Molecular Clocks and the Expansion of B2a in the Southwest

Publishing information related to DNA studies and our Book of Mormon model can be difficult. The subject matter itself is complicated and it’s very difficult to dive into technical discussions with an audience that is not necessarily composed of geneticists. Also, I am not a fan of disparaging the current state of science or the scientists involved in it, but the more I learn about modern DNA studies, the more I see that a significant number of peer-reviewed, prestigious studies are basing some of their conclusions on some very poor assumptions.

In this article, I want to address one of these assumptions in particular.

I know that many people will think that I just have sour grapes because no scientifically-accepted DNA studies seem compatible with the idea that any Native Americans are descended from Israelites. I can understand why a reader might be suspicious of my motives when they see me attacking the science itself, but please consider the thoughtful and informed nature of the arguments that I present before passing such judgements.

A Basic Understanding of DNA and Population Genetics

Delving into a full description of all of the relevant aspects of DNA research is far beyond the scope of this paper. I will briefly describe the broad basics of how DNA studies can reveal information about prehistoric populations and migrations, but I will rely on the reader to make sure that they take time to understand some of the technical terms that I use in this article.

Most of us understand that our DNA is a unique combination of the DNA provided by each of our biological parents. This is true, and this type of DNA is called “Nuclear DNA”, but there are also other forms of DNA in our bodies that are not derived from a combination of DNA from both of our parents. Mitochondrial DNA (mtDNA) is passed exclusively from mother to child and is far more abundant in our tissues than nuclear DNA. Yet another form of DNA gets passed from father to child and is called “Y-Chromosome DNA” (Y-DNA).

Nuclear DNA experiences drastic changes during the process of combining the DNA of our mother and father into our own unique DNA. This process is called “recombination”. Since mtDNA and Y-DNA are not affected by recombination, every child that is born receives an exact copy of their mother’s mtDNA and their father’s Y-DNA. This concept is fundamental to most historical genetic studies because it means that a modern person’s mtDNA is a copy of their mother’s mtDNA which is a copy of their mother’s mother’s mtDNA and so on all the way back through the evolutionary history of mankind (and likewise with Y-DNA through each person’s father, but to keep the discussion simple, we will only refer to mtDNA in this article).

Let’s take a moment now and describe what we mean by an “exact copy of their mother’s mtDNA”. This means that a mother passes on copies of her mtDNA to her child as it exists at that point in her life. Although this is often an exact copy of what that mother received from her own mother, please remember that many years pass by between the birth of a girl and the birth of that girl’s children. During those years, her mtDNA can experience what geneticists call “mutations”. Tracking mutations is fundamental in studies of population genetics.

To understand DNA mutations, we must first understand what Mitochondrial DNA is and what Mitochondrial DNA does. mtDNA is a long chain of things called nucleotides. Unlike Nuclear DNA, mtDNA’s nucleotide chain forms a loop. There is not really a “beginning” or an “end” of it in the same way that there is not really a “beginning or “end” of a circle. You can think of this loop as a chain that has roughly 16,600 individual links, all connected together. Geneticists call each link in this chain a “nucleotide position”.

There are four types of nucleotides that are relevant to our discussion, namely: Thymine, Cytosine, Adenine, and Guanine (labeled “T”, “C”, “A”, and “G” hereafter).

Each nucleotide position (each link in the chain) contains exactly one of those four nucleotides, but this brings us to our most important point: The exact nucleotide at each of the 16,600 nucleotide positions can occasionally change. For example, a “T” can get swapped out for a “C”. This brings us to our definition of the term “mutation”: A mutation is a change from one nucleotide to another nucleotide at one of the nucleotide positions.

Once a mutation occurs and is passed on to a mother’s daughter, that daughter will pass on that mutation to her children and the daughter’s daughters will pass it on to subsequent generations. After many generations, a process called “genetic drift” tends to make a small set of mtDNA lineages common within populations of people living in discrete areas of the globe.

Since mutations occur at different nucleotide positions and in different ways in one population of people compared to another, we can look at the mtDNA of a person and learn what population of people they are descended from on their maternal line. This is the basic theory behind most historical studies that are based on mtDNA (or Y-DNA) evidence.

What Are Modern Studies of Population Genetics Doing Right?

Before I dive into some things that I think are wrong with many current studies, I want to point out the main thing that modern scientific DNA studies have right.

Modern studies that use DNA information show us that different populations of people share patterns of mutations. This is an absolutely fundamental point and is the reason that we should continue to support genetic studies regarding human history. There is no doubt that we are learning many important things about human history through these studies.

In addition to the successes of these studies, the scientists involved are aware of many shortcomings in their research. In general, their studies tend to acknowledge many of the potential shortcomings of the science and they often provide relevant discussions to mitigate the risk that people might misinterpret their results.

Many of these well-recognized scientific shortcomings can significantly affect the results of DNA studies that are related to our model of the lands of the Book of Mormon, including:

  • The potential that genetic drift could hide entire populations of prehistoric Native Americans from studies of modern Native American DNA (This is a shortcoming that is only relevant to studies that use DNA samples from modern people. It is not a shortcoming of studies that obtain DNA from ancient tissue samples).
  • The fact that mtDNA and Y-DNA studies only tell us about two ancestors (the direct matrilineal and direct patrilineal lines) out of the thousands of people that are an individual’s actual ancestors.
  • Recognition that founder effects can easily mask important results.
  • Recognition that contamination of DNA samples is common and that proper precautions must be used.

I would also like to note some other potential shortcomings that are rarely mentioned in scientific papers because they are not likely to contribute significantly to the results of those papers including:

  • The potential that the father’s mtDNA might get passed to a daughter instead of the mother’s mtDNA. This has not been observed in humans, but since it has been documented in very rare circumstances in other species, scientists aren’t 100% certain that it never happens in humans. Although this potential is often highlighted by non-scientists who want to disparage scientific results, it is a weak argument at best. In order for it to significantly affect the results of a population study, not only would this very improbable thing have to happen, it would have to occur during the very short window when a lone outsider contributed DNA to the population being studied. Otherwise, the father’s mtDNA is still a reflection of the mtDNA of the population, just as the mother’s mtDNA is. This should not be used to argue against modern studies of population genetics.
  • The potential that a mother may pass on more than one version of her mtDNA. This is a rare, but well-documented phenomenon. The result is that the daughter’s mtDNA might not look like it matches the mother’s mtDNA, but the mtDNA still came from the mother and reflects something of her heritage. The potential for this occurrence to significantly skew the results of any population study decreases dramatically the farther away that it happens from a founder event. As a result, this should not be used to argue against modern studies of population genetics.

Some Well-Established Scientific Information is Currently Being Ignored by Many Researchers

Like I said at the beginning of this article, I do not like to criticize scientists and their work in broad strokes, but sometimes that kind of criticism is actually appropriate. I believe that this is one of those times.

Molecular Clocks

Virtually every study of population genetics includes an estimate of the age of the clades presented in the study. For instance, according to one prominent peer-reviewed study, mitochondrial haplogroup B2a experienced migrations and a population expansion centered around the Colorado River Delta which started roughly 100BC and which continued for several centuries. According to the authors:

The expansion seems to have been one that was region-wide, encompassing all of the diverse populations within the greater Southwest [ref]

The population expansion that they describe is a precise fit for our model of the Book of Mormon migrations into the land Northward followed by the collapse of the Nephite civilization at Cumorah.


A later study, based on more mtDNA information, gave us a completely different timeline for the expansion of B2a. It directly refutes the previous study. Here is an abbreviated version that highlights their conclusions:

A recent study, performed at the control-region level, proposed that B2a mtDNAs mark a population expansion within the American Southwest…Our analyses at the level of entire mitogenomes provide additional information that suggests a different scenario. The overall B2a coalescence time is at ∼12–13 ka…the main episode of population growth associated with B2a dates to 8–10 ka

Well darn. It looks like the original study was just plain wrong…but was it?

When we’re dealing with a topic as complicated as population genetics, most of us understand so little about what the professionals are saying that it is easy for a paper to gloss over important information without drawing attention to the real reasons that their conclusions are different than the conclusions of the original study. We’re going to delve deeper into what this second paper is really saying and a new picture will emerge.

Before I explain how the results themselves seem to avoid some inconvenient facts, we should give a little background information that may shed some light on the underlying conflict that the respective authors are addressing. The conclusions of the first paper were presented as supporting evidence of a very controversial linguistic hypothesis known as the “farming/language dispersal hypothesis”. This linguistic hypothesis is a clear target of the second study. This fact is evident if I provide the more complete version of the same quote as above:

A recent study, performed at the control-region level, proposed that B2a mtDNAs mark a population expansion within the American Southwest, and tested the hypothesis that this expansion was because of the spread of groups of Uto-Aztecan farmers who introduced maize agriculture into this area from Mesoamerica ∼4 ka…

With that background information in mind, we can see that the authors are directly refuting the farming/language dispersal hypothesis by giving us different dates for B2a’s emergence and expansion in the Southwest. There’s nothing wrong with this so far, so let’s continue reading the details of the statement from the second paper:

The overall B2a coalescence time is at ∼12–13 ka, and we obtained a similar estimate when combining the previously published B2a control-region data with the control-region sequences of our mitogenomes

So now the authors are saying that they didn’t just use their own data, they also included the data from the original study in their analysis. Again, there’s nothing wrong with this scientific approach yet, so let’s read on:

The network shows that B2a mtDNAs diverge from the root (central node) by 1.2 ± 0.3 control-region substitutions on average, which correspond to ∼11 ka [95% confidence interval (CI) 5.5–16.2 ka] when using the molecular clock of Soares et al. Therefore, the onset of B2a should be predated to 11–13 ka in the late Pleistocene. This finding is further supported by our BSP analyses. Indeed, the main episode of population growth associated with B2a dates to 8–10 ka; thus, it is likely too ancient to be associated with the farming/language dispersal hypothesis.

Ouch! That statement had some painfully technical words and phrases, but it’s not too hard to understand that all of those technical terms lead to the conclusion that the first study was wrong by thousands of years.

Unfortunately, there is something very wrong with what the authors just presented. They didn’t expressly lie to us, but they did leave out one very important point:

The reason that their dating of the emergence and expansion of B2a doesn’t match the first study is NOT because their study was more thorough. The reason it was different is because of this little tidbit hidden in the middle of that paragraph: “using the molecular clock of Soares et al”.

^^^^^This is a VERY CRUCIAL detail^^^^^

The reason that their dates are different is not because their data is different. It is because they analyzed it using a different molecular clock. Unfortunately, readers of their paper are very likely to miss that fact because its authors never once point it out directly. They talk a lot about how they analyzed more of the genome than the first study and they talk a lot about how their data sets were more complete than the first study, but they never draw attention to the fact that it was their choice of a different mitochondrial clock rather than the completeness or thoroughness of their data that was the single biggest factor influencing the difference between their results and the results of the paper that they are claiming to refute.

The very fact that they don’t draw attention to the most import factor influencing their dates is enough to give me pause, but it doesn’t necessarily mean that their results are wrong. After All, the molecular clock that they chose to use was published in 2009 by Soares and was well-received by the scientific community. Soares’ clock is based entirely on synonymous mutations in hopes that it will overcome many of the shortcomings of other published clocks. If I had to choose a clock based completely on its theoretical underpinnings, I would probably choose Soares’ clock also, despite the fact that it isn’t as supportive of my model as the clock used in the original study.

I want to repeat what I said earlier in this article. You need to understand a lot about population genetics to know when you should question the published results. It turns out that this is true of Soares’ clock. I recently noticed that one of the primary calibration points that Soares’ gave as evidence of the accuracy of his clock proved to be a poor marker. The geographical region where Soares’ conducts most of his research is in the Pacific Islands, so it is probably natural that he used an example from that area as a calibration point for his clock, but buried in the details of a subsequent, unrelated paper called “Ancient Voyaging and Polynesian Origins” (2011) Soares states that:

the virtual absence of B4a1a1 in Indonesia makes the motif’s origin in Wallacea very unlikely, contrary to our earlier suggestion that assumed a simple west-to-east progression

He goes on to tell us that “the motif is most likely at least 6.5 ka old”. What most readers don’t realize is that with this statement he is admitting that something he called a “clear-cut archaeologically based calibration point” which supposedly validates his clock in his 2009 paper was wrong. His clock’s calibration is based on a “clear-cut” date of 3.5 thousand years ago but he now believes that his clock should have shown a date of 6.5 thousand years ago instead.

That “clear-cut” calibration point turned out to be significantly wrong. It was nearly double the age that he now considers correct. In other words, Soares’ own calibration point proves the inaccuracy of his clock.

So, has the professional scientific community noticed this little discrepancy yet? Not as far as I can tell. They continue to publish papers based on Soares’ clock without the least acknowledgment that it doesn’t calibrate to it’s own “clear-cut” calibration point.

As one considers the history and state of affairs of molecular clocks in general, the problems with them are so obvious and so impactful that it is hard to understand why the professional community continues to publish study after study which use molecular clocks to estimate the age of DNA clades.

The good news is that some well-respected geneticists are starting to see the colossal errors that are being made. An article published in 2009 in the Journal “Molecular Ecology” could not have stated this and other related issues more clearly:

Over the last three decades, mitochondrial DNA has been the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of clonality, near-neutrality and clocklike nature of its substitution rate. Reviewing recent literature on the subject, we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like[ref] [Further evidenced in another article in 2011 available here]

So why is it that five years after the publication of that statement and the paper supporting it, the vast majority of peer-reviewed publications of population genetics still go to press proudly presenting age estimates based on molecular clocks?

I do not know the answer to that question. You don’t need to dig down to Soares’ inconspicuous little admission in 2011 in order to see that this is a BIG problem. All you have to do is take a look at Wikipedia and learn the difference between pedigree-based clocks and phylogeny-based clocks. The problems are readily apparent.

I hope that this article doesn’t come across like I just have sour grapes about the dates presented. I’m perfectly willing to accept scientific uncertainty when it’s treated properly by scientists, but this problem with molecular clocks has been too obvious for too long with too little progress towards changes in the way that studies of population genetics are presented to the public.

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