Hawks also has a teaching company course.
John Hawks intro physical anthropology course
Principles of Biological Anthropology. This has been up for a while, but apparently Hawks may be removing the videos in the near future, so watch soon if interested.
Men With Wider Faces Are More Generous to Their In-Group When Out-Group Competition Is Salient
Face Structure Predicts Cooperation: Men With Wider Faces Are More Generous to Their In-Group When Out-Group Competition Is Salient (abstract):
Male facial width-to-height ratio appears to correlate with antisocial tendencies, such as aggression, exploitation, cheating, and deception. We present evidence that male facial width-to-height ratio is also associated with a stereotypically male prosocial tendency: to increase cooperation with other in-group members during intergroup competition. We found that men who had wider faces, compared with men who had narrower faces, showed more self-sacrificing cooperation to help their group members when there was competition with another group. We propose that this finding makes sense given the evolutionary functions of social helpfulness and aggression.
Evolution and the psychology of intergroup conflict: the male warrior hypothesis
Free pdf here:
Evolution and the psychology of intergroup conflict: the male warrior hypothesis
Melissa M. McDonald1,*,
Carlos David Navarrete1 and
Mark Van Vugt2,3The social science literature contains numerous examples of human tribalism and parochialism—the tendency to categorize individuals on the basis of their group membership, and treat ingroup members benevolently and outgroup members malevolently. We hypothesize that this tribal inclination is an adaptive response to the threat of coalitional aggression and intergroup conflict perpetrated by ‘warrior males’ in both ancestral and modern human environments. Here, we describe how male coalitional aggression could have affected the social psychologies of men and women differently and present preliminary evidence from experimental social psychological studies testing various predictions from the ‘male warrior’ hypothesis. Finally, we discuss the theoretical implications of our research for studying intergroup relations both in humans and non-humans and discuss some practical implications.
TEDxCambridge: George Church on genomics and human diversity
Slide at 7:20:
"Rare [does not necessarily equal] Deleterious
MSTN: Lean muscles
LRP5: Extra-strong bones
PCSK9: Greatly reduced risk of heart disease
CCR5: Virus-resistance
Embrace the extremes: informative, easy, powerful"
Conclusion: "So anyway we and others are sequencing these long-lived animals and humans and we hope this will be part of a bigger project to measure and design humans going forward."
Eske Willerslev at the 2012 DOE JGI Genomics of Energy and Environment Meeting
'Eske Willerslev from the University of Copenhagen on "Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.'
"Asians are closer to Europeans than they are to aboriginal Australians, but at the same time aborigine Australians are closer to Asians than they are to Europeans." (23:10)
At the end, Willerslev mentions "we are also doing the genome of Clovis, the oldest skeleton in the Americas". I have no idea which skeleton in particular he's talking about, but any Paleo-Indian genome should be informative.
New York Times science writer Carl Zimmer: Oetzi genome "not important"
Ken Weiss links to this speech by Carl Zimmer.
"As I recall, the big news in the Oetzi genome I think was that he had brown eyes. I mean it just . . . it doesn't . . . that's not important." (31:42)
Obviously, that was not the biggest news to those who were paying attention. But even if it had been, I'd still be taken aback by a comment like this from a science reporter. In fairness, Zimmer's talk overall is reasonable and inoffensive compared to Weiss's blog post, and does not appear to be motivated by the same racial anxieties:
So just to conclude I would say that my experience in writing about genomes has firmly convinced me that we are in the middle of another scientific revolution like the one in the middle of the 17th century and that genomes are a big part of that. But it's important to focus on what makes that revolution so important. So in the 1600s, for example, one of the most important things that happened was the people invented microscopes. [. . .] But again it wasn't so much the microscopes themselves that mattered, but what people were seeing with them.
Some asshole named "Ken Weiss" wants whole genome sequencing to go away
Is whole genome sequencing fading? Will it rebound (or relapse)?
There are various informal indicators that funders are losing enthusiasm for human whole genome sequencing. [. . .] If this turns out to be more than a few anecdotes or personal opinions, and is actually occurring, it's understandable and to be lauded. As we think we can truthfully claim, we have for years been warning of the dangers of the kind of overkill that genomics (and, indeed, other 'omics' fads) present: promise miracles and you had better deliver!The same thing applies to evolutionary studies that seek whole genome sequences as well as to studies designed to use such data to predict individual diseases. There are too many variants to sort through, the individual signal is too weak, and too many parts of the genome contribute to many if not most traits, for genomes to be all that important--whether for predicting future disease, normal phenotypes like behaviors, or fitness in the face of natural selection.
The proper response to genomic complexity is of course not to throw ones hands up and go back to candidate gene studies, but to sequence lots and lots of genomes in full. This is what needs to happen, and falling sequencing costs mean this is what will happen, regardless of what Ken Weiss wants.
Note: Ken Weiss is "Evan Pugh Professor of Anthropology and Genetics at Penn State University". I can think of a few possibilities: (1) Weiss is sincere in believing medical science and evolutionary research would be better advanced with less whole genome sequencing; he's not malicious -- just short-sighted, unimaginative, and breathtakingly ignorant of the broader state of his supposed academic specialty. (2) Weiss is merely jealous that his colleagues are getting bigger grants than him, a frailty he could perhaps be forgiven. (3) "Anthropology and Genetics" professor Weiss, for some reason, prefers that human evolutionary and genetics research not advance.
Looking at some of his other posts, I see plenty of evidence ethnic and/or ideological considerations underpin Weiss's "warnings" about genomics.
Analysis of surname origins identifies genetic admixture events undetectable from genealogical records
In the name of the migrant father—Analysis of surname origins identifies genetic admixture events undetectable from genealogical records
M H D Larmuseau et al.
Patrilineal heritable surnames are widely used to select autochthonous participants for studies on small-scale population genetic patterns owing to the unique link between the surname and a genetic marker, the Y-chromosome (Y-chr). Today, the question arises as to whether the surname origin will be informative on top of in-depth genealogical pedigrees. Admixture events that happened in the period after giving heritable surnames but before the start of genealogical records may be informative about the additional value of the surname origin. In this context, an interesting historical event is the demic migration from French-speaking regions in Northern France to the depopulated and Dutch-speaking region Flanders at the end of the sixteenth century. Y-chr subhaplogroups of individuals with a French/Roman surname that could be associated with this migration event were compared with those of a group with autochthonous Flemish surnames. Although these groups could not be differentiated based on in-depth genealogical data, they were significantly genetically different from each other. Moreover, the observed genetic divergence was related to the differences in the distributions of main Y-subhaplogroups between contemporary populations from Northern France and Flanders. Therefore, these results indicate that the surname origin can be an important feature on top of in-depth genealogical results to select autochthonous participants for a regional population genetic study based on Y-chromosomes.
Keywords: admixture; genetic genealogy; historical gene flow; human population structure; Y-chromosome
http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy201217a.html
Ten Quite Interesting Things About Intelligence Test Scores - Prof. Ian Deary
"Doing research on intelligence is fascinating, and also sometimes frustrating. Like being a meteorologist, when you tell someone you work on intelligence you find that they start telling you about your own topic. So, Prof Ian Deary of the University of Edinburgh thinks that it is useful show people some real data that come from intelligence tests; opinions can then be founded on data, or at least one can query the data-gathering or its interpretations.
Without making assumptions about what intelligence tests measure or why people differ in their scores, he presents some results and invites people's reactions to them. He is still surprised by the fact that sitting down with one of these tests for three quarters of an hour or so and getting a score can have such far-reaching predictions, and cause so many arguments."
Miscellaneous links
Larger monkey groups lose fights because they contain more deserters
In the Battle of Rorke’s Drift, 150 or so British troops defended a mission station against thousands of Zulu warriors. At the Battle of Thermopylae, around 7,000 Greeks successfully held back a Persian army of hundreds of thousands for seven days. Human history has many examples of a small force defeating or holding their own against a much larger one. Among animals too, the underdogs often become the victors. One such example exists in the rainforests of Panama. There, capuchin monkeys live in large groups, each with its own territory. The monkeys often invade each other’s land. Numbers provide an obvious advantage in such conflicts, but small groups can often successfully defend their territory against big ones. Unlike human underdogs, they don’t win because of superior tactics or weapons. They win because their rivals are full of deserters.Whole genome sequences of a male and female supercentenarian, ages greater than 114 years
We show that: (1) the sequence variant spectrum of these two individuals’ DNA sequences is largely comparable to existing non-supercentenarian genomes; (2) the two individuals do not appear to carry most of the well-established human longevity enabling variants already reported in the literature; (3) they have a comparable number of known disease-associated variants relative to most human genomes sequenced to-date;Comparison of measures of marker informativeness for ancestry and admixture mapping.
BACKGROUND: Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases have been interrogated in an admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (FST), Informativeness for Assignment Measure (In), and the Absolute Allele Frequency Differences (delta). The objectives are to compare these measures of informativeness to select SNP markers for ancestry inference, and to determine the accuracy of AIM panels selected by each measure in estimating the contributions of the ancestors to the admixed population. RESULTS: FST and In had the highest Spearman correlation and the best agreement as measured by Kappa statistics based on deciles. Although the different measures of marker informativeness performed comparably well, analyses based on the top 1 to 10% ranked informative markers of simulated data showed that In was better in estimating ancestry for an admixed population. CONCLUSIONS: Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.Fluid insight moderates the relationship between psychoticism and crystallized intelligence
To elucidate potential relationships between personality and intelligence it is necessary to move beyond the ad hoc reporting of correlation coefficients and focus instead on testing deductions from well established theories. To this end the present paper references Eysenck’s (1995) theoretical work linking the dimension of psychoticism to both psychosis and creative genius. Drawing on this theory it was argued that the relationship between psychoticism and crystallized ability will be conditional on the level of fluid intelligence. Participants (N = 100) completed the Eysenck Personality Questionnaire-Revised (EPQ-R) and the Kaufman Brief Intelligence Test (K-BIT). Moderated multiple regression revealed a significant interaction effect. Crystallized ability (K-BIT vocabulary) was negatively related to psychoticism at low levels of fluid ability (K-BIT matrices) and positively related to psychoticism at high levels of fluid ability. These findings highlight the potential importance of psychoticism within GfGc investment theory.MH/CHAOS: The CIA’s Campaign against the Radical New Left and the Black Panthers
Operation MHCHAOS was the code name for a secret domestic spying program conducted by the Central Intelligence Agency in the late 1960s and early 1970s charged with unmasking any foreign influences on left wing protestors. CIA counterintelligence officer Frank Rafalko was a part of that operation. When The New York Times revealed MHCHAOS in 1974 and Congress investigated, MHCHAOS took its place in the pantheon of intelligence abuses. However, in his new book Rafalko says that the operation was justified and that the CIA was the logical agency to conduct it. Listen as he defends his perspective with dramatic intelligence collected on the New Left and black radicals. This event took place on 26 October 2011.
India paper
The paper, Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia, is free.
Summing up, our results confirm both ancestry and temporal complexity shaping the still on-going process of genetic structuring of South Asian populations. This intricacy cannot be readily explained by the putative recent influx of Indo-Aryans alone but suggests multiple gene flows to the South Asian gene pool, both from the west and east, over a much longer time span.Dienekes: "I haven't read the paper fully yet (it's open access), but the abstract seems to agree with what I've written both here and over at the Dodecad blog, about South Asians being primarily a West Asian/South Asian variable mix." In fact, the authors note in the body of the paper:
Another example of an heuristic interpretation appears when we look at the two blue ancestry components (Figure 2B) that explain most of the genetic diversity observed in West Eurasian populations (at K = 8), we see that only the k4 dark blue component is present in India and northern Pakistani populations, whereas, in contrast, the k3 light blue component dominates in southern Pakistan and Iran. This patterning suggests additional complexity of gene flow between geographically adjacent populations because it would be difficult to explain the western ancestry component in Indian populations by simple and recent admixture from the Middle East.Moreover:
Both PC2 and k5 light green at K = 8 extend from South Asia to Central Asia and the Caucasus (but not into eastern Europe). In an attempt to explore diversity gradients within this signal, we investigated the haplotypic diversity associated with the ancestry components revealed by ADMIXTURE. Our simulations show that one can detect differences in haplotype diversity for a migration event that occurred 500 generations ago, but chances to distinguish signals for older events will apparently decrease with increasing age because of recombination. In terms of human population history, our oldest simulated migration event occurred roughly 12,500 years ago and predates or coincides with the initial Neolithic expansion in the Near East. Knowing whether signals associated with the initial peopling of Eurasia fall within our detection limits requires additional extensive simulations, but our current results indicate that the often debated episode of South Asian prehistory, the putative Indo-Aryan migration 3,500 years ago (see e.g., Abdulla15) falls well within the limits of our haplotype-based approach. We found no regional diversity differences associated with k5 at K = 8. Thus, regardless of where this component was from (the Caucasus, Near East, Indus Valley, or Central Asia), its spread to other regions must have occurred well before our detection limits at 12,500 years. Accordingly, the introduction of k5 to South Asia cannot be explained by recent gene flow, such as the hypothetical Indo-Aryan migration.First, note that the k5 "light green" ADMIXTURE component does in fact extend into and throughout Europe (apart from Sardinia). The authors believe they've shown "k5" must have "spread" well before the Neolithic. What they've actually demonstrated is that ADMIXTURE (at least as used here) will not be the tool to disentangle complex recent population movements in Eurasia.
"Huge" Genographic Project ancient DNA study underway?
A reader forwards a comment posted to a mailing list yesterday by a project administrator attending FamilyTreeDNA's Houston conference:
Report from the mixer -- Spencer Wells was there and spoke enticingly of a huge ancient DNA research project that's been underway for some time, in which, instead of a simple replacement by incoming Neolithic populations, they are seeing wave after wave of peoples coming over thousands of years, each wave adding a stratum superimposed on those before it. The set of haplogroups seen in the earlier strata were not like the ones we see today. In particular he says mtDNA H was not there until a fairly recent, post-Neolithic date.It's clear from already-published ancient DNA results that at least some sublineages of H were present in Neolithic Europe -- but H does seem to have become much more common since then.
He is still apparently clinging to a rather old date for R1b, though. He seems to think it had a major expansion about 10,000 years ago. Haven't genetic genealogists mostly been arguing for a considerably more recent time frame? I hope to see some R1b experts engage him in dialog on that point.That's a 20,000 year step in the right direction. I won't begrudge him the other 5,000 years for now. I just hope the "huge" ancient DNA effort underway includes Y chromosomes. Another comment from the FTDNA conference:
Katherine, Emily, Joan and Bonnie are already tweeting from the FTDNA conference. Their Twitter accounts are: @khborges, @Genealem, @Luxegen and @GreenleafyYou can also follow the hashtag #FTDNA2011 though not all the tweets are going out with the hashtag. [. . .]
FTDNA has tested over 600,000 people.
The Genographic Project has 450,000 public participation samples and 75,000 indigenous samples.
The Genographic Project has two Basque papers going into journals this week and another paper which includes mtDNA haplogroup U5 is due out next year.
And a few more twitter comments:
khborges Katherine H. Borges SW-Phase 1 of Geno is wrapping up. Phase 2 to begin #FTDNA2011
khborges Katherine H. Borges #FTDNA2011 #Genographic SW- 1 in 17 men in Med are descended from Phoenician traders
khborges Katherine H. Borges #FTDNA2011 #Genographic SW-East Asian human migration patterns follow the rivers
khborges Katherine H. Borges #FTDNA2011 #Genographic SW-10 papers are going off to the journals next week and about a dozen more in the pipeline
Luxegen Joan Miller SW - teaser - big announcement coming in Genographic project next year. #FTDNA2011
Jewish Liberalism: the Allinsmith Study
Polling data is not kind to Moldbug's hilarious explanation for Jewish leftism. In a 1940s survey of eight religious denominations, Congregationalist respondents were least liberal. In Boston, high-SES Jews were more likely to vote for Adlai Stevenson for president in 1952 than low-SES non-Jews -- and low-SES non-Jews voted for Stevenson at twice the rate of high-SES non-Jews.
The degree of commitment of American Jews to liberalism is different from the degree of that commitment among other religious groups. The difference is that the Jewish devotion to liberalism is not correlated with economic or educational status. This was demonstrated almost 20 years ago by Wesley and Beverly Allinsmith.2Source: Nathaniel Weyl's The Jew in American Politics, pp. 6-8Toward the close of World War II, the Allinsmiths asked 8,820 members of eight religious denominations whether they believed that the most important postwar task of the U.S. Government was to provide opportunity for people to get ahead on their own or "to guarantee every person a decent and steady job and standard of living."
Nationally, 47% of the people questioned preferred security to opportunity. As the percentage of manual workers in each denomination increased, the proportion favoring security rose. Status, education and income were inversely related to the choice of security. As one proceeded from Congregationalists to Presbyterians to Episcopalians to Methodists to Lutherans to Baptists and finally to Catholics, the preference for security steadily increased from 26% to 58%.
The Jews were the only exception to this rule. Although they were a very high status group ranking first in occupational level, third in educational level and fourth in economic level, 56% of them preferred security to opportunity. This was almost as high as the Catholic preference for security.
Moreover, within each of the eight religious denominations, the preference for opportunity was greatest among those with most education, highest status and best occupational level. Again, the Jews were the only exception.
The 1944 presidential vote also revealed this marked difference between Jewish and Gentile political behavior. The upper-class and upper-middle-class Christian denominations voted heavily against Roosevelt and in favor of Republican standard-bearer Thomas Dewey. Only 31.4% of the Congregationalists, 39.9% of the Presbyterians and 44.6% of the Episcopalians backed Franklin Delano Roosevelt. The more working-class denominations, however, voted heavily for him, particularly the Catholics who were 72.8% in his favor. In terms of their combined educational, occupational and status rank in the Allinsmith survey-that of second place-the Jews might well have been expected to vote Republican. Actually, they were 92.1% for Roosevelt. This overwhelming support was greater than that of any of the Christian denominations. [. . .]
However, in the 1952 elections, despite the fact that the Republican presidential candidate, Dwight D. Eisenhower, had led the Western coalition to victory over the Nazis, 75% of the Jewish voters supported Adlai E. Stevenson, a man who had played no role of any importance in World War II. There was no difference in the attitude of the candidates toward Jewry or the state of Israel. The issue was clearly one of moderation vs. liberalism. In a situation where American voters as a whole gave decisive support to Eisenhower, three-fourths of the Jews backed his Democratic opponent. Moreover, interviews in depth of Boston voters showed that only 30% of the Gentiles with high socioeconomic status, as against 60% of those with low socioeconomic status, backed Stevenson. Among Boston Jews, 72% of those with high status voted for Stevenson.
Penny starting to drop for academics
From "Ancient DNA suggests the leading role played by men in the Neolithic dissemination" (pdf):
The high frequency of G2a haplogroup in Neolithic specimens, whereas this haplogroup is very rare in current populations, also suggests that men could have played a particularly important role in the Neolithic dissemination that is no longer visible today. This would imply that intra-European migrations related to the metal ages may have strongly affected the modern gene pool.
I was intending to comment more, but for now I'll just mention:
(1) I agree with Jean M.: "MtDNA haplogroups were K1a (3), T2b (2), and one each of H3 and U5. Since it seems very likely that all of these except the U5 arrived in the Neolithic, I cannot agree with the conclusions of the authors that the spread of farming was male-led."
(2) The confirmed presence of E-V13 in Neolithic western Europe reinforces for me that those wanting to attribute the reported elevated levels of E-V13 in NE Wales to "Roman soldiers" or the like are probably mistaken.
Dental morphological evidence for European admixture in Mongolia and western China
Lee, C. and Scott, G. R. (2011), Brief communication: Two-rooted lower Canines—A European trait and sensitive indicator of admixture across Eurasia. American Journal of Physical Anthropology, 146: 481–485. doi: 10.1002/ajpa.21585
With the exception of Carabelli's trait, the European dentition is better known for the morphological traits that it does not exhibit rather than the ones that it does. One root trait, however, runs counter to the characterization of reduced and simplified European crowns and roots. Although a rare trait in general, two-rooted lower canines are much more common in Europeans than in any other regional grouping and, given adequate sample sizes, can be useful in evaluating gene flow between Europeans and neighboring groups. In European samples, two-rooted lower canines consistently exhibit frequencies of 5–8%. In our sample from northern Spain, the trait attains a frequency of almost 10%. In contrast, in Sub-Saharan Africans the trait is virtually unknown while in Asian and Asian-derived populations, it varies between 0.0 and 1.0%. Here we show that two-rooted canine frequencies for new migrants along the western frontiers of China and Mongolia ranged from 0–4%. These data suggest European-derived populations migrated into western China (Xinjiang Province) and Mongolia (Bayan Olgii Aimag) sometime during the late Bronze age (1000–400 BCE). [. . .]One of the major concerns of Alexandersen (1963) regarding two-rooted lower canines revolved around the issue of ‘‘atavism.’’ This term, rarely used today, begs the question of whether or not this double rooted form was common at one time, then disappeared, only to reappear sometime later. Swindler (1995) notes that ‘‘the deciduous and permanent canines in the majority of living primates have a single root.’’ This suggests that two-rooted lower canines are not the ancestral condition in anthropoids or hominoids. Rather, the phenotype is a derived condition, found primarily in recent human populations distributed across Western Eurasia.
The presence of the two-rooted canines in East Asia may provide some clue as to the eastward migration of new populations into China and Mongolia. The largest numbers of individuals with this trait are concentrated along the western and northern frontiers of China and Mongolia. Archaeological excavations support the large scale movement of people into this area during the Bronze age (ca. 2200 BCE–400 BCE). Burial artifacts and settlement patterns suggest cultural and technological ties to the Afanasevo culture in Siberia, which in turn is linked archaeologically, linguistically, and genetically with the Indo-European Tocharian populations that appear to have migrated to the Tarim Basin ca. 4,000 years ago (Ma and Sun, 1992; Ma and Wang, 1992; Mallory and Mair, 2000; Romgard, 2008; Keyser et al., 2009; Li et al., 2010).
The appearance of a new population on the western frontier also supports the findings of previous research in cranial metrics, dental nonmetrics, and DNA. Using cranial metrics and archaeological dating, Han (1994) hypothesized the earliest large-scale migration into western China occurred during the early Bronze age (2000 BCE) from Central Asia or southern Siberia. Dental nonmetric data also support multiple migrations into western China (Xinjiang Province) from Central Asia during the Bronze age to Iron age (Lee, 2007; Zhang, 2010). mtDNA studies on archaeological and modern population samples from Xinjiang Province show heterogeneous Asian and European genetic signatures dating from the Bronze age to the present (Yao et al., 2004; Cui et al., 2010; Zhang et al., 2010; Li et al., 2010).
As the frequency of two-rooted canines is highest in European samples and low to nonexistent in Asians, we propose this trait was introduced into East Asia by Indo- European speaking groups or their affines crossing the western frontier of China and Mongolia. Further data are needed to clarify aspects of these population movements, including the identity of the migrants, along with the number, routes, and timing of the migrations.
Although two-rooted lower canines cannot offer the precision of DNA in evaluating the ancestry in individual skulls, this trait is a sensitive indicator of admixture wherever Europeans come in contact with Asian or African populations. As this distinctive trait can be scored with relative ease in large samples, it provides a useful supplemental tool in discerning gene flow between distantly related populations going back many millennia.
Daniel MacArthur twitter commentary from CSHL Personal Genomes meeting
This meeting took place a couple weeks ago -- dgmacarthur is presently posting from ICHG2011.
James Watson is asking a question. At least I think it's a question. #cshlpg
Yes, it was a question: hasn't ELSI just been a huge waste of money? Wait, no - he's back to talking again. #cshlpg
Manfred Kayser is talking about the genetics of human appearance, but his talk is untweetable. #cshlpg
Although Kayser's talk is untweetable it sounds as though a lot of this is close to publication - so stay tuned. #cshlpg
JV [Joris Veltman] discussing published analysis of de novo variants in mental retardation: http://bit.ly/olWpYK #cshlpg
JV: total number of de novo coding mutations is not higher in MR patients - but more likely to be in brain genes. #cshlpg
What fraction of the human genome is functional?
What fraction of the human genome is functional?
Chris P. Ponting1,3 and Ross C. Hardison2,3
Abstract
Many evolutionary studies over the past decade have estimated ?sel, the proportion of all nucleotides in the human genome that are subject to purifying selection because of their biological function. Most of these studies have estimated the nucleotide substitution rates from genome sequence alignments across many diverse mammals. Some ?sel estimates will be affected by the heterogeneity of substitution rates in neutral sequence across the genome. Most will also be inaccurate if change in the functional sequence repertoire occurs rapidly relative to the separation of lineages that are being compared. Evidence gathered from both evolutionary and experimental analyses now indicate that rates of “turnover” of functional, predominantly noncoding, sequence are, indeed, high. They are sufficiently high that an estimated 50% of mouse constrained noncoding sequence is predicted not to be shared with rat, a closely related rodent. The rapidity of turnover results in, at least, a twofold underestimate of ?sel by analyses that measure constraint across the eutherian phylogeny. Approaches that take account of turnover estimate that the steady-state value of ?sel lies between 10% and 15%. Experimental studies corroborate the predicted rates of loss and gain of noncoding functional sites. These studies show the limitations inherent in the use of deep sequence conservation for identifying functional sequence. Experimental investigations focusing on lineage-specific, noncoding, and functional sequence are now essential if we are to appreciate the complete functional repertoire of the human genome.
http://genome.cshlp.org/content/early/2011/09/30/gr.116814.110.abstract
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