We continue our review of the book, Adam and the Genome: Reading Scripture after Genetic Science, by Dennis Venema and Scot McKnight. Today, Chapter 3- Part 2
In Part 1 of Chapter 3- Adam’s Last Stand?, Dennis summarized two methods of estimating the size of ancestral populations based on the present characteristics of that populations genome. If there was a “bottleneck” of only two people then the genetic consequences would be severe: at maximum, four gene-forms (two from each parent) would be passed on by Adam and Eve. Interbreeding in the very small population after the bottleneck would result in the further loss of some alleles due to chance alone. In short, the genetic impact of such an event would leave a stamp on the genome of that species that would persist for tens of thousands of generations as mutations slowly generated genetic diversity.
This information can be used, then, to estimate the minimum number of people that could have existed at any point in time. First we ask how many different alleles there are for a number of genes within the current population. Correcting for the rate at which we know new forms of genes appear (mutation), we can calculate the minimum number of people needed to generate the current amount of diversity. Numerous studies analyzing many different genes all point to a bottleneck. However, these studies are all clear: during the bottleneck, there were several thousand individuals, not two.
The second method, independent of the first, is called “linkage disequilibrium”. In population genetics, linkage disequilibrium is the non-random association of alleles at different loci (i.e. where on the chromosome the genes are located). Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly. Based on the number of allele combinations that we observe in this population, how many ancestors do we need to invoke in order to explain what we observe? In this case, rather than estimating mutation frequency, the calculations require knowing how often crossing over happens between two loci. This is also something we can measure directly in humans and other animals, and there is a well-characterized relationship between chromosome distance between two loci and crossing over frequency. As Dennis says:
“We’ve now done this sort of analysis for millions of pairs of loci (yes—millions) for each chromosome pair in our genome (all 23 pairs). And what is the final tally after crunching all that data and counting up ancestors. The results indicate that we come from an ancestral population of about 10,000 individuals—the same result we obtained when using allele diversity alone.”
The third and last method that Dennis outlines is called “incomplete lineage sorting” or ILS. This method, like disequilibrium analysis, is virtually unaffected by varying estimations of mutation rates.
- While humans and chimpanzees are the closet living relatives as species, we expect that some human genes will be closer matches to other apes such as gorillas.
- When a population undergoes a speciation event some genes will have two or more alleles within the population as a whole.
- As populations separate, they will both inherit that diversity. The two alleles are represented as shaded boxes on a phylogeny or “family tree” in Figure 3-5
- The common ancestral population of gorillas, chimps, and humans has two alleles of one gene (“A” and “a”) within the population.
- As the population separates into 1) human-chimp and 2) gorilla, both populations inherit both alleles.
- In the gorilla lineage “a” is lost, leaving only variant “A”.
- As chimps and humans split, “A” is lost and “a” is retained in the chimp lineage while in the human lineage “a” is lost and “A” is retained down to the present day.
- The final pattern is:
- Humans and gorillas have “A”
- Chimps have “a”
- Gorillas and humans now have more closely related alleles than either does with chimps.
- This pattern lets us know that the common ancestral population of humans and chimps had both “A” and “a”
- Also the common ancestral population of gorillas, humans and chimps had both “A” and “a”.
- If you have a way to infer what genetic variants were present in a population, you have a way to estimate its population size.
- Scientists predicted in advance of sequencing the gorilla genome, an ILS of 25%.
- When gorilla genome was sequenced the observed rate was 30%.
- Scientists predicted in advance of sequencing the orangutan genome, an ILS of 1%.
- When the orangutan genome was sequenced the observed rate was 0.8%.
- Those results indicated that the estimation of ancestral population size leading eventually to humans was accurate.
“Put most simply, DNA evidence indicates that humans descend from a large population because we, as a species, are so genetically diverse in the present day that a large ancestral population is needed to transmit that diversity to us. To date, every genetic analysis analyses estimating ancestral population sizes has agreed that we descend from a population of thousands, not a single ancestral couple. Even though many of these methods are independent of one another, all methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last 3 million years or more—long before our lineage was even remotely close to what we would call “human”. Thus the hypothesis that humans descend solely from one ancestral couple has not yet found any experimental support, and it is therefore not one that geneticists view as viable.”
In the next section, Dennis addresses the question that genetics can’t answer: what did we look like and how did we behave? That question can only be answered by the fossil record, which because of its nature cannot conclusively reveal who our direct ancestors might be; it can only show remains that would be those of close relatives. At the time of publication of Origin of the Species by Darwin there were no known fossils that seemed to be intermediate between apes and humans. A few Neanderthal remains weren’t well understood and were also very similar to modern humans. At the time, there was a widespread expectation within the scientific community that an evolutionary lineage would be a ladder-like progression from one species to the next culminating in modern man. You know the one I’m talking about; that looks like a police lineup (that has been endlessly parodied).
From Darwin’s ideas, scientists and the public expected there to be a series of “missing links” connecting humans to apes that could be found in the fossil record and that any such species would be direct ancestors of humans. Since brain size was the obvious difference; scientist expected that “ladder” to show increasing cranial capacity i.e. evolution from the chin up and only then from the chin down. This expectation would hamper research into human evolution for many decades. One result of that false expectation was the fraudulent “Piltdown Man” with a human skull and an orangutan jaw with the teeth filed to shape them to the expected form. As the paleontological data continued to accumulate the data increasingly showed that Piltdown man did not fit the pattern; that the pattern was indeed evolution from the chin down first. Scientific suspicion of Piltdown man grew until the teeth filing was uncovered. It should be noted for the record, that careful scientific investigation by evolutionary anthropologists eventually uncovered the fraud, not creation scientists doing “creation research”; although the creationist literature loves to cite Piltdown man as an example of how “science gets it wrong” and how we should “doubt science rather than the Bible when they conflict”. It was “science” that eventually uncovered the fraud, but, as I’ve said before, the YEC are an irony-free community.
As we have seen for cetaceans, eventually a picture emerged that gives us a reasonable idea of how possibly our lineage changed as we parted ways with the lineage leading to chimpanzees. Though chimps are our closest living relatives, there are a number of species in the fossil record known as “hominins” that are more closely related to us than to chimps.
“Probable hominins” like Ardipithecus ramidus, a species that lived in Africa about 4 million years ago (mya) had skeletal characteristics intermediate between upright walking and the climbing of trees, and a small cranial capacity of 300-350 cubic centimeters (cc) (modern humans are about 1,300-1,400 cubic centimeters). Australopithecus afarensis (aka Lucy) about 3-4 million years ago shows further shifts toward walking and a cranial capacity of 400-550 cc. Later still we see pre-modern Homo erectus (“Upright Man”) dating to about 1.8 mya with full bi-pedalism and a cranial capacity of 700 cc.
In Dennis’ words:
“Similar to what we discussed regarding whales, we cannot be certain that any of these species is in fact a direct ancestor of present-day humans. What these species show us is the probable path of our actual lineage, since these species are at least close relatives of our ancestral line. The evidence thus suggests that our lineage over the past 4 million years passed through an Ardipithecine-like species, on to an Australopithecine-like species, and then through various shades of Homo until our species is first preserved in the fossil record 200,000 thousand years ago. And as we have seen for languages, the process was a continuous one of average change within a population over time. What we see in the fossil record matches up with what we see in our DNA.”
In other words, we have failed to reject the hypothesis that humans share a common ancestral population with apes.
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Other posts in the series: