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Saturday, 31 May 2014

Keith Crandall's Clanger

When a distinguished scientist like Keith A. Crandall claims on camera that Middle Eastern DNA has been identified in the Maya, one could excuse a lot of Mormons for getting excited. The Mayans live exactly where Mormon apologists have been claiming all along that Lehi's family established themselves in the Americas. I was troubled to hear a member of my extended family saying recently that Hebrew DNA has been found in Native Americans, and that their wayward Uncle Simon misunderstands the science. But a closer look reveals Keith Crandall has simply mistaken European admixture for Middle Eastern DNA and his claims are nothing more than wishful thinking. It appears Crandall has allowed his pre-determined conclusions to distort his interpretation of the facts.

For the last 180 years essentially all Mormon prophets, apostles and rank and file members have interpreted the Book of Mormon as it is plainly written. Migrating Hebrews established large civilizations in a Promised Land. No mention is made in the 1000-year record of what must have been massive neighbouring native populations. Many LDS apologists, in response to an enormous body of scientific knowledge of the colonization of the Americas, have shrunk the Book of Mormon territory to the region of Mesoamerica, the homeland of the Mayans. These apologists are desperate for scientific evidence that supports the "Mayans or Bust" Mesoamerican model. 


Professor Keith Crandall

Keith Crandall joined BYU in 1996 as an assistant professor in the biology department and has carved out a very successful career in invertebrate biology. He has research experience in a wide range of fields including statistical genetics, genomics, molecular evolution, population genetics, bioinformatics, computational biology and phylogenetics. Crandall was promoted to full professor in 2005 and Chair of the Department of Integrative Biology in 2006. He was department chair until 2012 when he resigned to lead the Computational Biology Institute at George Washington University in Washington D.C. Crandall and his family were baptised into the LDS Church in about 2004 and he was approached soon afterwards by representatives of the Foundation for Apologetic Information and Research. FAIR apologists have always been especially keen for high profile LDS scientists to appear in their DVDs defending the Book of Mormon, and Keith was just what they were looking for. 


Hebrew DNA in the Maya...really, Keith?

Crandall's claims appear prominently in the 2008 FAIR DVD entitled The Book of Mormon and New World DNA. The DVD is squarely aimed at defending the flagging Mesoamerican Limited Geography Theory (described here) and contains outrageous claims by a number of LDS scientists and apologists. To his credit, John Tvedtnes, who also appears in the DVD, requested that some of his earlier statements be removed in subsequent versions of the DVD, after some of his erroneous claims were pointed out to him (see FAIR errata page here). However, the statements made by Keith Crandall still remain. Crandall's unfounded claims now conveniently appear in a brief one-minute YouTube clip.  




Crandall makes this claim in the YouTube clip.
"…there is an interesting bit of data that probably only an LDS scientist would pick up…[chuckle]…which shows for the Mayan people and maybe one or two other cultures close geographically to the Yucatan area…there’s actually a nice infusion of Middle Eastern…what they call Middle Eastern genotypes in those populations." 
In the full length DVD Crandall tells us a little more about this amazing discovery.
“The most recent DNA evidence that I’ve seen, in terms of peopling of the Americas, shows this Middle Eastern haplotype at greatest frequencies in the Mayan people; so if that’s your perception of where Lehi and company set up shop then the DNA evidence would be consistent with that.”
Crandall also reassures viewers of the FAIR DVD that the DNA studies are very difficult to understand, and that because the critics are not population geneticists like himself, they couldn’t understand the research.
“The real issue is that these guys don’t actually look at the population genetic literature, they don’t understand the population genetic literature because they’re not population geneticists…so they couldn’t interpret these kinds of data. It's a very tricky kind of literature and a tricky kind of data to wrap your brain around. But it’s pretty patently obvious when you look at their data in this one figure in particular.  If that's what you’re looking for its there.” 
I must admit to growing tired of the repeated claims by LDS apologists that people like me don't understand population genetics. I have been actively engaged in forest tree population genomics research for well over a decade and I lead a group of 10 scientists who work in various aspects of this research field on eucalypts and pines. I am very familiar with the population genomics research that Keith Crandall misrepresents because we do identical types of analyses in eucalyptus trees. 


A tricky kind of data

Crandall based his claims on population genomics research published in two papers from the laboratories of Marcus Feldman and Richard Myers at Stanford University (Li et al. 2008 and Rosenberg et al. 2005). In contrast to earlier studies on mitochondrial DNA, Myers and Feldman's human genetics research was focussed on nuclear DNA variation. In the paper by Li et al. (2008) they studied the nuclear DNA of 938 unrelated individuals from 51 global populations at 650,000 common single-nucleotide polymorphisms (SNPs). SNPs are points in the genome where single base changes occur in the human genome sequence. 


   A SNP is a single-letter change in DNA
  Image courtesy of Lauren Solomon, the Broad Institute

SNPs are part of the natural genetic variation found within all human populations. In the research led by Richard Myers they were able to demonstrate that global populations can be clearly distinguished on the basis of variation at hundreds of thousands of SNPs. This is graphically illustrated in the figure below which is drawn from t
he paper by Jun Li. 


In the above diagram the information from 650,000 SNPs is condensed into a single thin vertical line for each individual. This line is partitioned into coloured segments whose length corresponds to the proportion of their DNA derived from particular global regions. Individuals are then grouped with other individuals who share similar DNA. 

If you look closely at the data for the Mayan population, which is expanded in the figure below, you will notice that their ancestry also includes DNA likely to have originated in East Asia (orange) and Europe (green). This is the DNA Crandall chooses to interpret as "Middle Eastern genotypes". However, this claim is incorrect. None of the authors of the papers Crandall cites conclude, as he suggested, that Middle Eastern DNA was found in the Maya. That is his misinterpretation of their research. 


Post-Columbus admixture confirmed

The most likely origin for the European DNA in the Maya is post-Columbus admixture, a common problem scientists encounter when studying the ancestry of Native Americans. After Columbus, large numbers of Europeans and Africans migrated to the Americas and many of these early colonists inter-married with indigenous Native Americans. Scientists try to avoid including individuals with this mixed ancestry, but it is especially hard to do this in populations that mixed with very early European and African colonizers. Figure 3 below shows evidence of admixture in numerous Native American populations. 



Admixture in the Maya has since been confirmed in a paper published in Science earlier this year (Hellenthal et al. 2014). Hellenthal was able to track the geographical origin of post-Columbian DNA admixture in the Maya to Europe and Africa (see figure below). None of the admixture came from the Middle East. What is especially telling is the DNA data Hellenthal used was obtained from the same individuals used in the Li et al. (2008) research. This report confirms that Crandall's "Middle Eastern genotypes" are in fact European and African admixture. See my Mesoamerican DNA post for more details on the Hellenthal study.

Figure 4. Geographical origins of Maya DNA. The orange circles represent post-Columbus admixture (European and African) that entered Mayan populations about 350 years ago. The blue circles represent much older ancestral links to other Native American, East and Central Asian populations. The area of each circle reflects the proportion of the donor population's contribution to the DNA of the Maya. Source: Chromosome Painting Collective / February 18, 2014


Given Keith Crandall's extensive population genomics experience, it is difficult to grasp how he has managed to misunderstand the genomic research on the Maya and why he refuses to retract his incorrect claims. In one email he accused me of basing my arguments not on science, but around a pre-determined conclusion that ignores the data. But it is clear that Crandall is seeing things in the data that are just not there. The truth is that scientific research has consistently failed to uncover reliable evidence for the presence of ancient Hebrews, or their genes, in pre-Columbian Mesoamerica or throughout the New World.