linkfest – 03/05/14

DNA USA*“[A]bout about 4 percent of whites have at least 1 percent or more African ancestry. Although it is a relatively small percentage, the percentage indicates that an individual with at least 1 percent African ancestry had an African ancestor within the last six generations, or in the last 200 years. This data also suggests that individuals with mixed parentage at some point were absorbed into the white population. Looking a little more deeply into the data, Kasia also found that the percentage of whites with hidden African ancestry differed significantly from state-to-state. Southern states with the highest African American populations, tended to have the highest percentages of hidden African ancestry…. Previous published studies estimate that on average African Americans had about 82 percent African ancestry and about 18 percent European ancestry. But in self-identified African Americans in 23andMe’s database, Kasia found the average amount of African ancestry was closer to 73 percent. Kasia found significant differences in state-to-state comparisons. African Americans in the northern and western states have more mixed ancestry than those in the southern states…. On average Latinos had about 70 percent European ancestry, 14 percent Native American ancestry and 6 percent African ancestry. The remaining ancestry is difficult to assign because the DNA is either shared by a number of different populations around the world, or because it’s from understudied populations, such as Native Americans.” – from 23andMe.

Common Variants in the CDH7 Gene are Associated with Major Depressive Disorder in the Han Chinese Population“Recent genome-wide association study also demonstrated that CDH7 was significant associated with bipolar disorder…. Our results support CDH7 to be a risk factor of MDD in the Han Chinese population. However, further studies with more markers and independent samples were suggested to validate our findings.”

Humans May Have Been Stuck on Bering Strait for 10,000 Years“In the new Perspectives article, published today (Feb. 27) in the journal Science, the researchers compile existing data to support the idea, known as the Beringia standstill hypothesis. Among that evidence is genetic data showing that founding populations of Native Americans diverged from their Asian ancestors more than 25,000 years ago. In addition, land in the region of the Bering Strait teemed with grasses to support big game (for food) and woody shrubs to burn in the cold climate, supporting a hard-scrabble existence for ancient people.” – razib is skeptical.

Was skin cancer a selective force for black pigmentation in early hominin evolution?“[D]ata on age-associated cancer incidence and lethality in albinos living at low latitudes in both Africa and Central America support the contention that skin cancer could have provided a potent selective force for the emergence of black skin in early hominins.”

Neanderthal Introgression at Chromosome 3p21.31 Was Under Positive Natural Selection in East Asians“Studies of the Neanderthal and Denisovan genomes demonstrate archaic hominin introgression in Eurasians. Here, we present evidence of Neanderthal introgression within the chromosome 3p21.31 region, occurring with a high frequency in East Asians (ranging from 49.4% to 66.5%) and at a low frequency in Europeans. We also detected a signal of strong positive selection in this region only in East Asians…. [S]uggestive evidence supports latitude-dependent selection, implicating a role of ultraviolet-B.”

Neanderthals challenge the origins of speech“Neanderthals, may well have spoken in languages not dissimilar to the ones we use today…. [I]n terms of mechanical behaviour, the Neanderthal hyoid was basically indistinguishable from our own, strongly suggesting that this key part of the vocal tract was used in the same way. ‘From this research, we can conclude that it’s likely that the origins of speech and language are far, far older than once thought.'” – h/t billare (who is 0.1% neanderthal)!

READ THIS (yes, there *will* be a pop quiz on the material later in the week (~_^) )!: Environmental Hereditarianism“[T]here is little evidence linking most ‘measurable’ aspects of the environment to human physical or behavioral traits…. Most of the solid evidence we do have for environmental impacts come in the forms of things that do physical damage (e.g., maiming limbs or traumatic brain injury) – a category which includes poisons; or are developmental deficits, such as malnutrition. Much of the rest of it (take your pick) is lacking.” – from jayman. – previously: it’s not nature and nurture….

Outliers – from greg cochran.

New evidence confirms link between IQ, brain cortex“Rate of change in the thickness of the brain’s cortex is an important factor associated with a person’s change in IQ, according to a collaborative study by scientists in five countries…. This study is the first to show the association between cortical thickness and development in full scale IQ, and has potentially wide-ranging implications for the pedagogical world and for judicial cases in which the defendant’s IQ score could play a role in determining the severity of the sentence.”

The Germ Theory of Democracy, Dictatorship, and All Your Most Cherished Beliefs“What kind of government do you live under? Who are your sexual partners? How do you treat strangers? All of these questions may mask a more fundamental one: What germs are you warding off?” – h/t jason collins! – but see this previous post: pathogens and consanguinity“the BIG outliers, though, are the arabs and all their middle eastern/north african/south asian muslim buddies. they are the ones throwing off the correlation completely…. these societies are amongst those that have the highest consanguinity rates, and yet some of their pathogen index scores are *very* low.” that part of the world also does not do well when it comes to (liberal) democracy. – see also jayman’s response.

Nicholas Wade Takes on the Regime – jared taylor reviews nicholas wade’s upcoming book on race. – h/t hbd bibliography! – see also this comment from jayman. – and see also Harmful, toxic equalism from the awesome epigone.

The Nature of Race – from karl boetel and john furest. see also here.

12,000 year old prehistoric art shows woman hunting – maybe. kinda/sorta. (not really.) – from adam benton.

Altruism and the Dark Side of Agreeableness“[B]eware of really nice people. If they seem too good to be true, they usually are.” – from staffan.

Forgotten fathers: paternal influences on mammalian sex allocation“A growing body of evidence suggests that the assumption that males produce an unbiased proportion of X- and Y-chromosome-bearing spermatozoa is not always valid with significant between- and even within-individual variation.” – a mechanism for trivers-willard? – h/t lars penke!

Digit Span: the modest little bombshell and What does IQ 70 mean for black and white kids? – from dr. thompson.

The paradox of the Visual Word Form Area“The VWFA functions differently in different human populations. The difference is striking between people who use alphabetical script, where each symbol represents a sound, and those who use logographic script, where each symbol represents an idea. Chinese subjects process their idea-based symbols with assistance from other brain regions, whereas Westerners process their sound-based symbols only in the VWFA.” – from peter frost.

The man who destroyed America’s ego“How a rebel psychologist challenged one of the 20th century’s biggest—and most dangerous—ideas…. Among the most egregious errors they discovered were those in the papers that focused on academic performance. A correlation had been repeatedly found between high self-esteem and good grades. So, the logic went, if you boosted self-esteem you’d also boost grades. But the authors had made one of the most elementary mistakes in science. ‘When they tracked people over time,’ says Baumeister, ‘the grades came first, and then the self-esteem. High self-esteem was a *result* of good grades, not a cause.'” – h/t matthew wygant!

Genetic Influences on Political Ideologies: Twin Analyses of 19 Measures of Political Ideologies from Five Democracies and Genome-Wide Findings from Three Populations“Here we present results from original analyses of a combined sample of over 12,000 twins pairs, ascertained from nine different studies conducted in five democracies, sampled over the course of four decades. We provide evidence that genetic factors play a role in the formation of political ideology, regardless of how ideology is measured, the era, or the population sampled…. We then present results from one of the first genome-wide association studies on political ideology using data from three samples: a 1990 Australian sample involving 6,894 individuals from 3,516 families; a 2008 Australian sample of 1,160 related individuals from 635 families and a 2010 Swedish sample involving 3,334 individuals from 2,607 families. No polymorphisms reached genome-wide significance in the meta-analysis. The combined evidence suggests that political ideology constitutes a fundamental aspect of one’s genetically informed psychological disposition, but as Fisher proposed long ago, genetic influences on complex traits will be composed of thousands of markers of very small effects and it will require extremely large samples to have enough power in order to identify specific polymorphisms related to complex social traits.”

Why Americans Are So Polarized: Education and Evolution“Improvements in learning — which correlates with stronger partisanship — and the tendency to choose likeminded mates may be helping to create divided politics.” – from avi tuschman. – h/t eddy elmer!

Conservatives generally more willing to take business risks, study finds

Paternal Age at Childbearing and Offspring Psychiatric and Academic Morbidity“In the study population, advancing paternal age was associated with increased risk of some psychiatric disorders (eg, autism, psychosis, and bipolar disorders) but decreased risk of the other indexes of morbidity.”

A Genotype-First Approach to Defining the Subtypes of a Complex Disease – h/t kevin mitchell who tweeted: “Increasing recog’n that ‘common disorders; like autism really umbrella terms for many rare diseases.”

Researchers look at boy-girl differences in autism“Boys, it seems, can develop autism from a relatively small genetic hit, according to a study published today in the American Journal of Human Genetics. It takes more of a genetic wallop, though, to cause autism in girls – so when they do get it, they’re worse off. The same explanation holds true, researchers think, for the gender imbalance in ADHD (attention-deficit hyperactivity disorder), intellectual disabilities and schizophrenia.” – see also: A Higher Mutational Burden in Females Supports a “Female Protective Model” in Neurodevelopmental Disorders.

China Cracks Down on DNA Testing – h/t jayman!

Epigenetics: The sins of the father – big story in nature today. – “The roots of inheritance may extend beyond the genome, but the mechanisms remain a puzzle.” – but swedish scientist on twitter says: “But Rando misquotes Swedish human data in his Cell paper on mice. Caution for epigenetic hype!” – hmmmm. =/

The Consequences of Natural Morality“Good and Evil are not objective things. They exist as subjective impressions, creating a powerful illusion that they are objective things. This illusion that Good and Evil are objects independent of the conscious minds that imagine them exists for a good reason. It ‘works.’ In other words, its existence has enhanced the probability that the genes responsible for its existence will survive and reproduce.” – from helian.

Digit ratio predicts eminence of Polish actors – this one’s for sisyphean! (^_^) – h/t ben southwood!

Sex differences in color preferences transcend extreme differences in culture and ecology.

In Academia, Women Collaborate Less With Their Same-Sex Juniors“‘Some older women treated us younger women almost worse than some men did,’ she says. ‘We called it the “Queen Bee syndrome.”‘” – heh. – h/t claire lehmann!

Women Can Keep the Vote: No Evidence That Hormonal Changes During the Menstrual Cycle Impact Political and Religious Beliefs – behind paywall.

Women ‘subconsciously outdo other females’ during ovulation“But what the researchers found really surprising is that ovulating women did not appear to want a higher standing over men – they became kinder to them. When playing the dictator game, non-ovulating women shared 45% of their money with men, while ovulating women were willing to share 60% of their money with men. These findings are unlike anything we have ever seen in the dictator game. You just don’t see people giving away more than half of their money,’ says Prof. Durante.” – (~_^)

Women Outperform Men in Ultra-Distance Swimming – The ‘Manhattan Island Marathon Swim’ From 1983 to 2013. – because we float better (because we have that extra layer of fat)? (~_^)

Sameness and the self: philosophical and psychological considerations.“[H]ow can a person maintain a belief in the sameness of self over time in the face of continual psychological and physical change?” – h/t neuroskeptic!

Young Children Can Be Taught Basic Natural Selection Using a Picture-Storybook Intervention – but not politically correct people, apparently. (~_^) – h/t stuart ritchie!

Study: Racial bias in pain perception appears among children as young as 7 – see also: Psychologists use baby-cam to study infants’ exposure to faces.

Mixed-race children ‘are being failed’ in treatment of mental health problems“Children of mixed race are at greater risk of suffering from mental health problems and are not getting the support they need, says a report.” – in the u.k.

Inferring Character From Faces: A Developmental Study.“This research suggests that the predisposition to judge others using scant facial information appears in adultlike forms early in childhood and does not require prolonged social experience.”

Los europeos no inventaron la desigualdad en Hispanoamérica – from eduardo zugasti.

Native American city on the Mississippi was America’s first ‘melting pot’carcosa cahokia. – “By analyzing the teeth of those buried in different locations in Cahokia, Emerson, state archaeological survey bioarchaeologist Kristin Hedman and graduate student Philip Slater discovered that immigrants formed one-third of the population of the city throughout its history (from about AD 1050 through the early 1300s).”

Two-hundred-year drought doomed Indus Valley Civilization“Monsoon hiatus that began 4,200 years ago parallels dry spell that led civilizations to collapse in other regions.”

HBD 101 – from malcolm pollack. (*^_^*)

bonus: A ‘Second Great Wave’ of immigration?“‘Once again, the country is approaching a percentage of foreign-born not seen since the late 1800s and early 1900s,’ the Census Bureau wrote on its blog this week.” – =/ – h/t ray sawhill!

bonus bonus: Muhammad’s birthplace to be razed – remember that the najdis hate the hejazis and vice versa.

bonus bonus bonus: Giant Virus, Awakened From 30,000-Year Slumber, Is Still Infectious – ruh roh (if you’re an amoeba)!

bonus bonus bonus bonus: Crawling Through The Brain Without Getting Lost“Do the wasps taste their way through a cockroach brain?” – mmmmmm! =/

bonus bonus bonus bonus bonus: Australia: Snake eats crocodile after battle – WITH PICTURES! =o – h/t ed west!

(note: comments do not require an email. g-8 selfie. (~_^) )

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chinese cleaners smarter than western professionals

here’s the latest re. the most recent pisa test results (various news outlets are reporting that the below also applies to the u.s. and canada – check google news for pisa+oecd):

“China’s poorest beat our best pupils”

“Children of factory workers and cleaners in Far East achieve better exam results than offspring of British lawyers and doctors, says OECD.

“British schoolchildren are lagging so far behind their peers in the Far East that even pupils from wealthy backgrounds are now performing worse in exams than the poorest students in China, an international study shows.

“The children of factory workers and cleaners in parts of the Far East are more than a year ahead of the offspring of British doctors and lawyers, according to a report by the Organisation for Economic Co-operation and Development….

“As part of the study, children were asked to name their parents’ occupation to determine its effect on pupil performance. Across the world, children whose parents work in professional careers generally outperform those in elementary jobs such as caterers, cleaners, factory workers and labourers.

“The study, involving more than 500,000 pupils worldwide, found children of elementary workers in many Far Eastern nations outperformed the sons and daughters of professional British children.

“The children of UK professionals scored an average of 526 points in maths. But this was overshadowed by an average score of 656 registered by the children of professionals in Shanghai-China and 569 among children of the country’s elementary workers. The children of parents in unskilled jobs in the UK scored an average of 461, the equivalent of two and a half years behind.

“Elementary workers’ children in Hong Kong (542), South Korea (538) and Singapore (534), also outperformed more affluent British peers. In Japan, Vietnam, Liechtenstein, Japan and China-Taipei, relatively poor children were only marginally behind the wealthiest British pupils.

“The report said: ‘In the United States and the United Kingdom, where professionals are among the highest-paid in the world, students whose parents work as professionals do not perform as well in mathematics as children of professionals in other countries — nor do they perform as we as the children in Shanghai-China and Singapore whose parents work in manual occupations….'”

no idea if any of these results were broken down by race, ethnicity, etc.

and a related story from a while back:

“Report: Chinese Third-Graders Falling Behind U.S. High School Students in Math, Science”

“According to an alarming new report published Wednesday by the International Association for the Evaluation of Educational Achievement, third-graders in China are beginning to lag behind U.S. high school students in math and science.

“The study, based on exam scores from thousands of students in 63 participating countries, confirmed that in mathematical and scientific literacy, American students from the ages of 14 to 18 have now actually pulled slightly ahead of their 8-year-old Chinese counterparts.

“‘This is certainly a wake-up call for China,’ said Dr. Michael Fornasier, an IEA senior fellow and coauthor of the report. ‘The test results unfortunately indicate that education standards in China have slipped to the extent that pre-teens are struggling to rank among even the average American high school student….'”

(~_^)

(note: comments do not require an email. or an average pisa score above ca. 450.)

linkfest – 11/13/13

oops! it happened again. =/

Deletion of Any Single Gene Provokes Mutations Elsewhere in the Genome“Johns Hopkins researchers report that the deletion of any single gene in yeast cells puts pressure on the organism’s genome to compensate, leading to a mutation in another gene…. ‘The deletion of any given gene usually results in one, or sometimes two, specific genes being “warped” in response….'”

Self-heal like Wolverine? Gene discovery might hold clues“In a discovery by a Harvard researcher, a reactivated gene found in embryos helps mice regrow clipped parts of their ears and toes. Could the ‘fountain of youth’ gene hold promise for humans too?” – i want one! – h/t mike anissimov!

Gene Variants Up CKD [chronic kidney disease] Risk in Blacks“A high-risk genetic variant conferred a significantly increased risk of progressive kidney disease in African Americans, at least partly explaining a racial disparity in end-stage renal disease (ESRD), investigators reported here. Analysis of black and white patients in another trial — half with diabetes — showed kidney function declined almost three times as fast in blacks with the high-risk APOL1 profile as compared with whites….”

Genetic clue to high heart risk of black Americans“The gene that produces the protein [PC-TP which activates a clotting factor called PAR4] is four times more active in the platelets of black Americans than it is in white Americans.” – h/t hbd bibliography!

Europeans and South Asians share by descent SLC24A5 light skin allele“‘We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.'” – @dienekes’.

The ancestors with no descendants“On the eve of the last ice age, Siberia was home to a people who were related to modern Europeans and Amerindians but not to modern native Siberians. So concludes an analysis of DNA from the remains of a boy who lived 24,000 years ago at Mal’ta near Lake Baikal, Siberia…. [T]he Mal’ta people probably looked very much like native Indians with a more European skull shape, perhaps like the Ainu of northern Japan or the Kennewick humans of North America.”

Political colour is half genetic“New study provides definitive evidence that heritability plays a significant role in the formation of political ideology, regardless of how ideology is measured, the time period or population sampled.” – @ScienceNordic.com – the photo caption is pretty funny/telling: “Imagine if scientists could identify the ‘liberal’ genes and genetically modify babies so that they all voted liberal when they grow up? Brave new world?” (and the first comment is priceless!) – h/t ray sawhill!

It’s not just conservatives that support discrimination against their ideological foes“‘Discrimination by liberals has received scant attention in the literature, despite this being a prevalent concern in conservative rhetoric. By only examining conservative biases, social scientists fail to fully explore political intolerance in America. This research helps fill that gap….’ When opposing groups were seen as violating core values, liberals were just as likely to support discrimination against same-sex marriage opponents, religious fundamentalists, Tea Party protestors, and prolife people as were conservatives against feminists, atheists, leftist protestors, and prochoice people.”

Politics Has an Odor“[C]onservatives are significantly more likely than liberals to detect [bitter tasting] PTC [phenylthiocarbamide].” – h/t jayman!

Study: Your brain sees things you don’t“Our brains perceive objects in everyday life of which we may never be aware, a study finds, challenging currently accepted models about how the brain processes visual information.”

New evidence on the biological basis of highly impulsive and aggressive behaviors“Physical and chemical changes in the brain during development can potentially play a role in some delinquent and deviant behaviors.”

Root of maths genius sought“Entrepreneur’s ‘Project Einstein’ taps 400 top academics for their DNA.”

Has a 15-year-old explained the Flynn Effect? – on elijah amstrong and michael woodley’s newly published paper! – from steve sailer.

Is young Woodley down for the count? – never! (^_^) – from dr. james thompson.

Religions of the American Nations“[T]hese differences [regional cultural and political divisions in america] stem from the *genetic* differences in the descendants of these initial settlers (suffused with the genes of subsequent immigrants, particularly in the old North).” – from jayman.

In Hookups, Inequality Still Reigns“[A] study of 24,000 students at 21 colleges over five years found that about 40 percent of women had an orgasm during their last hookup involving intercourse, while 80 percent of men did.” – h/t john durant!

The Co-Villains Behind Obesity’s Rise“Not everyone, however, has the same gut bacteria. And, interestingly, the composition of this bacteria correlates with obesity…. [T]he bacteria study found that the ‘obese gut bacteria’ had an impact only when the mice were fed diets heavy in saturated fats.” – h/t jayman!

Rich Chinese Couples Turning To American Surrogates For Easier Immigration And ‘Designer Babies’“Another factor that has some Chinese couples choosing American surrogates is a desire for ‘designer babies.’ While most couples still use their own eggs and sperm, making the child biologically theirs, Reuters reports that more and more people are open to egg donation, to get what some clients believe are smarter and better-looking children. ‘Lots of clients that are Chinese do use tall, blond donors,’ Jennifer Garcia, who works at Extraordinary Conception in California, where 40 percent of clients are Chinese, said in the report.” – h/t mark krikorian!

CRISPR gene therapy: Scientists call for more public debate around breakthrough technique“‘I’m sure there will be some concern about the possibility that the technology could be used for “enhancement” rather than repair, veering from medicine towards eugenics,’ [professor wells] warned.” – oh noes! not “enhancement”! *swoon!* h/t anatoly!

Should state education be abolished?“New York City adopting Finland’s education system is not going to make New York like Finland…. In the game of life the dice are loaded and trying to make teachers responsible for making life fair is deluded and unfair to them….” – from ed west.

Shaker Heights – from greg cochran.

John Derbyshire’s Modest Proposal On Politics and Intelligence“And the too-dumb-to-vote segment is only a part of the problem we conservatives have with universal suffrage. Here’s another part: too *smart* to vote…. At the very highest levels of intelligence, the correlation between IQ and sensible political opinions may actually be *inverse*: the more brilliant you are, the dumber your politics. Albert Einstein thought well of Stalin; Hitlerism got its first mass following in the highly-selective German universities.”

Amid austerity and debt, Denmark remains happiest nation“The second pillar of happiness is a high level of trust between people, even for a stranger on the street….” – crazy danes! (~_^)

Introducing the Mongol Project“‘I will now tell you all about the Tartars and how they acquired their empire and spread throughout the world.'” – excellent! – from t.greer.

Early uses of chili peppers in Mexico“Chili peppers may have been used to make spicy beverages thousands of years ago in Mexico….”

Case of Insect Interruptus Yields a Rare Fossil Find“[T]he oldest fossil of two insects copulating.” – 165 million years old!

This Is How Much Money You’ll Make Based on Your Personality – d*mn. =/

bonus: Another Word for “Holocaust”“[O]ne would have to be smoking banana peels dipped in formaldehyde and sprinkled with PCP to assert that both events [the holocaust and the holodomor] receive a similar amount of attention in Western media and academia.” – from jim goad. of course.

bonus bonus: Swedish cinemas launch feminist movie rating – hahahahahaha!!! heh. wait. (*hbd chick wipes tears from eyes*) heh. – “To get an ‘A’ rating, a movie must pass the so-called Bechdel test, which means it must have at least two named female characters who talk to each other about something other than a man….” – hahahahahaha!! – “The entire ‘Lord of the Rings’ trilogy, all ‘Star Wars’ movies, ‘The Social Network,’ ‘Pulp Fiction’ and all but one of the ‘Harry Potter’ movies fail this test,” – so, except for The Social Network, all of my faves. this is going to be a REALLY handy movie rating system. whatever movies they FAIL, i will go see! (^_^)

bonus bonus bonus: Strange Doings on the Sun“Sunspots, Which Can Harm Electronics on Earth, Are Half the Number Expected” – ruh roh.

bonus bonus bonus bonus: Large magma reservoir gets bigger – ruh roh.

bonus bonus bonus bonus bonus: This amazing fruit fly evolved to have pictures of ants on its wings – srsly! – h/t jayman!

(note: comments do not require an email. rupee – first dog to climb mt. everest. woof!)

inbreeding and cognitive ability among whites in the u.k.

via dienekes via jayman:

Genome-wide estimates of inbreeding in unrelated individuals and their association with cognitive ability

“INTRODUCTION

“Research on consanguineous marriages, and other forms of inbreeding, has long shown a reduction in cognitive abilities in the offspring of such unions. The presumed mechanism is that detrimental recessive mutations are more likely to be identical by descent in the offspring of such unions and so have a greater chance of being expressed. To date, research on the relationship between inbreeding and cognitive ability has largely been restricted to recent inbreeding events as determined by pedigree…. It has been suggested that intellectual disability is under negative selection, and that recent deleterious mutations have an important role in the underlying aetiology. The wealth of molecular genetic data currently available allows estimates of inbreeding on a genome-wide level and to examine the effects of long-term ancestral levels of inbreeding. Such an association with inbreeding, as measured by runs of homozygous polymorphisms (ROH), has previously been identified with several behavioural traits, such as schizophreniz, Parkinson’s disease and personality measures, as well as non-behavioural traits such as height.

“The relationship between inbreeding on a population level and cognitive ability is particularly interesting due to assortative mating, non-random mating, which is greater for cognitive ability than for other behavioural traits, as well as physical traits such as height and weight. Positive assortative mating has been reported for cognitive ability, particularly for verbal traits, with spousal correlations generally around 0.5. Assortative mating should lead to greater genetic similarity between mates at causal loci for cognitive ability and to a lesser extent across the genome, which in turn reduces heterozygosity at these local. In other words, in contrast to the genome-wide reduction of heterozygosity caused by inbreeding, the reduction of heterozygosity due to assortative mating for a trait is limited to loci associated with the trait…. Another difference between inbreeding and assortative mating is that the effects of inbreeding are expected to be negative, lowering cognitive ability, whereas the effects of assortative mating affect the high, as well as the low end of the ability distribution, thus increasing genetic bariance, that is, when high-ability parents mate assortatively, their children are more likely to be homozygous for variants for high ability, just as offspring of low-ability parents are more likely to be homozygous for variants for low ability….

“MATERIALS AND METHODS

“Participants

“The Twins Early Development Study (TEDS) recruited over 11 000 families of twins born within England and Wales between 1994 and 1996…. In this analysis, individuals were excluded if they reported severe current medical problems, as well as children who had suffered severe problems at birth or whose mothers had suffered severe problems during pregnancy. Twins whose zygosity was unknown or uncertain or whose first language was not English were also excluded. Finally, analysis was restricted to twins whose parents reported their ethnicity as ‘white’….

“Cognitive measures

“Verbal and non-verbal tests were administered using web-based testing. The verbal tests consisted the Similarities subtest and the Vocabulary subtests from the Wechsler Intelligence Scale for children (WISC-III-UK). The non-verbal tests were the Picture Completion subtest from the WISC-III-UK and Conceptual Grouping from the McCarthy Scales of Children’s Abilities. A general score was derived from the test battery as the standardized sum of the standardized subtest scores, which correlates 0.99 with a score derived as the first principle component of the test battery score.

“Runs of homozygosity

“FROH was defined as the percentage of an individual’s genome consisted of runs of homozygosity (ROH)…. [O]nly ROH with a minimum of 65 consecutive SNPs covering 2.3Mb were used when calculating the total proportion of the genome covered by ROH. In addition, the required minimum density in a ROH was set at 200kb per SNP, and the maximum gap between two consecutive homozygous SNPs was set at 500kb….

“RESULTS

“Table 1 includes descriptive statistics for FROH and the three measures of cognitive ability (general, verbal, and non-verbal). FROH is slightly positively skewed, as it represents the total percentage of the genome that includes runs of homozygosity (ROH). The average percentage of genome covered by ROH was 0.7% (95% CI 0.65-0.72%). Verbal and non-verbal abilities correlate 0.49; because general cognitive ability is the sum of the standardized verbal and non-verbal subtests, they correlate much more highly with general ability (0.87 and 0.86, respectively).

inbreeding and iq - table 01

“Table 2 presents the results of the linear regression analyses. No significant regression was found between FROH and the cognitive measures after correction for multiple testing, although the association with non-verbal cognitive ability was nominally significant (P=0.03). Although this association was not statistically significant, it is noteworthy that every regression in Table 2 is *positive*, indicating that increased homozygosity tends to be associated with *higher* cognitive scores across different measures of cognitive ability (general, verbal and non-verbal).

inbreeding and iq - table 02

“Our analysis identified 87 loci where ROH overlapped in 10 or more individuals. For these overlapping regions we tested for association with each of the cognitive measures and again showed no significant associations after correction for multiple testing (P-values of less than 5.7 x 10-4). A sign test of the direction of effect across all ROH showed a disproportionately large number of *positive* associations, indicating that ROH are associated with higher cognitive ability (P=0.002). The sign test was non-significant for verbal ability but highly significant for non-verbal ability (P<10-6). The sign test for non-verbal ability alone remained significant after correcting for an individual’s genome-wide FROH score (P<10-6).

“As explained earlier, positive assortative mating can also lead to genome-wide homozygosity for trait-specific loci, and, unlike inbreeding, assortative mating can affect the high as well as the low end of the ability distribution. One possible explanation for the trend suggesting a positive correlation between homozygosity and cognitive scores in our data is that positive assortative mating on intelligence might be greater for high cognitive ability individuals….

“DISCUSSION

“Our results show that within a representative UK population sample there was a weak nominally significant association between burden of autosomal runs of homozygosity and higher non-verbal cognitive ability. This nominal association with *increased* cognitive ability is counterintuitive when compared with the results from more extreme inbreeding based on pedigree information. A potential explanation for this direction of effect is that individuals with higher cognitive ability might show greater positive assortative mating, which would lead to increased homozygosity at loci for higher cognitive ability in their offspring. However, in a separate sample we showed that greater positive assortative mating was not associated with higher cognitive ability. While these findings seem to provide clear evidence against this hypothesis, it is possible that the genome-wide genetic finding reflect historical mating habits that no longer exist today. It should also be noted that there was a reduction in the standard deviations for spousal correlations in the increased cognitive ability groups by an average of 6% compared with the decreased cognitive ability group (see Table 3), which could reflect less genetic variability in the high ability couples or a ceiling effect on the cognitive tests. This lesser phenotypic variability at the high ability end would have a small effect in reducing the spouse correlations and potentially confound our analysis….

“Overall, these results highlight the importance of understanding mating habits, such as inbreeding and assortative mating, when investigating the genetic architecture of complex traits such as cognitive ability. The results certainly suggest that there is no large effect of FROH on reduced cognitive ability, the expected direction of effect. The nominally significant associations found in this study may even suggest that in the case of non-verbal cognitive ability, beneficial associations with homozygosity at specific loci might outweigh the negative effects of genome-wide inbreeding and that the relationship between inbreeding and cognitive ability may be more complicated than previously thought.
_____

so, although obviously Further Research is RequiredTM, these researchers have concluded that both the absence of reduced cognitive ability and the slight increase in cognitive ability which they found in individuals who had runs of homozygosity (roh) in their genomes (evidence of matings between genetically similar individuals) were probably NOT due to assortative mating (i.e. smart people mating with smart people).

furthermore, they suggest that the inbreeding-causes-reduced-cognitive-ability meme is incorrect — or at least that the situation is more complicated than the idea that it’s the accumulation of recent deleterious mutations which haven’t been selected away that is the (whole) problem. in fact, a little inbreeding seems to have a positive effect on some cognitive abilities!

i’ve suggested a couple of times one way in which inbreeding might result in a low average iq in a population, and that is if the inbreeding leads to clannish, altruistic behaviors between extended family members which then result in the deleterious mutations NOT being weeded out.

one real world example i’ve offered is how life works in egyptian villages and how the more successful and affluent (and, presumably, more intelligent) members of a clan are obliged to help out their less successful and poorer (and, presumably, less intelligent) clan members. so, apart from mentally retarded individuals not reproducing, where is the negative selection for deleterious mutations here? there is none. or it’s a lot weaker than in more individualistic societies (like gregory clarks’ medieval england) where it’s more every man for himself — in clannish societies, deleterious mutations might be able to hang around for a long time, riding on the coattails of those with fewer deleterious mutations.

(note: comments do not require an email. i’m my own grandpa! [no, I’M not! it’s just the song.])

western europeans, runs of homozygosity (roh), and outbreeding

i know, i know — it’s easier to spot inbreeding (or outbreeding) from the presence (or absence) of a lot of long runs of homozygosity (roh) in the genomes of individuals in a population rather than short roh (see for example the central/south and west asians in this post, populations which everyone knows are regular inbreeders), but i haven’t got any data on long roh for separate, sub-populations (like italians vs. europeans), so we’re gonna have to make do with short roh (for now). and anyway, even the amount of short roh is reduced via outbreeding (and increased via inbreeding), so you can use it as a tool to try to work out a population’s mating history. it’s just not as easy/obvious as with longer roh.

so … the map below is taken from Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans.

the samples come from:

the rotterdam study – the netherlands
popgen – northern germany – specifically the schleswig-holstein region (in deutsch if you like)
– the monica augsburg surveys – southern germany – from the city of augsberg and two neighboring counties
– and popres, which, since this is a study of europeans, i presume must mean that the samples came from both the lolipop study in london and the colaus study, lausanne, switzerland — i discussed those two studies in this previous post (scroll down).

again, the problem with taking samples from people living in big cities is that, even if they may be natives of whatever country they happen to live in, they, or some of their recent ancestors, may have migrated to the city — so, who knows, for instance, if the samples from rotterdam tell us anything about rotterdam or even the region of the country in which rotterdam is located. probably tells us something about the dutch, but even then….

these researchers — nothnagel et al. — chose to look at roh that were 1Mb in length. that’s shorter than the 1.5Mb roh as delineated by the researchers who looked at the roh in russian populations. also, nothnagel et al. weighted the average roh in each population according to how much linkage disequilibrium was (estimated to be) present in each population. don’t ask! no, really — don’t ask, because i don’t really understand why they did this. here’s the wikipedia page for linkage disequilibrium. i know that you can have more ld in an inbreeding population and — you guessed it! — less in an outbreeding one. and, of course, other things like bottlenecks can affect how much ld is present in a population. nothnagel et al. found different amounts of ld in the populations in this study and compensated for that, but again i’m not exactly sure why.

anyway … here’s what they found. this map shows the subpopulation averages of the weighted number of roh per individual (the contour lines are guesstimates — educated guesstimates, but still guesstimates):

europe roh - average weighted ROH number per individual

if you look closely, you’ll see that there’s a sort-of central band of a relatively low average number of roh (between 37-39) that runs from southern england down through beligum/the netherlands (rotterdam) and northeast france, southern germany and switzerland. and, as the researchers observed, and as we saw in the previous post on russia, the numbers of roh increase going northwards and decrease going south. until you get to southern spain and southern italy, southern greece, and (probably) a central spot in the balkans there, all regions where the average number of roh increases again. the researchers suggest that, perhaps, migration from northern africa to the iberian peninsula (that’s the only region for which they offer a possible explanation for this anomaly) explains the longer roh there — presumably they’re thinking of a bottleneck. maybe. but perhaps it’s due to greater historic inbreeding in southern spain — and southern italy and greece and the balkans. some data showing longer roh would help us tell one way or the other.

the researchers, btw, acknowledge that the areas indicated as having very low amounts of roh — colored in the lightest shades of yellow — i.e. northwest spain and eastern europe — are probably artifacts of the interpolation method that they used. also, for all you scots out there (you know who you are! (^_^) ), while i do predict that the average numbers of roh in scotland ought to be higher there than in england, note that there was no data for scotland included in this study, so the shades of the contours up there are wild guesses as well.

i’m quite surprised by the very low levels of roh in romania, but remember that one has to read this map with the underlying north-south differences in numbers of roh in mind, so perhaps the roh in romania really indicates an inbreeding/outbreeding rate in romania that is more like that found in, say, france/germany. dunno. in any event, it’s very interesting.

now i want to compare the average number of roh in eastern europe with western europe. that’s going to be kinda hard to do since 1) the two studies used different roh lengths (1Mb vs. 1.5Mb), and 2) the numbers from this study have been weighted. still, i think we can get at something of a (very!) rough picture by taking the numbers from germany as our starting point and using them to calibrate the results from the two studies. we can do this, i think, since the samples from germany came from the same sources in both studies — the popgen study for northern germany and the monica study for southern germany.

in the russian study, the samples from northern and southern germany were combined, so we only have one number for germany — which was lower than all the results from eastern europe, typically much lower (see map from previous post). the number of roh in the polish sample, for instance, was more than twice that found for the germans. the average number of roh in russia (Rus_HGDP) was also twice that of the germans. czechs, latvians, estonians — all higher than the germans.

now if we work westwards from germany using the results from the study in this post — the english, the dutch (rotterdam), and the swiss are all in the same range as the southern germans, while the southern french have an even lower average number of roh — and the irish (in dublin) and the czechs are in the same range as the northern germans. so all of these populations — and even the spanish and italians — have fewer roh on average than eastern europeans. which is what i would’ve guessed given what we know about the historic mating patterns of europeans beginning in the early medieval period (see mating patterns in europe series below ↓ in left-hand column).

maybe there’s another explanation for this difference between western and eastern europe — and for the apparent differences between central and southern europe. like i said above, a study or two looking at longer roh would help to clear up the picture one way or the other.

previously: russians, eastern europeans, runs of homozygosity (roh), and inbreeding and ibd and historic mating patterns in europe and ibd rates for europe and the hajnal line and runs of homozygosity and inbreeding (and outbreeding) and runs of homozygosity again

(note: comments do not require an email. ruh roh!)

russians, eastern europeans, runs of homozygosity (roh), and inbreeding

greying wanderer (thanks, grey!) pointed out to me (via) a very interesting study of russian/eastern european genetics which includes some runs of homozygosity (roh) data (which can provide clues of inbreeding/close matings among other things): A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe. (dienekes has a really good explanation of roh here.)

in this latest study, khrunin et al. took a look at a handful of different ethnic russian sub-populations (from different locations in russia) as well as some other eastern european groups. most of the samples from russia they collected themselves — the rest came from other studies. here’s a list of which groups were included and where they came from:

– russians (n=384) from the archangelsk (mezen district, n = 96), vladimir (murom district, n = 96), kursk (kursk and oktyabrsky districts, n = 96), and tver (andreapol district, n = 96) regions
veps (n=81) from the babaevo district of the vologodsky region
komi (n=150) from the izhemski (izhemski komi, n = 79) and priluzski (priluzski komi, n = 71) districts of the komi republic.

all of these samples were collected by the authors — except for those from tver — and the researchers ensured that the subjects AND their parents were originally from whatever region in which they happened to find them (i like that!).

the data from other studies which they used are described in this paper and include:

– finns – samples from helsinki (n = 100) and kuusamo (n = 84) – kuusamo is really remote
– estonians (n = 100) – samples collected across the entire country
– latvians (n = 95) – samples collected in riga – parents had to be latvians
– poles (n = 48) – from the west-pomeranian region, so just on the border with germany
– czechs (n = 94) – from prague, moravia, and silesia
– germans (n = 100) – from schleswig-holstein in the north and the augsburg region in the south
– italians (n = 88) from tuscanyhapmap
– russians (n = 25) from the human genome diversity panel (hgdp) – i believe from the vologda oblast.

the data collected by khrunin et al. are really good, imho, since 1) they went to all the trouble of collecting samples from different regions of russia, and 2) the researchers tried to control for ethnic/regional origin. the quality of the data from all the other studies is kinda mixed, for my interests anyway. for instance, taking in samples in large, capital cities — meh — not so great. the residents of those cities could’ve come from all over the country. the northern versus southern sampling in germany is better; unfortunately, those data sets were combined together in this study (they’re kept separate in another really cool study which i will post about soon!). the estonian data set is interesting because the samples came from across the country. otoh, the polish data set is also interesting because it’s from such a specific region (and right on the border with germany).

ok. one last thing before i show you the results (i made a map!). different researchers define roh differently (*sigh*) — while there do seem to be some standards, there’s also quite a bit of variation, and different researchers choose to look for roh of varying lengths. in this study, the researchers looked for roh that were 1.5Mb in length (i’ve seen other researchers look for 1Mb in length). 1.5Mb is pretty short as far as roh go. if you recall, when a population has a lot of longer roh (like 4-8Mb or more), that’s a pretty good indicator of inbreeding. 1.5Mb — not so much. lots of short roh are a better indicator of something like a population bottleneck in the distant-ish past. but, what’s a girl to do? gotta work with what’s available, and if it’s short roh, so be it.

here (finally!) is the map. i took the data from this table. the map (first column of data) is of the average number of roh (of 1.5Mb) found in individuals in the different populations (nROH):

russia nroh

the most obvious thing to note is that the small, endogamous groups (the veps and the komi) have more roh than any of the other populations, except for the finns up in kuusamo (and i think that that’s probably due to a bottleneck — ethnic finns really only migrated to, and began to settle in, the area seriously in the 1600s, and i imagine it wasn’t very many of them — and being so far away from anybody else!). the veps and the komi are small populations and, historically, they didn’t marry out much (that’s why we have veps and komi people today), so they are somewhat inbred. definitely more so than the surrounding population.

another curious thing is the pretty high number of rohs in the baltic populations: latvians=0.58, estonians=0.61, and finns in helsinki=1.13. wow! what happened there? that’s something like three to five times the number of roh we see in italians (from tuscany) or germans.

the most interesting point for me, though, is that there is an east-west divide. it’s kinda vague, maybe, but i think it’s there: italians (tuscans) and germans at ca. 0.20, and then the czechs and poles right next door at 0.35 and 0.51 respectively. and everyone to the east, except the russians in kursk, higher again than those two figures. i think these results hint at what i’ve found in the history books on medieval europe, i.e. that western europeans began outbreeding earlier than eastern europeans and as a result wound up being more outbred. (see, for example, here and here — and the “mating patterns in europe series” below ↓ in left-hand column.)

finally, the authors of the study point out how it appears that the average number of roh in individuals in a population increases with latitude — and they mention that this has also been shown elsewhere (i’ll be posting on that paper — very soon!). if you look at the various ethnic russian populations, for instance, the russians down in kursk (Rus_Ku=0.28) and murom (Rus_Mu=0.39) have fewer roh than the russians further to the north in tver (Rus_Tv=0.49) and way up in mezen (Rus_Me=1.63!). however, the hgdp russian samples, apparently from the vologda oblast which is pretty far north, have relatively low numbers of roh (Rus_HGDP=0.44), so that doesn’t seem to fit. still, it does look like a real pattern to me. the authors suggest that this is due to the general pattern of how europe was settled (from the south to the north), as well as the fact that the farther north you go, the fewer people there are to mate with (so the more inbred you wind up being).

as i’ll show in my next post, though, while there does seem to be a north-south pattern to roh frequency in europe with more roh in populations to the north than the south, curiously the numbers seem to increase in southern europe as well (as compared to places in central europe like germany and france) — and strangely in the balkan region as well. i can’t imagine why! (^_^)

previously: ibd and historic mating patterns in europe and ibd rates for europe and the hajnal line and runs of homozygosity and inbreeding (and outbreeding) and runs of homozygosity again

(note: comments do not require an email. kuusamo traffic jam!)

libya update

been a while since i checked on events in libya. so, how are the rebel alliance those democracy-loving freedom fighters doing in libya, anyway?:

“Libyan rebel leader is killed, and tribal fissures emerge”

ruh roh.

“The top rebel military commander in Libya was killed yesterday [july 28th], and members of his tribe greeted the announcement with gunfire and angry threats. The violent outburst stirred fears that a tribal feud could divide the forces struggling to topple the Libyan dictator, Moammar Khadafy.

“The leader of the rebels’ provisional government, Mustapha Abdul Jalil, announced yesterday evening that assassins killed the commander, General Abdul Fattah Younes, and two other officers. But he provided few details.

“Younes, a former officer and Cabinet member in the Khadafy government, had long been a contentious figure among the rebels, some of whom doubted his loyalty. He had been summoned to Benghazi for questioning by a panel of judges, and members of his tribe – the Obeidi, one of the largest tribes in the east – evidently blamed the rebel leadership for having some role in the general’s death.

The specter of a violent tribal conflict within the rebel ranks touches on a central fear of the Western nations backing the Libyan insurrection: that the rebels’ democratic goals could give way to a tribal civil war over Libya’s oil resources….”

see also: “Assassination of Libya’s rebel military leader brings tribal divisions to forefront”“The murky death of Gen. Abdul Fateh Younes, who led Libya’s rebel forces, has called into question rebels’ ability to transcend tribal divisions and their credibility to lead a democratic transition.”

previously: inexplicable rifts in libyan rebel forces and libya – land o’ tribes and consanguinity in libya…

(note: comments do not require an email. or a rebel alliance tattoo.)