randomly adding pieces to simple structures. With this context in mind, let's look at a recent Nature Genetics paper that studied germline mutations and their implications for human-chimp divergence from their common ancestor.

The authors investigated de novo or germline mutations. These mutations come from either the mother or of the father and are due to a mutation in a germ cell, the egg or sperm. These types of mutations are the bread-and-butter of the evolutionary theory of the origin of novel biological structures. The authors identified candidates for germline mutations within the genomes of two parent-child trios of differing nationalities. They selected several genetic mutations that could have come from a germline mutation. They subjected their candidates for germline mutations to a developed experimental procedure that puts the candidates through a more rigorous test to see whether they are truly germline (as opposed to somatic mutations) and whether the mutations where from the material line or the paternal line. Using their more precise methods, they found that there are more false-positives than what has been shown in previous studies: They found 49 and 35 de novo germline mutations and 952 and 643 non-germline mutations in each of the trios. They report that this 20:1 ratio of non-germline to germline is larger than the 1:1 ratio that had been previously published.

The authors made the following conclusions:

  • There are fewer germline mutations than was once thought. They found that there are about 60 mutations per generation as opposed to the 100 (or more) mutations estimated before.
  • In one of the parent-child trios, more mutations came from the father, while in the other parent-child trio, more mutations came from the mother. This contradicts the theory that most germline mutations come from the paternal side due to male germ cells undergoing more cell divisions.
  • The number of germline mutations was drastically different for the two families. It seems that some families are more prone to mutations than other families.

From an interview with one of the researchers, Phillip Awadalla:
This makes us think about what are the underlying mechanisms of these mutations, other than just a random process...Why are there differences in the rate or accumulation of mutations in individuals? (emphasis added).

The mechanisms that Awadalla is talking about are presumably environmental pressures; however, the authors are not sure what causes some families to have more mutations than others. This study seems to show that these are not necessarily random mutations, but mutations that occur for some reason.

The authors of this study emphasized in their research paper their findings of the widely variable sex-specific mutations as well as the variable number of mutations per family. They were interested in how this may help our understanding of the factors that cause mutations as well as assist in diagnosis of genetic disease. But there is another implication to their studies that the popular press focused on in their interview, and the authors briefly mentioned in their paper: The study implies that humans must have evolved slower than was thought because there are fewer (at least half) de novo germline mutations passed from parents to offspring. For this rate of mutation to be consistent with the prevailing theories of human-chimpanzee divergence from a common ancestor, the authors contend that the human-chimp divergence must have occurred 7 million years ago:

Averaging across these four studies gave a more precise sex-averaged mutation rate of 1.18x10-8 (+_ 0.15 x 10-8(s.d)) which is less than half of the frequently cited sex-averaged mutation rate derived from the human-chimpanzee sequence divergence of 2.5 x 10-8. These apparently discordant estimates can be largely reconciled if the age of the human-chimpanzee divergence is pushed back to 7 million years, as suggested by some interpretations of recent fossil finds, and by considering more recent (and slightly lower) robust genome-wide estimates of sequence divergence (references removed).

Evolutionary theory states that humans and chimps, because of similarities in their DNA, have a common ancestor that diverged several million years ago. However, genetic studies have proved inconclusive as to how long ago this happened. There are several factors to consider in predicting human-chimp divergence. The fossil record, genetic similarities in the genomes, and differences in the Y chromosome can all point to different theories at to the time line of human-chimp divergence. What the fossil evidence seems to show is that the homo line appeared suddenly and distinctly in the fossil record and that there is a lack of transitional evidence connecting the homo line to the chimpanzee (see here for a description of the various fossil findings including ambiguities in the human fossil record).

This study, based on mutations in the genome, assumes that humans evolved slower than was once thought, but time lines based on other fossil data show a rapid evolutionary transition in skull size and body structure. To say that human-chimp divergence needs to be pushed back to seven million years implies re-thinking some of the other criteria used to determine human origins and its time line.

There's another issue that has not been fully addressed. These 60 mutations per generation are very few mutations for natural selection to work with. But humans have a very long generational time. And finally the authors reported that most of these mutations, particularly in the family with the higher mutation rate, occur in the non-coding part of the DNA. Finally, from what we know about mutations that do occur and have a noticeable effect on the person, they are often deleterious or serve to remove some type of function. Rarely are they beneficial and rarely do they add function. The question is, is this really enough mutations and enough time for natural selection to produce novel body plans? Is this even enough time to see the changes that have occurred in an evolutionary model of the Homo lineage?

Human ancestry is a highly contentious subject. Interpretations of the fossil record seem to be full of presuppositions, while the genetic studies seem to go back-and-forth between a fast human-chimp divergence and a slow one. With only 60 mutations per generation, even given that some families may mutate more and others less, it does not seem feasible that mutations coupled with natural selection had enough time to create the divergence that we see today.