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Tuesday, 13 September 2016

Misleading FAIR video


In 2013 the Foundation for Apologetic Information and Research (
FAIR) published a video entitled DNA and the Book of Mormon Explained. The video is aimed at defending the flagging Mesoamerican Limited Geography Theory and contains amazing claims by a number of LDS scientists and apologists. By far the boldest claims in the video are those of Keith Crandall who was a BYU professor at the time. Crandall joined BYU in 1996 and was baptised in 2004. He was Chair of the BYU Department of Integrative Biology from 2006 until 2012, when he resigned to take up a position at George Washington University in Washington D.C.   

Three times in the video Keith Crandall claims Middle Eastern DNA has been found in the Maya.


28 seconds 
“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.”

25 minutes 07 seconds  
"…the fact is, based on this paper by Noah Rosenberg from the University of Michigan that there are in fact Middle Eastern haplotypes in where we as Latter-day Saints would expect them to be; in the Mayan population, as opposed to across all North and South America.  

37 minutes 37 seconds 
"…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." 


Crandall's claim that Middle Eastern DNA has been found in the Maya is not true.

Crandall also tells viewers the DNA studies are very difficult to understand, and because the critics are not population geneticists like himself, they couldn’t understand the research.

3 minutes 25 seconds 
“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 it's there.” 

The truth is these studies are now routine and they are performed in hundreds of plant and animal populations. My own research team has been actively engaged in forest tree population genomics for well over a decade and have published numerous research papers in the field. Consequently, I am quite familiar with the population genomics research that Keith Crandall cites because we did identical types of analyses in trees. 

A tricky kind of data

When asked for references to his claims Crandall directs people to two published papers, Li et al. 2008 and Rosenberg et al. 2005). In contrast to earlier studies on mitochondrial DNA, this 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 differences occur in the human population.


   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 Li's research they  showed that global populations can be clearly distinguished on the basis of the hundreds of thousands of SNPs they carry. This is illustrated in the figure below


In the above diagram the information from 650,000 SNPs is condensed into a single thin vertical line for each individual. This line has 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 focus on 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 interprets as "Middle Eastern genotypes". However, this claim is incorrect, and none of the authors of the papers Crandall cites conclude, as he suggested, that Middle Eastern DNA was found in the Maya.


If we look at more Native American populations we see exactly the same pattern. European, Asian and African admixture is found in many Native American populations (Figure 3). 







The most likely origin for the European and African DNA in the Maya is post-Columbus admixture. After Columbus, large numbers of Europeans and Africans migrated to the Americas and many of these early colonists intermarried 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 very early with European and African colonizers. 



Post-Columbus admixture confirmed

Admixture in the Maya has since been examined in much more detail in a paper by Hellenthal et al. 2014. Hellenthal tracked the geographical origin of post-Columbian DNA admixture in the Maya to Europe and Africa (see figure below). None of the admixture came from Middle Eastern populations which were included in his study. 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


It appears that in his eagerness to please his FAIR colleagues Keith Crandall was tricked into seeing things in the research that are simply not there. The truth is that scientific research has consistently failed to uncover reliable evidence for the presence of any ancient Hebrews, or their genes, in pre-Columbian Mesoamerica or throughout the New World.

Tuesday, 2 February 2016

Response to the claim 1/3 of Native American DNA came from the Middle East - now that would be a Great Surprise



Some Mormons have been claiming that a recently published human genomics research paper offers support for the belief that Native Americans have Jewish ancestors. The paper causing the excitement was published in the Jan 2013 issue of Natureone of the most prestigious scientific journals. The article in question was written by Raghavan et al. and entitled “Upper Palaeolithic Siberian Genome Reveals Dual Ancestry of Native Americans.”  The paper would have gone unnoticed by Mormons had a National Geographic journalist not sensationalised it with the following hyperbole.


"Great Surprise"—Native Americans Have West Eurasian Origins.

Oldest human genome reveals less of an East Asian ancestry than thought.
Nearly one-third of Native American genes come from west Eurasian people linked to the
 Middle East and Europe, rather than entirely from East Asians as previously thought, according to a newly sequenced genome.


Many Mormons reading these headlines have seized upon this research as conclusive proof that Native Americans have Middle Eastern, and thus potentially Jewish, DNA (1234). Even President Newsroom cited Raghavan's research in the Church's official "Book of Mormon and DNA Studies" essay, claiming it challenges previous conclusions and proves the picture isn't clear. But the conclusions being challenged have nothing to do with recent Hebrew migrations. The Raghaven study is focussed on a 25,000-year-old paleolithic DNA sample which tells us something about major human migration events that took place over 20,000 years ago. There is nothing in the Raghavan research that supports the Book of Mormon or challenges the mainstream scientific views about the colonization of the New World. Native Americans are still all descended from ancient Asian ancestors.

The Context of the Research 


Raghavan's research adds another detail to a broad scientific understanding of the timing and route our ancestors took as they colonised the globe. The common ancestors of all humans lived in sub-Saharan Africa. They began migrating "out of Africa" about 80,000 years ago and by about 50,000 years ago had colonized Western Asia, India and Southeast Asia and Australia (Fig.1). Eastern Asia was colonised by people derived from this southern migration event. By about 40,000 years ago people arrived in Europe and Central Asia via a northern route, finally reaching the Americas between 15 and 25,000 years ago.

Fig.1.   Major routes and timing of human colonisation of the world 
(Wellcome Trust, www.sanger.ac.uk

Scientists have found no evidence that we all descend from a single man and women (Adam and Eve) who lived on the earth about 6,000 years ago. This is simply not what happened. The volumes of evidence in support of the mainstream scientific views are vast and span numerous disciplines. It is the truth and Mormons should face it. When the individual Raghavan's team studied was alive, humans had not even reached the Americas so it is difficult to comprehend how it tells us anything about mythical Jewish migrations in the last few thousand years. 

Fig. 2.  The extent of human colonization of the world 25,000 years ago 
and the location of Raghavan's Siberian sample.


The 2014 Raghavan Study 

Raghavan's team isolated DNA from the bones of a 24,000-year-old individual and sequenced its entire genome. They then examined 156,000 DNA markers (SNPs) to reveal how closely related this individual is to hundreds of other people from contemporary populations (Fig. 3). The more DNA markers two individuals share the more closely related they are. 


Fig. 3.  Heat map of relatedness between the Siberian (MA-1) and individuals from numerous 
geographical locations around the world. The graded heat key on the left indicates the 
degree of relatedness with red indicating high relationship and black low relationship. 
(See Raghavan et al. 2014)

The major finding of the study is that the Siberian individual (MA-1) is not closely related to other Central and Eastern Asians (dark blue dots) and much more closely related to Native Americans (red dots). In addition, this Siberian appears to be related to people now living in Europe and Western Asia (yellow, light blue-green dots). This suggests that this Siberian individual's ancestors had migrated from Western Eurasia into Siberia, but when they arrived they did not mix very much with Asian populations living further east. Consequently, when some of this Siberian's descendants migrated on to the Americas, they didn't carry many DNA markers found in East Asian populations.

Another way of illustrating the results of the study is shown in Fig. 4 below. All Eurasians and Native Americans descend from people who lived in West Asia (near modern day Afghanistan and Pakistan) about 50,000 years ago (see also Fig. 1.). These people carried with them large numbers of DNA markers that can be defined as West Asian. When the ancestors of the Siberians and Europeans/Middle Easterners migrated away from each other, both groups carried the same set of West Asian (blue) DNA markers with them. This is why the Siberian individual carried DNA markers also found in Europeans and Middle Easterners. They shared common ancestors about 15,000 years earlier (50,000 years ago).   

However, once they became separated from each other, each group began to accumulate DNA markers that were unique to each group. This is indicated by the green (Eur/ME) and purple (Siberian) shading on the tree (Fig. 4). Once the Siberian groups encountered East Asians some of their DNA lineages (red) also entered Siberian populations, and some of these DNA markers found their way to the Americas.


Fig. 4.  Origin of DNA markers in Native Americans and some Eurasian populations 
and the approximate timing of their occurrence 

Summary

Virtually all Eurasian and New World populations descend from populations that migrated out of Africa and colonised West Asia about 50,000 years ago. Eastern Asia is likely to have been first colonised by populations that split away from a southern migration through India that ended in Australia. The Raghavan study tells us that Siberians are mostly derived from people who migrated into Central Asia via a northern route that resulted in little admixture with Eastern Asian populations. The research paper is focussed on very ancient migrations and tells us nothing about the likelihood or occurrence of recent Jewish migrations to the pre-Columbian New World.

Thursday, 21 January 2016

Response to Rodney Meldrum's Incredible "New" DNA Evidence for the Book of Mormon


A YouTube clip entitled “DNA vs Book of Mormon (INCREDIBLE New Evidence)” is causing a stir among Mormons as it has appeared on websites such as LDS.net, LDSLiving, Prepare to Serve (YouTube site) and LDS Smile. Over 66,000 people viewed the video in the two weeks after it appeared. In a bizarre turn of events the YouTube clip has subsequently been removed from the LDS.net, LDSLiving and LDS Smile websites. A cached version of the original LDS.net page used to be saved here, but someone with serious connections has even had the cached page removed!  

In the video Rodney Meldrum claims there is DNA evidence that proves the Book of Mormon is true. He boldly claims there is now concrete DNA evidence linking Native Americans to Jewish populations in the Middle East.






Rodney Meldrum presents himself as a scientific authority who has worked on a university-level science textbook. The truth is Rodney Meldrum has no scientific qualifications and the unpublished textbook he was working on was a Creationist textbook masquerading as science. Meldrum entered the DNA apologetics arena in about 2003 after first learning of the Book of Mormon DNA issue.

The video's claims

In the video Meldrum claims that North American Indians from the Algonquin language group carry high proportions of Jewish mitochondrial DNA. This DNA carries five unique “markers” that only appear in Jewish populations. While not stated in the interview, the mitochondrial DNA Meldrum is referring to is lineage X2a. (Mitochondrial DNA is widely used by scientists to track related populations. It is passed from mothers to offspring, much like a molecular maiden name.)  

I have thoroughly critiqued Rodney Meldrum’s DNA claims elsewhere on my blog. 

However, you don’t have to take my word for it. Meldrum has come under attack from other believing Mormons. 

Mormons attacking Mormons 

Meldrum’s spurious DNA claims have been heavily criticized by other Mormons, including Ugo Perego, an LDS scientist who has made a major contribution to our understanding of the origins of Native American DNA. Here are Ugo’s comments after viewing Rodney Meldrum's video. This response appeared on Ugo Perego's personal Facebook page on Saturday 24th Jan 2016 at 7.11am.  

I want everyone to know that I do not support the views presented in this video. I personally believe the Book of Mormon to be sacred scripture, but not based on genetic evidence.

It is my opinion that the presenter in this video (Rod Meldrum) is oversimplifying and stretching complex scientific data to fit its own view and purposes. This is dangerous because some people might actually believe in what he is saying and take for granted his conclusions. I have listened to Rod Meldrum in the past and spoke with him on several occasions. I have also tried to explain to him the mistakes with his approach, but to no avail. Here are in a short few points the main problems with the information presented in this video:
1. Lineage (haplogroup) X in the America is an unusual marker, but there is absolutely no evidence to link it to Book of Mormon people.
2. As far as science has been able to determine to date, lineage X has been in the Americas probably long before Book of Mormon times (based on both carbon dating and the molecular clock).**
3. It is not true that the first four lineages in the Americas prior to the discovery of haplogroup X are identical to lineages found in Asia. They are related with each other, but the ones in the Americas have their own unique characteristics. 
4. Likewise, lineage X in Northern North America has its own unique characteristics and it is not found anywhere else in the world. The one in the Americas is know has lineage X2a.
5. There are other lineage X's in the world (Europe, North Africa, Middle East and Asia) but none of them is the same as their American counterpart X2a.
6. It is not true that lineage X was identified in the Americas in 2003. Data on a fifth lineage in the America has been widely published since 1991.
7. All the DNA that has been talked about in this video is referred to a genetic molecule known as mitochondrial DNA that is transmitted exclusively along the unbroken maternal line. This means that this approach cannot be easily used to determine the genetic ancestry of male lineages such as those described in this video and in the Book of Mormon. In other words, this is not the DNA we would expect to find today from Abraham, Isaac, Joseph, Lehi, Nephi, etc.
8. The LDS Church does not support DNA evidence in favor of the Book of Mormon. Here is something more official found on the LDS.org website: https://www.lds.org/topics/book-of-mormon-and-dna-studies


**Recent research has revealed the presence of the X2a lineage in the DNA of a famous ancient skeleton named Kennewick Man. The skeleton was found in the banks of the Columbia River, Washington state. Numerous dating methods, including carbon-14, revealed that Kennewick Man lived about 8,500 years ago. This discovery adds further compelling evidence that the X2a lineage is not Jewish. It arrived in the Americas thousands of years BEFORE the Israelite nation came into existence.


Note:
If you are prepared to wade through dozens and dozens of pages of Mormon apologetics (active Mormons attacking active Mormons) then feel free to take a look at FAIR's response to Rodney Meldrum