Teaching Evolution in the Middle East

The teaching of evolution has been under attack by creationists in many parts of the world. In the United States the idea of intelligent design has been pushed by creationists in school boards and local legislatures and led to the familiar court case of Kitzmiller versus Dover Area School District and the now overturned 1999 decision by the Kansas State Board of Education to change their science education standards to remove any mention of “biological macroevolution, the age of the Earth, or the origin and early development of the universe”. In Kentucky, the Department of Education replaced the word “evolution” with “change over time” in state school standards. In Louisiana, the 2008 passing of the bill named the “Louisiana Academic Freedom Act” allows teachers to teach the controversy regarding evolution rather than evolution as a scientific theory. The Tennessee state legislature has similarly passed a bill (HB 368/SB 893) protecting “teachers who explore the ‘scientific strengths and scientific weaknesses’ of evolution and climate change”.

However, despite controversies, and much political resistance to evolution education in some parts of the US, the teaching of evolution is by now an integrated part of most science teaching in the US. In fact, the new national US science curriculum, the Generation Science Standards, teaches evolution as a fundamental principle of life sciences, and is expected, despite some political resistance, eventually to be adopted by all states. The state of Tennessee was involved in the development of this curriculum and Kentucky has already opted to adopt the curriculum.

The teaching of evolution has been much less controversial in most other parts of the world. There is not much of a creationist movement in Central and South America and the teaching of evolution in these and countries has largely been uncontroversial. The same is true for most other predominantly catholic countries, particular after the 1996 declaration of Pope John Paul II that “new knowledge has led to the recognition of the theory of evolution as more than a hypothesis”. In Asian counties such as India, China and Japan, the teaching of evolution has been largely uncontroversial, with the possible exception of the teaching of certain Darwinian ideas during the Cultural Revolution in China. In Europe, evolution has for long been an integrated part of all science curricula, and despite occasional controversies in a few countries, remains so. Evolution is taught as an integrated part of the science curriculum in almost all countries in the world. However, there is one area of the world where the evolution teaching remains highly controversial and is banned in several countries: the Middle East and North Africa.

The most egregious example is perhaps Saudi Arabia, which in effect has a complete ban against the teaching of evolution. Evolution is not mentioned in K-12 education, except in the more advanced biology course in 12th grade, where in textbooks it is introduced as a fallacious and blasphemous theory, using the following introduction to the topic: “Nevertheless in the West appeared what is called ‘the theory of evolution’’ which was derived by the Englishman Charles Darwin, who denied Allah’s creation of humanity, saying that all living things and humans are from a single origin. We do not need to pursue such a theory because we have in the Book of Allah the final say regarding the origin of life, that all living things are Allah’s creation (1)”. One might wonder how it is possible to provide more advanced biology education while altogether avoiding the topic of evolution. However, even concepts such as adaptation can find alternative definitions that agree with creationism. For example, the standard Saudi Arabian secondary 10th grade obligatory text on biology explains adaptation as follows: “There exist structural, functional and behavioral characteristics in organisms that help them to survive in their environment. Allah, glory to him, created for organisms those characteristics and structures that enable them to live in their different environments (2)”.

While Saudi Arabia represents an extreme in terms of evolution teaching, another extreme in the opposite is provided, perhaps surprisingly, by Iran. In Iran, evolution is an important part of the K-12 biology curriculum. The standard Iranian text book in biology at the high-school level has been analyzed by Elise Burton who writes: “The evolution chapter, divided into three sections, provides a comprehensive introduction to the development of evolutionary theory, with the first section devoted primarily to Darwin and his influences and culminating in the formulation of the new synthesis; the second section to evidence of evolution, including paleontology, molecular and structural homology, and embryology, with discussion of evolutionary rates and punctuated equilibrium; and the third section to examples of natural selection, such as peppered moths and the work of Peter and Rosemary Grant on Darwin’s finches (3)”. The high-school curriculum in evolution in Iran appears to be at par with the education in most countries in Europe, the Americas, and East Asia.

Most other countries in the Middle East and North Africa fall somewhere between these extremes, and often evolution and creationist theories are taught side-by-side. Turkey, arguably the most highly educated and secularized Muslim country in the Middle East, has been immersed in a constant struggle between scientists and creationists, which to some degree reflects a greater culture war in the country. In Turkey, creationism is now a semi-official position of the government and is taught side-by-side with evolution in the standard High School text books. Turkish creationism will be familiar to many western scientists, including myself, who received Harun Yahua’s book, Atlas of Creation, free in the mail. While Turkey remained officially fiercely secular since the establishment of the republic in 1923, a new policy of “Turkish-Islamic synthesis” in the 1980s drove science education towards creationism. The Minister of Education, Vehbi Dinçerler, established a relationship with the US-based Institute for Creation Research (ICR), seeking help in modifying Turkish science education (3). This led to the production of biology textbooks that were openly critical of evolutionary theory and which often mimicked the arguments against evolution produced by American creationists. Decisions in the late 1990s reversed this, and Turkey today adopts a policy of neutrality between evolution and creationism in the science curriculum. The teaching of evolution is often not prioritized in Turkish universities: many biology programs (<40%), most science education programs, and nearly all molecular biology programs lack undergraduate courses on evolution.

Ambiguous school curricula, lack of appropriate education of teachers, and systematic creationist propaganda by religious networks, have resulted in a widespread rejection of evolution in Middle Eastern and North African societies. Multiple studies conducted in Turkey, Egypt, Lebanon, and Tunisia within the last ten years have consistently found that a large proportion (from 25% to 75%) of students and teachers in these countries reject evolution; some explain this on religious grounds, but others claim that “evolution is scientifically disproven” (4-7). Even among those who do accept evolution, severe misconceptions about the mechanisms of evolution can be found.

The majority of Middle Eastern and North African scientists are, like scientists in the rest of the world, firmly convinced about the principles of evolution. However, they are often isolated and lack scientific networks. Examples of researchers that do great work on teaching evolution, often in isolation, include Rana Dajani at the Department of Molecular Biology at Hashemite University in Jordan and my good friend and former postdoc Mehmet Somel from the Middle East Technical University in Ankara, Turkey. Mehmet is a stellar new young researcher who is building up a very strong research group in evolutionary biology in Ankara, in the middle of increased direct and indirect pressure on the universities from Davutoğlu and Erdoğan’s Islamist government. There are serious worries that the government in Turkey is engaged in a process of reducing intellectual freedom at Turkish universities.

Sadly, researchers in evolutionary biology in the Middle East are often poorly integrated into international networks and lack support from the international community. These researchers are often engaged in a cultural war that expand beyond just teaching of evolution, but involve a fundamental clash between secular and fundamentalist religious ideas. Arguably, the future of the Middle East, and to some degree therefore the rest of the world, is tightly linked to this struggle.   We are all too familiar with the violent images from the Middle East in the news media, typically involving sectarian conflicts between different religious groups, or between secular and religious groups. Revolutions in Syria and Libya against local dictators were hijacked by jihadist forces leading to prolonged civil wars that now greatly affect, not only the Middle East, but the entire world. The consequences of these conflicts, including increased flow of refugees and terrorism, dominates the political discourse in much of the western world.   In the West we have a strong tradition for intervening in the Middle East militarily, often with arguably counter-productive results. Our strongest allies, Saudi Arabia and Qatar, are some of the most regressive countries in the region in which suppressive Salafist religious ideology is used to maintain extreme economic and political privilege for a small elite. We have chosen not to support moderate secular forces, but instead to build economically convenient alliances with presumably stable rulers of oil rich countries. And to maintain our perceived strategic and economic interests we have not hesitated to act militarily. But progressive and secular movements in the Middle East have been left high and dry, locally accused of promoting a Western agenda, but without support from the West.

Debates regarding evolution are in the Middle East embedded in this environment. They are part of a larger cultural (and often physical) war between modernist secular ideas, and fundamentalist religious ideas. And once again, there have been no effort from the rest of the world to lend support to individuals in the Middle East who are promoting teaching and research in evolutionary biology.   Perhaps once we could try to promote development in the Middle East by providing infrastructure and support for forward thinking intellectual leaders, instead of just treating the Middle East as a place where we have to act militarily when the bombs start going off in Paris, London or New York, or when our perceived strategic and economic interests are threatened. As researchers in evolutionary biology we can contribute to this. Obviously, supporting evolutionary biologists in the Middle East is not going to eliminate the threat from Daesh or convert Syria into a stable and peaceful democracy tomorrow, but it can be one little step towards a modern political development in the region. After all, good science education is one of the most powerful weapons against religious fundamentalism. As Western evolutionary biologists, we have the opportunity to help put that weapon into the hands of local educators and scientists. For that reason, I had, together with collaborators from the Middle East, proposed to the Society of Molecular Biology and Evolution (SMBE) to support an initiative to start a network of evolutionary biologists in the Middle East, and requested funding for an initial conference and for local meetings for promoting evolution education to college level educators. SMBE is ideally suited for this because it is an international society and because it is quite rich primarily due to the revenues generated by the society journals MBE and GBE.   Now there are many reasons I could see why one might not want to support such a proposal. For example, the proposal might be too vague, the Society might want to see a competition between many proposals, or there might be a shortage of funds. However, the proposal was rejected, not for any of these reasons, but because the Society simply does not want to support activities in the Middle East. This is the reply I received:

SMBE council discussed your proposal on Evolution in the Middle East and North Africa. The council appreciates the importance of bringing modern molecular evolutionary research and education to this part of the world, but has widespread concerns about the political stability and safety in the region. For this reason, your proposal was not approved. 

However, the council recognizes the value of having occasional meetings in regions/countries where SMBE annual meetings do not typically go (e.g., Africa, South America, India, and China), and has decided to create a new category of meetings called regional comprehensive meetings that will be held in such countries/regions. The call for proposals of regional comprehensive meetings will go out later this year, and you are welcome to submit proposals at that time”. 

Notice that the rejection includes a statement that the Society wishes to support occasional meetings in “…Africa, South America, India, and China…” – a list of regions that explicitly does not include the Middle East. The reason given is that the society has “…has widespread concerns about the political stability and safety in the region”. So we choose not to support our evolutionary biology colleagues in the Middle East because of safety concerns? If I am to take this literally, I can only interpret it as an extreme form of cowardice. But perhaps it is really not fear but other concerns that really underlie this decision. I will refrain from second-guessing the council’s decision.

However, this leaves us now without funds for our efforts to support evolution research and education in the Middle East. If you have any suggestions for how to move forward with this initiative or would like to get involved, then please send me an email. We are not giving up – the stakes are too high. We should not leave our colleagues in the Middle East who daily struggle to promote teaching of evolution without support. We have a historic opportunity here, for one times sake, to do what is right, rather than what is convenient.

Rasmus (rasmus_nielsen@berkeley.edu)

 

Referenced literature:

  • Sulaiman bin Muhammad al-Habib et al. al-Ahyā’ lil-ṣaff al-thālath al-thānawī: al-faṣl al-darāsī al-awwal [Biology for Secondary Grade Three: First Semester]. Riyadh. Translation by Elise Burton.
  • Fahd bin Nasir al-Aqiyyal et al. al-Ahyā’ lil-ṣaff al-awwal al-thānawī [Biology for Secondary Grade One] Riyadh. Translation by Elise Burton.
  • Elise Burton. 2010. Science, Religion and the State: Teaching Evolution in the Middle East. Honor’s Thesis, Department of Middle Eastern Studies, UC Berkeley.
  • Saïda Aroua, Maryline Coquide, Salem Abbes. 2009. Overcoming the Effect of the Socio-cultural Context: Impact of Teaching Evolution in Tunisia. Evo Edu Outreach 2:474–478
  • Saouma BouJaoude, et al. 2011. Muslim Egyptian and Lebanese Students’ Conceptions of Biological Evolution. Sci & Educ 20:895–915
  • Pelin Yalcinoglu. 2009. Impacts of Anti-Evolutionist Movements on Educational Policies and Practices in USA and Turkey. Elementary Education Online 8(1), 254-267
  • Gülsüm Akyol, Ceren Tekkaya, Semra Sungur. 2010. The contribution of understandings of evolutionary theory and nature of science to pre-service science teachers’ acceptance of evolutionary theory. Procedia Social and Behavioral Sciences 9: 1889–1893

 

BAPG XIII at UC Berkeley

Screen Shot 2016-02-05 at 11.33.58 AM

Join the BAPG Google Group if you want to be in the loop

Registration is FREE but REQUIRED: 

This conference is generously supported by Ancestry.com and the Center for Computational Biology.

Date: Saturday 02/13/16

Place: University of California-Berkeley, Stanley Hall, Room 105

Schedule:

program

Refreshments: Coffee Breaks and Lunch will be included with registration. Alcohol will be available, by donation, in the afternoon.

Directions and Parking: 

Screen Shot 2016-02-05 at 10.01.07 AM

Driving: Most parking meters in Berkeley have a one to two hour maximum.  Please follow the link below for information about parking garages near campus:

http://www.cityofberkeley.info/Public_Works/Transportation/Off_Street_Parking.aspx

BART: The Downtown Berkeley BART station (http://www.bart.gov/stations/dbrk/) is the closest BART station to campus.

Amtrak: There is an Amtrak station in Berkeley.  The 51B (Rockbridge Bart) bus picks up nearby and and makes stops near campus.

 

Why do African-Americans have increased cholesterol levels?

There is a well-established difference in cholesterol levels between Americans of European and African descent. In particular African Americans generally have higher HDL levels. HDL is known as the “good” cholesterol and has in many studies been associated with protection against cardiovascular disease. Curiously, African Americans generally have higher rates of cardiovascular disease – their high HDL levels do not seem to provide them much protection. Although socio-economic and environmental factors including diet certainly contribute, these factors alone do not appear to fully explain the difference. There appears to be genetic variants that cause African Americans to have higher HDL levels but less protection against cardiovascular disease. Finding these genetic causes is an area of much active research, and some studies suggest that the reduced HDL protection in African-Americans is related to paraoxonase activity. With the increase in GWAS studies focusing on African-Americans we will likely learn more about these factors within the next few years. But there is another question buried here – an evolutionary question. Why would there be differences in HDL levels and HDL functionality in different geographic areas of the world? One possibility is that it is purely random; genetic drift has caused these differences. A perhaps unlikely explanation, but an explanation that we nonetheless want to rule out before speculating too much about the adaptive reasons for the observed differences.

A new study from our group published in Molecular Biology and Evolution with Anna Ferrer-Admetlla as lead author, sheds some light on this. Behind the technical title “On detecting incomplete soft or hard selective sweeps using haplotype structure” hides a few results that might help us better understand the evolutionary underpinnings of HDL biology in African Americans. Using a new haplotype based statistic, we show that APOL1, the gene encoding the major protein component of HDL, is one of the genes showing the strongest signature of natural selection in Yorubans – a group from which most African Americans descent. We do not see a similar pattern in any other group investigated, including Maasais from East Africa. Most other groups show evidence for selection primarily in immune and defense related genes, except for the Maasais which show most evidence for selection relating to the lactase genes – a story that has already been investigated in great detail by Sarah Tishkoff. In addition, we find several other genes relating to cholesterol metabolism which also show strong evidence of selection in Yorubans, including CD36, a gene implicated in the binding and internalization of oxidized LDL (the “bad” cholesterol). So clearly, something serious happened evolutionarily with cholesterol in Yorubans. We can probably rule out that the differences in HDL levels and functionality between African Americans and other groups are simply a consequence of genetic drift – natural selection most likely caused these differences.

This then raises the next question: which phenotypes did selection act on? Without a time machine we will never know. Even though we can identify certain phenotypic effects of the genetic variants that selection has acted on, we cannot conclude that selection worked to change these specific phenotypes. Many, if not most, genes are highly pleiotropic – they affect multiple different phenotypes. Which of these phenotypes where the primary target of selection can be difficult to discern. However, one obvious explanation for the selection acting on APOL1 and other cholesterol related genes in Yurubans, might be changes in diet. Demands on cholesterol activity may depend on diet, and there may be trade-offs relating to the efficacy of fatty acid uptake, energetic costs, and risk of cardiovascular disease that have imposed different selective regimes in different parts of the world. While this explanation seems obvious, it doesn’t really explain why selection has targeted only people in West Africa. Many other groups around the world have experienced changes in diet. Our hypothesis is instead that the selection is driven by pleiotropic effects relating to defense against parasites. APOL1 is involved in parasite killing, particularly trypanosome killing. APOL1 triggers uncontrolled osmotic swelling of the lysosome in the parasite, an effective mechanism for elimination of parasites. Similarly, CD36 harbors genetic variants associated with susceptibility to malaria. The pathogenic environment differs greatly between different geographic regions, and West Africa has certainly historically been one of the areas of the world with highest parasitic load. So one likely explanation is that the selection on genes such as APOL1 and CD36 observed in Yurubans is in response to selective pressures imposed by parasites – not by changes in diet. When African Americans today have different HDL levels and functionality than other groups, it may be a byproduct of past selection acting on their ancestors in Africa in defense against parasites.

I decided to write this rare blog entry, in part because I wanted to draw attention towards these results from the Ferrer-Admetlla paper – results that otherwise might remain buried in the technical aspects of the paper. But this example also well illustrates the challenges in evolutionary biology in identifying adaptive causes. It is often quite easy to identify the footprints of natural selection in DNA data, at least when natural selection is very strong. We have a slew of good methods for detecting natural selection. Unfortunately, we will in most cases never know for sure which phenotypes were targeted by selection. Evolutionary biology is in part a historical science – and as such we have to live with some ambiguity: we can detect the footprints of past selection – but we may never know for sure which phenotypes selection acted on. There is not a simple experiment that can determine what happened in the past.

Familial [mis]identification rates and experiments in video

Happy to say that a paper I wrote along with Erin Murphy, Yun Song, and Monty Slatkin is out today over at PLoS ONE (and on the arXiv).  In the paper, we implement the familial searching method of Myers et al. and estimate power, false positive rate, and rates of distant relatives misidentified as near relatives.  Short story: we find very high power and low false positive rate, however we also see high rates of relative misidentification.

These results are relevant to people inside and outside of the scientific community involved in decisions about the implementation of familial searching methods.  With that motivation [and generally], I’m experimenting with explaining my research through different media apart from technical manuscripts.

Adhamh Hoeltzel, Alex Safron, Mosaic Project youth leadership, and I collaborated to make a charismatic and informative general audience video explaining the idea and impact of familial misidentification in social context.  I’m hoping to see this video used in high school classroom or other educational contexts to introduce ideas and stimulate questions about forensic genetics.

For a quick technical overview, I made a short video abstract which outlines the basic questions and results for a scientific audience (video abstract idea thanks to Eline Lorenzen, more information coming soon).

Finally, I wrote a guest post for Haldane’s Sieve to motivate and explain the work to population geneticists without background in forensic science.

I’m curious to learn how these different formats are received and see other scientists’ alternate-media projects.  Most importantly, I’m excited to see more engaged discussion of forensic identification methods and their implementation.

Clarence Thomas got it right!

I know – that’s a first.  The supreme court made a wise and unanimous decision on the Association for Molecular Pathology v. Myriad Genetics case.  You can no longer patent a gene. However, the supreme court upheld Myriad Genetics’ rights to patent cDNA from BRCA1 and BRCA2 – which might explain why Myriad Genetics’ stock jumped after the ruling.  Apparently, the investors had feared worse.  Exactly what a patent on cDNA entails may be up to future litigation, but it should not preclude many common genotyping platforms as a diagnostic tool for BRCA1 and BRCA2 mutations.

What are the long term consequences of the ruling?  We can probably expect private companies to invest less in basic research on the molecular genetics of disease.  It might be harder to make a profit on discovering disease related mutations.  On the other hand, it will be easier to develop new diagnostic tools based one existing knowledge.  We might expect a shift in focus in private companies from basic research towards development of diagnostics. That is not necessarily a bad thing.  But somebody else has to pick up the slack on basic research.

The mantra for funding of genomics research at the National Institute of Health (NIH) – the major funding body of genomic and medical research – has been ‘translational’.  Apparently, the phase in genomic research in which we focus on basic discoveries is over.  Now we need to focus on translating these discoveries into medical applications – diagnostics and treatments.  That is all good – but with the expected fallout of the supreme court ruling,  somebody has to continue the drive for basic research.  It is time for NIH to once again step up on funding for basic research in the genomic sciences.

—————-

Addendum:  Hilariously, while Scalia voted in favor of the ruling – he dissented on the basic principles of molecular biology. Apparently, it is not only global warming and evolution that is being challenged.  I expect soon to see a dissent on the shape of the earth or the placement of the earth in the solar system.

 

BAPG meeting in Berkeley Oct. 5th

The next Bay Area Population Genetics meeting will be hosted by our group at UC Berkeley on October 5th.  You are hereby invited.  Please
register and sign up for talks/posters at http://tinyurl.com/lglzosw.

For more information about previous meetings, see here.

 

 

Register for Bay Area Population Genomics

From Ryan Hernandez:
Hello Everyone,
We are excited to be hosting the 8th meeting of the Bay Area Population Genomics group at UCSF Mission Bay on June 8th!  Thanks to support from Ancestry.com and the Institute for Quantitative Biosciences (QB3 @ UCSF), this conference will include breakfast and lunch.  In addition, we will also have a reception during the poster session, so we highly encourage you to preview your work at BAPG before heading out to summer conferences.
Please register at http://tinyurl.com/a8h6uo8, and sign up to give a talk or poster.  Registration is again free, but required by June 3rd.
There is paid parking in the lot/garage at the corner of 4th and 16th streets, and we have a limited number of parking passes for people that sign up to present and/or make a strong effort to carpool (please email me for details).
We are very much looking forward to seeing you at UCSF in a few weeks!
Best,
Ryan

This is an excellent opportunity to share ideas, learn about new topics, and meet other researchers! Unfortunately, this is the same weekend as the Miller Symposium that I’ve been co-organizing, but I encourage you all to participate.

Do it: 2013 Workshop for Young Researchers in Mathematical Biology

You know you want to go…
2013 Workshop for Young Researchers in Mathematical Biology (WYRMB)
August 26 – 29, 2013
Application deadline: May 1, 2013
The workshop is intended to broaden the scientific perspective of young researchers
(primarily junior faculty, postdocs, and senior graduate students) in mathematical biology and to encourage interactions with other
scientists.
Workshop
activities include plenary talks and poster sessions, as well as group
discussions on issues relevant to mathematical biologists. Several
abstracts will be chosen
for short talks as well as poster presentations.
Limited funding is available on a competitive basis.
We
cordially invite young mathematical biologists to participate. For full
consideration, please apply by May 1, 2013. To apply, click this link
http://www.mbi.osu.edu/wyrmb/wyrmb2013.html

Plenary Speakers

Lisa Fauci, Tulane University

Kresimir Josic, University of Houston

Claudia Neuhauser, University of Minnesota

Sebastian Schreiber, UC Davis

Arthur Sherman, Laboratory of Biological Modeling, NIDDK, NIH

John Tyson, Virginia Tech

Lani Wu, Southwestern University

Thoughts on an extremely ancient root of the human Y tree

I was recently interviewed by Alan Boyle at NBC to comment on:

An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

Fernando L. Mendez, Thomas Krahn, Bonnie Schrack, Astrid-Maria Krahn, Krishna R. Veeramah, August E. Woerner, Forka Leypey Mathew Fomine, Neil Bradman, Mark G. Thomas, Tatiana M. Karafet and Michael F. Hammer

The American Journal of Human Genetics, 28 February 2013
doi:10.1016/j.ajhg.2013.02.002

I do think the paper is very exciting. The identification of a new Y lineage is always interesting, and this one appears to be very long-lived. However, after a more careful reading, and some thought, I am not sure I agree with the way the TMRCA (Time to the Most Recent Common Ancestor) of the Y chromosomes was computed. And the ancient TMRCA depends quite a bit on the TMRCA. I have written up my thoughts and submitted them to the American Journal of Human Genetics, AJHG. The AJHG has a pretty strict pre-print policy (emphasis is mine):

“Work intended for submission to AJHG, currently under consideration at AJHG, or in press at AJHG may not be discussed with the media before publication. Providing preprints, granting interviews, discussing data with members of the media, or participating in press conferences in advance of publication without prior approval from the AJHG editorial office may be grounds for rejection.

But, I have gotten permission from the editor to discuss my thoughts about the submitted manuscript with colleagues (and in blog form). I am sharing the full AJHG manuscript with Mendez, but want to summarize here:

Mendez et al. identify a Y chromosome haplotype that has not been characterized before and, with more work, they determine that it is nearly identical to a small group of Y chromosomes from Cameroon. They also estimate the TMRCA for the Y haplotype phylogeny, including this new Y chromosome and find it to be at least twice as large as anyone else, and as noted by the authors themselves, this TMRCA is inconsistent with what is known in the human fossil record.  While the new Y haplotype does increase the diversity, and thus the TMRCA, the TMRCA calculation is extremely sensitive to the mutation rate used. Mendez et al. advocate for using a mutation rate from human pedigree data instead of from comparative genomics. They then derive a mutation for the human Y chromosome from the mutation rate estimated from autosomal pedigree data. The equation they use assumes a linear correlation between the mutation rate on the autosomes, and the mutation rate on the Y chromosome.

I present a case in my response that: 1) it is not appropriate to assume a linear correlation between the mutation rate on the autosomes and the mutation rate on the Y chromosome; 2) the mutation rate Mendez et al. computed for the Y from autosomal data is an order of magnitude lower than the mutation rate that was measured for the Y chromosome from a pedigree analysis in 2009; 3) the resulting TMRCA is inconsistent with what is known about diversity on the mtDNA, autosomes and X chromosome. Further, our own research suggests that selection is acting to reduce diversity on the Y chromosome relative to the autosomes, X, and mtDNA, which would make an extremely high TMRCA on the Y even more incompatible with observed data.

As such, I am curious why the mutation rate measured from Y chromosomes in a pedigree analysis was not used. I think the results would still be quite exciting and novel. Given what we expect to be strong purifying selection acting to reduce diversity on the Y, the same arguments, of ancient population structure  or even archaic introgression may still apply to this unique Y haplotype.

Cross-posted at my blog.

Natural selection reduced diversity on human Y chromosomes


Authors:
Melissa A. Wilson Sayres, Kirk E. Lohmueller, and Rasmus Nielsen

Abstract:
The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

We have submitted to PLoS Genetics, and I plan to present (as a talk or a poster) at SMBE 2013.

Cross-posted from my website.