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Misconceptions Around Mitochondrial Eve

 

A Critique of Carl Wieland's AiG article on Mitochondrial Eve

 

Alec MacAndrew

 

 

 

This is a response to an article written by Carl Wieland and published on the Answers in Genesis website about the concept of 'Mitochondrial Eve' published here:

 

http://www.answersingenesis.org/docs/4055.asp (1)

 

The AiG article attempts to claim that the mitochondrial evidence is that the Most Recent Common Ancestor of extant humans in the matriarchal line is 6,500 years old.  The AiG article begins with a reasonable definition of an MRCA (see link for definition) but then grasps at two relatively recent papers assessing mutational rates in the mitochondrial DNA and rushes to a prematurely triumphant conclusion about them.  

 

 

The Underlying Science

 

Most of the DNA in the cell of non-bacterial organisms lies in the nucleus. But in eukaryotes there are structures in the cell outside the nucleus called the mitochondria. The mitochondria have several functions, the most obvious of which is that they are responsible for converting 'food' into energy within the cell. The mitochondria also have their own DNA. (There is strong evidence that the complex cells of eukaryotes, which are organisms that have cells with a nucleus, arose originally as a result of parasitism or symbiosis of one simpler organism with another which developed into what's called an obligate relationship - that is one in which the different organisms were so closely bound that they became unable to live without one another and thence became one organism. But, that's a different story).  (2), (3), (4)


DNA material in the nucleus, in the 46 chromosomes in humans for example, comes almost equally from the father and mother - 23 chromosomes from each. (I say almost, because the Y chromosome in mammals is much smaller than the X chromosome). But the mitochondrial DNA comes only from the mother. This means that the mitochondrial DNA follows the female line exclusively. If a woman has no daughters, her mitochondrial DNA (called mtDNA) line dies out.

Nuclear DNA (the 23 pairs of chromosomes in the nucleus) goes through a process called recombination whereby the chromosomes that are passed on to offspring, say through the mother, are a mixture of the genes in the mother's parent's lineage. However the mtDNA is not a mixture like this, but comes exclusively from the mother. This makes mtDNA a good way to study lineages and to estimate dates of divergence of different groups. The way this is done is to study differences between the mtDNA sequences in different individuals. The nature of the differences provides clues about the relationship between individuals, and the magnitude of the difference indicates how long ago the lineages of the two individuals
in the maternal line diverged. There are complications with this process, but that is the basic principle (5)

This is the way that the age of what has been called mitochodrial Eve is calculated. I don't like the term mitochondrial Eve, because it implies things that it is not - it is simply misleading. So what is it? It is properly termed the most recent common (matrilineal) ancestor (MRCA).

That means the
most recent individual that lived that stands in the direct line through mothers with the entire set of individuals in question. If we are looking at the entire population of people today, the MRCA of that set is called mitochondrial Eve. The matrilineal MRCA of humans is estimated to have lived between 150,000 to 200,000 years ago (note that there are other MRCAs; eg the MRCA as measured by the X-chromosome - since the X-chromosome descends through fathers and mothers, the lineage is different - but there is still the concept of the individual from whom the X-chromosomes of all people alive today descended. That concept is not the same as matrilineal MRCA or Mitochondrial Eve).

Anyway, the estimate of 150,000 to 200,000 years for matrilineal MRCA was called into question not by one challenge (as Carl Wieland suggests) but by two challenges. However, Carl Wieland's implication that it is now considered to be likely that the matrilineal MRCA lived 6,500 years ago is very misleading.

 

There are many other creationist sites which use this research to claim a young (~6,500 year) age for the origin of humans, and many do so with less care than Wieland.  Many go so far as to say that these papers make it settled question that biblical Eve existed and that she lived 6500 years ago. Here are a few:

 

An article by Charles Creager

Institute for Creation Research

The Apologetics Press

Creation Research Society

Creation Digest

 

Let's look at this in more detail.

 

 

The Challenges to the view of a 175,000 year date for matrilineal MRCA.

 

A Challenge which would make the date of matrilineal MRCA earlier

CHALLENGE 1: In Science 286, 2524 - 2525, Philip Awadalla, Adam Eyre-Walker, and John Maynard Smith (6)   reported evidence of some mixing of paternal with maternal DNA in the mitochondria. They looked at a measure called linkage disequilibrium (which determines the degree of 'randomness' between alleles at different loci) and concluded that there was evidence of recombination between the father's and mother's mitochondria. This is radical as it would call a lot of conclusions based on assessing mtDNA into question. This occurred in 1999. If it were to be true, then it would mean that estimates of matrilineal MRCA age would be too low, as recombination tends to make DNA sequences more like one another over time, so it would take longer for the differences that we observe in people from around the world to evolve.

However, we soon saw Awadalla et al's study called into question: The following researchers published direct challenges to the Awadalla et al paper:

Toomas Kivisild and Richard Villems: "In sum, likely errors in the sequence data used by Awadalla et al. and the possibility that straightforward phylogenetic explanations can explain the observed correlations make the conclusions drawn [in the reference below] weaker than such an exceptionally important problem deserves"

LB Jorde and M Bamshad: "The possibility of recombination in mtDNA is intriguing and deserves further evaluation. Six of the eight mtDNA data sets examined here fail to show a significant decline of LD with physical distance using the r2 statistic, however, and none show a decline using the more appropriate D' statistic. Thus, LD patterns provide little support for the hypothesis of mtDNA recombination"

Sudhir Kumar, Philip Hedrick, Thomas Dowling and Mark Stoneking: "Our reanalysis thus contradicts the contention by Awadalla et al. (1) that recombination is occurring in human mtDNA. Extensive family studies have likewise failed to find any exceptions to strict maternal clonal inheritance of human mtDNA (9-12). There is no need to reconsider inferences about human or mtDNA evolution that have assumed that recombination does not occur in human mtDNA."

Thomas J. Parsons and Jodi A. Irwin: "In light of that finding, it seems unlikely that our understanding of the pattern and relative rates of sequence evolution within the mtDNA CR will require substantial revision based on the Awadalla et al. report. Our analysis also suggests that mtDNA forensic testing will be negligibly impacted by recombination; forensic applications already deal successfully with intergenerational mutation [in the references below], clearly a far more significant effect."

All of these were published in Science 288 p1931
(7) . At the moment this question has not been settled. The bulk of the opinion is that recombination does not occur, but there has also been some further evidence for it. Note that if recombination does occur, the matrilineal MRCA of humans would be OLDER than the current estimate of 150,000 to 200,000 years

 

.

A Challenge which would make the date of matrilineal MRCA later

CHALLENGE 2: This is the challenge that Carl Wieland was referring to. There have been two papers that have measured unexpectedly high short term mutational rates in the control region of the mitochondrial DNA. The control region is a part of the mitochondrial DNA that does not code for proteins. The normally accepted rate is one mutation every 300 to 600 generations (6000 to 12000 years) and this is calibrated, as Wieland correctly says, by counting mutations in great ape and human mitochondria and regressing back to the age of their divergence as determined by fossils dated by radiometric dating.

 

(Note the control region is also known as the D-loop)

 


The two papers are:

 

A high observed substitution rate in the human mitochondrial DNA control region (8) :

 

The rate and pattern of sequence substitutions in the mitochondrial DNA (mtDNA) control region (CR) is of central importance to studies of human evolution and to forensic identity testing. Here, we report direct measurement of the intergenerational substitution rate in the human CR. We compared DNA sequences of two CR hypervariable segments from close maternal relatives, from 134 independent mtDNA lineages spanning 327 generational events. Ten substitutions were observed, resulting in an empirical rate of 1/33 generations, or 2.5/site/Myr. This is roughly twenty-fold higher than estimates derived from phylogenetic analyses. This disparity cannot be accounted for simply by substitutions at mutational hot spots, suggesting additional factors that produce the discrepancy between very near-term and long-term apparent rates of sequence divergence. The data also indicate that extremely rapid segregation of CR sequence variants between generations is common in humans, with a very small mtDNA bottleneck. These results have implications for forensic applications and studies of human evolution...

....The observed substitution rate reported here is very high compared to rates inferred from evolutionary studies. A wide range of CR substitution rates have been derived from phylogenetic studies, spanning roughly 0.025-0.26/site/Myr, including confidence intervals. A study yielding one of the faster estimates gave the substitution rate of the CR hypervariable regions as 0.118 +- 0.031/site/Myr. Assuming a generation time of 20 years, this corresponds to ~1/600 generations and an age for the mtDNA MRCA of 133,000 y.a. Thus, our observation of the substitution rate, 2.5/site/Myr, is roughly 20-fold higher than would be predicted from phylogenetic analyses. Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA of only ~6,500 y.a., clearly incompatible with the known age of modern humans.'

'The rate and pattern of sequence substitutions in the mitochondrial DNA (mtDNA) control region (CR) is of central importance to studies of human evolution and to forensic identity testing. Here, we report direct measurement of the intergenerational substitution rate in the human CR. We compared DNA sequences of two CR hypervariable segments from close maternal relatives, from 134 independent mtDNA lineages spanning 327 generational events. Ten substitutions were observed, resulting in an empirical rate of 1/33 generations, or 2.5/site/Myr. This is roughly twenty-fold higher than estimates derived from phylogenetic analyses. This disparity cannot be accounted for simply by substitutions at mutational hot spots, suggesting additional factors that produce the discrepancy between very near-term and long-term apparent rates of sequence divergence. The data also indicate that extremely rapid segregation of CR sequence variants between generations is common in humans, with a very small mtDNA bottleneck. These results have implications for forensic applications and studies of human evolution...

...The observed substitution rate reported here is very high compared to rates inferred from evolutionary studies. A wide range of CR substitution rates have been derived from phylogenetic studies, spanning roughly 0.025-0.26/site/Myr, including confidence intervals. A study yielding one of the faster estimates gave the substitution rate of the CR hypervariable regions as 0.118 +- 0.031/site/Myr. Assuming a generation time of 20 years, this corresponds to ~1/600 generations and an age for the mtDNA MRCA of 133,000 y.a. Thus, our observation of the substitution rate, 2.5/site/Myr, is toughly 20-fold higher than would be predicted from phylogenetic analyses. Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA of only ~6,500 y.a., clearly incompatible with the known age of modern humans 


The second paper is:

How rapidly does the human mitochondrial genome evolve? (9)

 

 

Analysis

So it is the Parsons work that mentions an matrilineal MRCA of 6,500 years that Wieland and other creationists have latched on to. Note that Parsons says: 'Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA of only ~6,500 y.a.,
clearly incompatible with the known age of modern humans'

Both Parsons and Howell use a technique called restriction fragment length polymorphism (RFLP) analysis. This technique uses restriction enzymes (enzymes which cut sequences of DNA between short identical sequences). The length of the cut pieces is analysed and the presence of mutations will cause the length of the excised sequences to vary.  This does tell us a lot about the different alleles on mitochondrial DNA, but since RFLPs can be created by events other than single base pair substitutions, it can be misleading.

 

Nevertheless, on the face of it, there is a substantial discrepancy between the mutational or substitution rates as determined by phylogenetic analysis (comparing the mtDNA sequences of chimp and human, foe example) and pedigree analysis (data based on allelic differences between close family members).


Others who attempted to repeat Parson's results with pedigree data were unable to do so
(10) and derived a rate little different from the rate given by phylogenetic data which yields an MRCA of 150,000 years. In order to help resolve these discrepancies, all the scientists have pooled their data and the result is a mutation rate of one every 1200 years based on the pedigree data - a rate which is still faster by a factor of five than the rate given by the phylogenetic approach.


So there is a substantial issue in how to resolve the rate of mutations in mtDNA, which appear to occur between one generation and the next, and the much lower rate of mutations that seem to be fixed after several million years in the genomes of the great apes.  There is a further issue, that the data based on pedigree analysis of the D-loop gives widely varying mutation rates in different studies.

 

There is, therefore, a number of considerations:

 

  1. We need to explain the variation in mutational rates in pedigree studies based on analysis of the D-loop.  It is clear that at least some of this variation can be explained by statistical variations in small samples of a stochastic process.  However, pooling all the data still leads to a 'factor of five' discrepancy, between the rate measured by pedigree and phylogenetic studies
  2. We need to consider whether the mitochondrial DNA does, in fact, mutate at a fixed rate, and therefore whether it will provide a good 'clock' for dating genomic events.  Furthermore, we must consider whether some parts of the mitochondrial genome are more 'clock-like' than others.
  3. We need to consider the fundamental differences between pedigree and phylogenetic studies.  Pedigree studies, particularly those that compare the genetic make-up of close relatives, measure a rate of mutation from one generation to the next  Phylogenetic studies, or pedigree studies that compare broad populations that have been in existence for many generations will yield a rate of fixed mutations or permanent substitutions in that lineage's genome.  These rates might be different, because mildly deleterious mutations will be eliminated over time from the gene pool, and because in some cases, a particular mutation might mutate back to the original sequence
  4. We need to consider the possibility that mitochondrial mutations usually occur in some, but not all, of the thousands of copies of mitochondrial DNA present in each cell.  Such a condition is called mitochondrial heteroplasmy, and, if it occurs in the germ line, can result in tissue mosaicism (different mitochondrial DNA in different tissues). It is frequently deleterious
  5. We need to consider whether restriction fragment length polymorphism analysis (RFLP) is a good technique for estimation of mutation rate

 

Discussion

 

It has been shown by Hasegawa et al (11) that the non-synonymous to synonymous rate ratio of mitochondrial polymorphisms is much higher within species than between species. What does this mean?  Synonymous mutations make no difference to the protein encoded and therefore are not acted on by natural selection.  Synonymous mutations are therefore neutral and their incidence in the population depends on the population dynamics of the lineage possessing them.  Non-synonymous mutations do cause changes in protein, and the probability of their survival over many generations depends on whether they are deleterious, neutral or beneficial.  Since most mutations are deleterious, the ratio of non-synonymous to synonymous mutations is less than one.  In fact the study found that the ratio within primate species varies from five to 10 times the ratio between species.  (Human ratio = 0.2, chimpanzee = 0.5, gorilla = 0.4, between species = 0.033 - 0.04).  Hasegawa et al conclude that this is due to the elimination of slightly deleterious mutations from the population.  Since synonymous rates have no effect on the phenotype, they are expected to be the broadly the same rate across all primate species.  Differences in the ratio are therefore to be explained by differences in the fixing of non-synonymous mutations over time.  Hasegawa et al also note that the D-loop is functional and that the high mutational rate obtained in pedigree analyses is because more deleterious mutations are observed in this type of study, compared with long term phylogenetic studies, where deleterious mutations would be expected to be eliminated over time.

 


Max Ingman et al, Nature 408, 708 - 713, Mitochondrial genome variation and the origin of modern humans (published in 2000)
(12) address the issues of:


Ingman et al point out that there is a big variation in mutational rates on the control region or D-loop, for different populations. They point out that the mutational rate of the mitochondrial genome,
excluding the D-loop, has evolved at a constant rate in humans, and, by analysing data across primate species, and using gorilla as an out-group, they demonstrate that there is no significant difference between the evolutionary rate of human and chimpanzee mtDNA, excluding the D-loop.  Hence they specifically exclude the D-loop from their analysis.

 

Ingman et al study a representative sample of the human population.  They analyse the complete mtDNA of 53 humans of diverse origins. They also use a technique for sequencing using specific PCR primers and direct sequencing chemistry (specifically BigDye from Applied Biosystems) to sequence the entire mitochondrial genome (as opposed to looking at RFLPs). By comparing the variation within the human population with the difference between human and chimpanzee mtDNA, they obtain a mutational rate across the whole mitochondrial genome, excluding the D-loop, of 1.7x10-8 mutations per site per year.


On the basis of the humans in this study with the greatest difference in their mitochondrial DNA, the authors say that: 'The age of the most recent common ancestor (MRCA) for mtDNA, on the basis of the maximum distance between two humans (5.82 x 10
-3 substitutions per site between the Africans Mkamba and San), is estimated to be 171,500 50,000 yr BP'.

So the most recent study using the most appropriate techniques confirm the date of matrilineal MRCA at between 150,000 and 200,000 years.


A similar exercise has also been performed on the Xq13.3 region of the X-chromosome of the same individuals used in this study by Kaessmann et al
(13).

The X-chromosome is the female sex chromosome in the nucleus, but because it is 'paired' with the tiny male Y-chromosome, it mostly doesn't recombine and is similar to mitochondrial DNA in that respect; but it is passed on by both fathers and mothers to offspring and so is different from
mitochondrial DNA in that respect. Because the effective population size of the X-chromosome is three times that of mitochondrial DNA, the X-chromosome MRCA is predicted to be three times older than the matrilineal or mitochondrial MRCA. The age of the MRCA of Xq13.3 is found to be in agreement with the mtDNA data (mtDNA MRCA age: 171,500 years BP; Xq13.3  MRCA age: 479,000 years BP)

Ingman et al conclude:'Our results indicate that the field of mitochondrial population genomics will provide a rich source of genetic information for evolutionary studies. Nevertheless, mtDNA is only one locus and only reflects the genetic history of females. For a balanced view, a combination of genetic systems is required. With the human genome project reaching fruition, the ease by which such data may be generated will increase, providing us with an evermore detailed understanding of our genetic history.'

 

 

Conclusion

 

No-one in the science community thought that the Parsons et al study supported a matrilineal MRCA of 6,500 years.  Nevertheless their work did result in discrepancies between the known date of human geographic dispersion (at least 60,000 years BP) and the apparently very high rate of mitochondrial mutation, which, if taken at face value, would yield a matrilineal MRCA 6,500 years ago.

 

Subsequent studies have shown the following:

 

 

It seems to be the nature of creationist apologists to misrepresent and misuse scientific work.  The fact that so many creationists and creationist websites latch on to the Parsons et al paper ,and claim that it is proof for a biblical Eve living 6500 years ago, (even though Parsons et al claim no such thing), demonstrates two things:

 

  1. They do not understand or they deliberately misrepresent the concept of the matrilineal Most Recent Common Ancestor which does not point to the only female human ancestor
  2. They ignore the fact that subsequent research has largely resolved the issues that the Parsons et al paper raised.

 

It is my confident prediction that both ill-informed creationists and those who should know better will be using this discredited argument 20 years from now.  They will be as wrong then as they are now.

____________________________________________________________

Wieland replied to this article in 2005. My response to his reply is here. (October 2006)

 

 


 

 

1.  Answers in Genesis at this web address:

http://www.answersingenesis.org/docs/4055.asp   Return to text

 

2.  Lynn Margulis, Michael F. Dolan, and Ricardo Guerrero: The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists, PNAS 97, 6954 -6959 Return to text

 

3.  Gray, Burger and Lang, Mitochondrial Evolution, Science 283, 1476 - 1481 Return to text

 

http://biology.unm.edu/faguy/teaching/margulis.pdf  Return to text

 

4.  Gray et al, The Origin and Early Evolution of Mitochondria, Genome Biology 2001, 2(6):reviews1018.11018.5;  Return to text

 

5.  Cann, Stoneking and Wilson, Mitochondrial DNA and Human Evolution, Nature 325 (1987) 31 - 36 Return to text

 

6.  Philip Awadalla, Adam Eyre-Walker, and John Maynard Smith, Science 286, 2524 - 252  Return to text

 

7.  Various authors, Science 288 p1931  Return to text

 

8.  Parsons TJ et al, A high observed substitution rate in the human mitochondrial control region, Nat Genet 15, 363-368 Return to text

 

9.  Howell, Kubacka and Mackey, How rapidly does the human mitochondrial genome evolve?, Am J Hum Genet 59, 501 - 509 Return to text

 

10.  Gibbons, Calibrating the Mitochondrial Clock, Science 279, 28 -29 Return to text

 

11.  Hasegawa, Cao and Yang, Preponderance of Slightly Deleterious Polymorphisms in Mitochondrial DNA:  Nonsynonymous/Synonymous Rate Ratio is Much Higher within Species than Between Species, Mol Biol Evol 15, 1499 -1505  Return to text

 

12.  Ingman et al, Mitochondrial genome variation and the origin of modern humans, Nature 408, 708 - 713 Return to text

 

13.  Kaessmann, H., Heissig, F., von Haeseler, A. & Paabo, S. DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nature Genet. 22, 78-81 (1999). Return to text

 


 

 

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