Archives for posts with tag: genetics

well this seems important! via race/history/evolution notes, an abstract from the society for molecular biology and evolution 2014 conference (in puerto rico! – teh scientists are always good to themselves whenever they can be (~_^) ):

Evidence for different mutation rates across human populations
Ron Do, David Reich
Department of Genetics, Harvard Medical School, Boston, USA

Although mutation rates (per base pair) have clearly changed across primate evolution, many analyses continue to assume that all present-day human populations have the same mutation rates. Recently, William Amos analyzed 1000 Genomes Project and Complete Genomics sequences and found evidence of significantly higher divergence rates on African than on non-African lineages since separation (W. Amos, PLoS One 4, e63048). The detected pattern was strongest in genomic regions of high polymorphism rate, a pattern that the author hypothesized was due to ‘heterozygote instability’, whereby gene conversion events surrounding heterozygous sites increase the mutation rate. To further test this observation, we measured the relative accumulation of mutations in lineages drawn from two different populations, using 25 deep genome sequences generated according to the same experimental protocol using the Illumina technology. We carried out pairwise comparisons of five sub-Saharan African (Dinka, Mandenka, Mbuti, San, Yoruba) and eight Non-African populations (Australian, Dai, French, Han, Karitiana, Mixe, Papuan, Sardinian) on all divergent sites. We observed statistically significant differences in the relative accumulation of mutations for many pairs of African and Non-African populations. Among the strongest differences is significantly more lineage-specific mutations in Mbuti than in Han Chinese (R=1.044, standard error (SE) =0.0015). On average, we observed about 1% more mutations on African lineages compared to Non-African lineages. We also observed some significant differences across non-African populations, with the Han Chinese who have experienced extreme expansions in population size associated with agriculture having more mutations than the Karitiana, a hunter-gatherer population from Amazonia who did not experience such expansions (R=1.015, SE=0.0014). The results are consistent across both European and African segments of the human reference sequence, so are not an artifact of reference sequence bias. Taken together, these results support the view that per-base pair mutation rates may be dynamically and substantially changing across humans.

cool!

wrt to greater number of mutations in african lineages: polygamy (and, therefore, older fathers)? life in the tropics?

(note: comments do not require an email. old san juan. (^_^) )

holy toledo! two week’s worth of links! happy friday! (^_^)

John Derbyshire On Nicholas Wade’s A TROUBLESOME INHERITANCE – A Small, But Significant, Step For Race Realism“Wade raises high the banner of race realism and charges head-on into the massed ranks of the SSSM. He states his major premise up front, on page two: ‘New analyses of the human genome have established that human evolution has been recent, copious, and regional.’ Those last four words are repeated at intervals throughout the narrative. They are, as it were, the keynote of the book; Wade returns to them many times to anchor his observations — and some speculations — on the history and development of human societies.” (my emphasis there – h.chick)

henry harpending on science“[T]his is perhaps at the heart of the slander of the so called hbd-crew that circulates. Most of us are really interested, in our hearts, in theory and models. This is the way that most of science works…. You state somewhere that the hbd crew is obsessed with IQ. Seems so, but wait! IQ is literally the only thing that can be reliably measured of a whole constellation of interesting traits. It really does work in the sense of telling one whom to hire or whom to admit to graduate school. You also speak of what we ‘believe’ but the whole fun of science is falsifying hypotheses, not believing them. I would give my eye teeth (if I had them) to come up with something besides IQ to look at.” (my emphasis again – h.chick)

Digging For Gold: Study Says Your Race Determines Your Earwax Scent – h/t hbd bibliography!

Austronesians Out of the Cauldron“…the emergence of Austronesians. Linguistics and archaeology already were rather clear on the pattern of expansion, and when. But now an ancient DNA remain from off the coast of Fujian dated to ~8,000 years ago solidifies in totality the where and when. This is not an argument anymore.” – from razib.

New Diet, Sexual Attraction May Have Spurred Europeans’ Lighter Skin“[A] new study of ancient DNA concludes that European skin color has continued to change over the past 5000 years, suggesting that additional factors, including diet and sexual attraction, may also be at play.” – see also: Natural selection has altered the appearance of Europeans over the past 5,000 years.

It made their brown eyes blue…“A recent report in PNAS shows the inhabitants of the Ukraine and its environs had much darker hair, skin, and eyes back in the Bronze Age and earlier.” – from greg cochran.

Did Europeans become white in historic times? – from peter frost.

Pause Is Seen in a Continent’s Peopling“Using a new method for exploring ancient relationships among languages, linguists have found evidence further illuminating the peopling of North America about 14,000 years ago. Their findings follow a recent proposal that the ancestors of Native Americans were marooned for some 15,000 years on a now sunken plain before they reached North America.”

The place of the Armenian language in the Indo-European family“A very interesting talk at the Library of Congress making a good case for a Greek-Phrygian-Armenian clade within the Indo-European family.” – from dienekes.

One Million Brits ‘Descended from Vikings” DNA Study Claims“Around one million Britons, or one in 33 men across the UK, can claim direct descent from Vikings, according to a new DNA study. Men from the far north of Scotland were most likely to provide a direct match with almost a third (29.2%) of the men from the Shetland Islands testing positive for Viking blood.” – h/t ed west!

Genetic Architectures“The point is that the genetic architecture of a quantitative trait does not have to be the same in different populations of the same species. For example, I have the impression that height is not as highly polygenic in Pygmies as it is most other human populations. There’s a particular region on chromosome 3 that seems to influence height- you don’t see such a concentration in Europeans.” – another from greg cochran.

Molecular genetic contributions to socioeconomic status and intelligence – h/t billaire! who tweeted: “21% of the var. in education level, 18% of SES, 29% of cognitive ability explained by COMMON SNPs in Scottish sample.”

Study finds genetic link between height and IQ“A team of researchers at Edinburgh University in Scotland has found a correlation between genes associated with height and those associated with intelligence. In their paper published in the journal Behavior Genetics, the group describes how they studied the DNA of 6,815 unrelated people and discovered what they describe as a direct correlation between height and intelligence—taller people are smarter, they say.”

HVGIQ: Puerto Rico – from jason malloy.

Population differences in intellectual capacity: a new polygenic analysis – peter frost on davide piffer’s work.

Evidence for the general factor of personality as social-effectiveness

Intelligent people are more likely to trust others“Intelligent people are more likely to trust others, while those who score lower on measures of intelligence are less likely to do so, says a new study. Researchers based their finding on an analysis of the General Social Survey, a nationally representative public opinion survey carried out in the United States every one to two years.” – h/t mr. mangan, esq!

Openness to experience and aesthetic chills: Links to heart rate sympathetic activity“These results suggest links between openness to experience and sympathetic nervous system activity explaining, at least in part, relationships of openness to such traits as aesthetic chills.” – h/t stuart ritchie!

Psychological refractory period in introverts and extraverts“Evidence for faster stimulus analysis in extraverts compared to introverts.”

‘Free to Be’ Boys and Girls: 40 Years After the Failed Gender Revolution“1974’s ‘Free to Be…You and Me’ feels like an eternity ago. And, amazingly, kids and adults have yet to morph into mutually respectful, non-gendered human persons.” – from christina hoff sommers.

Personality Regions: The Friendly Midwest, the Left Coast and the Wicked (Possibly Irish) Witch of the Northeast – from staffan.

Want Success? Choose the Right Parents“Gregory Clark’s startling new book, ‘The Son Also Rises,’ asks you to rethink everything you thought you knew about social mobility. His research, if it’s correct, isn’t good news. It says that socio-economic status is mostly a matter of nature not nurture, and suggests that trying to help the disadvantaged move up won’t make much difference.” – h/t alice teller! – see also: Social mobility: Have and have not“Mr Clark follows his logic to an unexpectedly egalitarian end. Redistribution is sensible, he argues, not in order to boost mobility but because mobility is intractably low. The cream will rise regardless, and so paying extraordinary salaries to capable workers is unnecessary. If high rates of mobility are used to excuse or justify inequality, he suggests, then the reality of low mobility implies something quite different: t hat great inequality serves little purpose and redistributing income from the rich to the poor might raise overall welfare at little economic cost. This makes for uncomfortable reading for those of all ideological persuasions.”

Why HBD“As I have tired to explain in my earlier post, Environmental Hereditarianism, the behavioral and physical traits of people are environmentally context-dependent. The broad environmental context regulates the expression of the genes. There is *not* a dichotomy between genes and ‘environment’. Nor could there be one – we are always ‘with’ both. The broad environment includes geography, climate, technology, and prevailing social landscape (otherwise known as ‘culture’). When the social-technological-geographic landscape changes, you can have broad behavioral change all without genetic change. This explains secular changes that occur too quickly to be a result of evolution, such as the sexual revolution, the modern rise in irreligiosity, the increase in the obesity rate, etc.” – from jayman.

Key connection“Biologists zero in on role of plasticity in evolution. For more than a century, scientists have suggested that the best way to settle the debate about how phenotypic plasticity — the way an organism changes in response to environment — may be connected to evolution would be to identify a single mechanism that controls both. Harvard researchers say they have discovered just such a mechanism in insulin signaling in fruit flies. Cassandra Extavour, an associate professor of organismic and evolutionary biology, and grad student Delbert André Green II were able to show that a single molecular pathway plays a role in both heritable changes in the flies’ number of ovarioles — egg-producing compartments in the ovaries — and in how they react to their environments by shutting down some ovarioles. The study is described in a paper published this month in the Proceedings of the Royal Society B. ‘This is the first example, to my knowledge, that shows this link — between heritability and plasticity — being controlled by the same mechanism,’ Extavour said. ‘What we’ve done with this paper is show that an important trait that controls how many offspring a fruit fly will have exhibits both heritable variation and phenotypic plasticity, and that both are controlled by insulin signaling.'” – h/t steven pinker!

Morality and the Lament of the Liberal Atheists“Moral relativism is the ground state of living things. It doesn’t work for a social species like ours. If every one of us tried to monopolize all the available resources within his grasp at the cost of everyone else, the chances that any given individual would survive and reproduce would be drastically reduced. Therefore, morality. It exists because, from an evolutionary perspective, it works. It will continue to function just as it always has, even if 100,000 philosophers shout at the top of their lungs that it’s irrational. Of course it is, but it doesn’t matter. We will continue to perceive the good and evil that seem so real to our imaginations as absolutes. It is our nature to do so….” – from helian

coolest. story. ever. (in the past two weeks.): The Woman Who Can Will Herself Out Of Her Body – h/t keith laws!

Hypothesis on Why Northwest Europe Began Outbreeding“It could just be coincidence that the outbreeding areas that coincide with other positive hajnal line traits were also lands conquered by men from tribes with the traditions of Germanic kingship. These kings were illiterate barbarians seeking legitimacy and thinking long term at the security of their line ruling…. This is a hypothesis, but the position these rulers were in was one of new conquerors in foreign lands. They needed to create and encourage loyalty in the natives as well as find a way to secure their individual line as king in a manner that was different from what their people, the conquerors, were accustomed to. The Church, an institution eager for power in a new area as well, offered an opportunity to import a political infrastructure and change the social make up of their new lands. Even moreso in England than the rest of core Europe, the Church and the elite’s motivations and goals overlapped perfectly. Christianity was new to them and new to the Britains, but as conversions mounted, it was a shared trait amongst them all. That shared identity was the warrior-chiefs’ way to have rule and kingship legitimized. That shared identity made the natives and newcomers men of Kent or East Anglia, later England, and not of the clan.” – good stuff from son of brock landers!

Rise of the West and the Hajnal line – from mr. mangan, esq.

The Low Fertility Of Urban Liberals Is A Feature Not A Bug – from heartiste.

The Achilles’ Heel of Northern Europeans: Outbreeding? – from alfred clark.

The Medieval Mind“The medieval character was not just about poisoning rivals and raping their daughters. That picture misses the raw and unquestioned nationalism, the impulsivity, the superstition, the childishness (in Barbara Tuchmann’s words), the present time-orientation.” – from elijah.

On Digit Ratio and its Implications – from sisyphean the mad contrarian.

psychO – from the awesome epigone. linking to this mostly for the pictures – awwww! (^_^)

The genes that mean you have a good ear for music“Musical aptitude may be partly down to genes that determine the architecture of the inner ear.” – h/t simon makin! – alternatively: you, too, can have perfect pitch! (~_^)

The Origin of Ideology“Are left and right a feature (or bug) of evolution?” – review of a couple of books.

Do Women’s Mate Preferences Change Across the Ovulatory Cycle? A Meta-Analytic Review – answer: yes. – see also: Intersexual conflict across women’s ovulatory cycle“Results indicate that (a) men are particularly self-assertive toward partners when their partners are fertile; (b) similarly, women are especially self-assertive toward partners when they are fertile; (c) women report engaging in more behaviors that resist male vigilance and mate-guarding when they are fertile, especially in ways that are unobservable to male partners; (d) these effects are especially strong when women themselves report greater attraction to men other than partners when they are fertile, compared to the luteal phase.” – h/t robert burriss!

Study finds less cooperation among women than among men where hierarchy is involved“‘When I studied young children, I noticed that boys were typically interacting in groups, and girls tended to focus on one-on-one relationships,’ said Benenson, the study’s lead author, who explored similar questions in her book Warriors and Worriers. ‘There is even evidence that these differences exist in six-month-olds – but you can see it with the naked eye by about five or six years old, where boys form these large, loose groups, and girls tend to pair off into more intense, close friendships.’ What makes those differences particularly provocative, Benenson said, is that chimpanzees organize their relationships in nearly identical ways. ‘Chimpanzee males usually have another individual they’re very close with, and they may constantly battle for dominance, but they also have a larger, loose group of allies,’ Benenson said. ‘When it comes to defeating other groups, everybody bands together. I would argue that females don’t have that biological inclination, and they don’t have the practice.'”

The Reason Early Humans May Have Practiced Infant Cannibalism – mmmmmmm! – h/t diana fleischman!

Personality Traits and Body Mass Index in a Korean Population“Compared with the normal weight groups, overweight and obese men scored higher on openness to experience and lower on conscientiousness. Overweight and obese women scored lower on neuroticism and openness to experience and higher on agreeableness. Extraversion was positively associated with BMI in men (β = 0.032, P<0.05). BMI and waist circumference were significantly increased in individuals who were less dutiful. In women, neuroticism was inversely associated with BMI (β = −0.026, P<0.05). Openness to experience was negatively, and agreeableness was positively, associated with BMI (openness to experience: β = −0.072, agreeableness β = 0.068) and waist circumference (openness to experience: β = −0.202, agreeableness: β = 0.227) (P<0.05).”

The Supergene That Paints a Liar

This Island Life“The strange biology of island populations highlights the role of chance, not just selection, in evolutionary change.” – h/t john belmont!

Competition May Not Be the Driving Force of Species Diversity After All – h/t robert ford!

Big Testicles Drive Genetic Evolution: Size Does Matter After All“[A]nimals with larger testis having an increased speed of genome evolution, researchers have found.”

Bye bye RNA world

The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota!

Genomics/Bone Marrow Donation: Next-gen DNA sequencing enables reliable donor matching service

Is Ed Houben Europe’s most virile man?“Ed Houben has an unusual pastime. He has slept with scores of women who seek him out for his legendary powers of insemination…. Ed Houben has come to see his daughter for the first time. He talks gently to the six-week-old baby, and little Madita looks up at him. She is, he says, his 98th child.”

The Costume of Shangri-La: Thoughts on White Privilege, Cultural Appropriation, and Anti-Asian Racism – it’s worth quoting the whole abstract: “This piece poses cultural appropriation as an undertheorized aspect of white privilege in White Privilege Studies. By way of narrative exploration, it asserts that a paucity of scholarship on Orientalism and anti-Asian racism has created a gap in White Privilege Studies that curbs its radical transformative potential. It argues for the value of a structural and historically focused lens for understanding the issue of cultural appropriation, and extends questions of culture and race relations beyond the borders of the United States. It also explores the complex ways that interracial and transnational relationships can influence white racial identity, and illustrates the disruptive potential that queer interracial relationships can offer to dominant historical patterns of white behavior.” – (~_^) h/t ben southwood!

bonus: mr. mangan’s book! (^_^): Smash Chronic Fatigue: A Concise, Science-Based Guide to Help Your Body Heal, and Banish Fatigue Forever

bonus bonus: Backing the Big Bang“In breakthrough, astronomers find evidence of speedy ‘cosmic inflation’ of universe”

bonus bonus bonus: Does Time Flow? (video) – d*mn physicists! (~_^)

bonus bonus bonus bonus: Elephants Hear Age, Gender, Ethnicity in Human Voices – elephants are awesome!

bonus bonus bonus bonus bonus: Dinosaurs are not Extinct – YAAAAAAAAYYYYY!!!! – h/t steve stewart williams!

bonus bonus bonus bonus bonus bonus: The stripy stick insect that walked with dinosaurs“This is the earliest known plant-mimicking stick insect, its fragile body preserved for 126 million years in the dusty rocks of north-east China.” – h/t jason moore!

bonus bonus bonus bonus bonus bonus bonus: Flies That Do Calculus With Their Wings“The wings of fruit flies beat about 250 times a second.” – h/t kyle hill!

bonus bonus bonus bonus bonus bonus bonus bonus: Portolan Charts ‘Too Accurate’ to be Medieval – h/t heresiarch!

(note: comments do not require an email. polite elephant steps over fence.)

Your Ancestors, Your Fate“The notion of genetic transmission of ‘social competence’ — some mysterious mix of drive and ability — may unsettle us. But studies of adoption, in some ways the most dramatic of social interventions, support this view. A number of studies of adopted children in the United States and Nordic countries show convincingly that their life chances are more strongly predicted from their biological parents than their adoptive families. In America, for example, the I.Q. of adopted children correlates with their adoptive parents’ when they are young, but the correlation is close to zero by adulthood. There is a low correlation between the incomes and educational attainment of adopted children and those of their adoptive parents. These studies, along with studies of correlations across various types of siblings (identical twins, fraternal twins, half siblings) suggest that genetics is the main carrier of social status.” – from gregory clark. see also The Son Also Rises: Surnames and the History of Social Mobility.

Reductionism! Determinism! Straw-man-ism!” The main problem, it seems to me, is a fundamental misunderstanding of what genetics as a science studies and how it relates to the function of complex systems. The following statements are not contradictory: 1. The function of a complex system emerges from the complex and dynamic interactions between all of the components of the system, in a context- and experience-dependent manner. 2. Variation in single components of the system (or in multiple components) can affect how it functions. Geneticists investigate the second question. Showing that variation in Gene X affects the behaviour or outcome of a system is not the same as saying that Gene X fully determines that behaviour or fully accounts for the entire system. Gene X is just a piece of DNA sitting in a cell somewhere – it doesn’t do anything by itself. But a *difference* in Gene X can account for a *difference* in how the system works. – from kevin mitchell.

The Problem with HBD, the Dark Enlightenment, Neoreaction, Alt-Rightism, and All That Jazz – READ THIS! – from jayman (and misdreavus).

There’s nothing wrong with looking for ‘gay genes’“The Left loves to tell the Right that it’s anti-science, pointing (not without reason) to the correlation between conservative beliefs and a failure to come to terms with the scientific facts of evolution and human-caused climate change. But there’s a subtler tendency on the Left; a fear of research into human nature, in case the findings are in some way politically uncomfortable.”

Evolution equally efficient in removing deleterious variants in Europeans and West Africans“…but apparently not in Denisovans who accumulated deleterious mutations at a higher rate than modern humans.” – @dienekes’.

Scientists unlock a ‘microbial Pompeii’“An international team of researchers have discovered a ‘microbial Pompeii’ preserved on the teeth of skeletons around 1,000 years old. The key to the discovery is the dental calculus (plaque) which preserves bacteria and microscopic particles of food on the surfaces of teeth, effectively creating a mineral tomb for microbiomes.”

The effect of paternal age on offspring intelligence and personality when controlling for paternal trait level [pdf] – “We examined the effect of father’s age at birth on offspring intelligence, head circumference and personality traits. Using the Minnesota Twin Family Study sample we tested paternal age effects while controlling for parents’ trait levels measured with the same precision as offspring’s. From evolutionary genetic considerations we predicted a negative effect of paternal age on offspring intelligence, but not on other traits. Controlling for parental intelligence (IQ) had the effect of turning an initially positive association non-significantly negative. We found paternal age effects on offspring IQ and Multidimensional Personality Questionnaire Absorption, but they were not robustly significant, nor replicable with additional covariates. No other noteworthy effects were found.” – from lars penke.

Reversed hierarchy in the brain for general and specific cognitive abilities: A morphometric analysis“Here, we analyze gray matter with three morphometric indices (volume, cortical surface area, and cortical thickness) at three levels of the intelligence hierarchy (tests, first-order factors, and a higher-order general factor, g)…. The key finding reveals substantial variability in gray matter correlates at the test level, which is substantially reduced for the first-order and the higher-order factors. This supports a reversed hierarchy in the brain with respect to cognitive abilities at different psychometric levels: the greater the generality, the smaller the number of relevant gray matter clusters accounting for individual differences in intelligent performance.” – h/t ben southwood!

A nice bunch of flowers“The general factor of intelligence is strongest at lower levels of intelligence. It may be a case of ‘All neurones to the pump’. When abilities are low, most problems are difficult. In such cases, all resources have to be thrown at the problem. When abilities are higher there is more spare capacity for differentiation of abilities. Brighter persons have a lower proportion of their abilities accounted for by a common factor, even though the have higher absolute abilities.” – from dr. james thompson.

GED scores by Ethnicity and Nation – from chuck @human varieties.

The Unfortunately Innate Nature of Intelligence“You cannot blame people for being what they were born, and you cannot expect them to do what they cannot.”

Psychologist on a mission to give every child a learning chip“Prof Robert Plomin wants educators to take notice of genes, and has a new big idea – personalised learning.”

Fruit-loving lemurs score higher on spatial memory tests“Food-finding tests in five lemur species show that fruit-eaters may have better spatial memory than lemurs with a more varied diet. The results support the idea that relying on foods that are seasonally available and far-flung gives a competitive edge to individuals with certain cognitive abilities — such as remembering where the goodies are.”

What Does Our DNA Say About How We Look?“A biologist aims to profile suspects from genetic material left at crime scenes.’ – h/t matthew wygant!

Four Lame Responses to Sam Harris’ Moral Landscape Challenge“Moral emotions, like every other evolved trait, exist because their presence increased the probability that the genes responsible for the existence of those traits would survive and reproduce. Moral emotions, and the associated illusions of the existence of Good and Evil as things in themselves, exist as subjective impressions in the minds of individuals.” – from helian.

Free will beliefs and motivation to punish“In a paper forthcoming in the Journal of Personality and Social Psychology, Cory J. Clark and co-authors provide evidence that widespread belief in the existence of free will is bolstered by a fundamental desire to punish wrongdoers…. As Clark et al. put it, ‘There seems little doubt that the subjective experience of choosing and acting supports people’s belief in free will, but our findings suggest another powerful motivating factor: the human impulse to blame and punish. People believe in free will – at least in part – because they wish to affirm that people who do immoral things could have and should have acted differently’.”

A small contribution to the free-will thingy – from elijah.

Is there a ‘dark intelligence’? Emotional intelligence is used by dark personalities to emotionally manipulate others“Narcissism and psychopathy increased link between emotional intelligence facets and emotional manipulation.” – h/t claire lehmann!

Theory of mind: did evolution fool us?“Although sophisticated ToM is believed to have high adaptive fitness, broad experimental evidence from behavioural economics, experimental psychology and linguistics point towards limited recursivity in representing other’s beliefs.” – h/t neuroskeptic!

Creativity and personality in classical, jazz and folk musicians“[J]azz musicians are more frequently engaged in extracurricular musical activities, and also complete a higher number of creative musical achievements. Additionally, jazz musicians show higher ideational creativity as measured by divergent thinking tasks, and tend to be more open to new experiences than classical musicians. This study provides first empirical evidence that jazz musicians show particularly high creativity with respect to domain-specific musical accomplishments but also in terms of domain-general indicators of divergent thinking ability that may be relevant for musical improvisation.” – h/t mary louise cowan!

Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa“In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia, and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations.”

Silver Blaze“[I]n most parts of Europe, it looks as if modern populations inherited the three EEF/WHG/ANE groups (Levantine farmers, West Hunters and Sibermen) via only two proximate ancestral populations. Europe at the time was almost entirely occupied by Sardinian-like farmers – then another population moved in, one that had about 3 times as much West Hunter as Sibermen.” – from greg cochran.

Replacement or continuity?“Ancient DNA seems to promise a clearer picture because the only source of uncertainty is the age of the skeletal material. Unfortunately, this new method is more sensitive to uncertainty from another source: natural selection. Late hunter-gatherers and early farmers had to adapt to different environments. There certainly was a genetic divide between the two, but did it result from differences in origin or from differences in natural selection?” – from peter frost.

Dystopian diversity – from the awesome epigone.

“I regret studying social anthropology” – me, too. *sigh* – see also the original post.

The parasite that escaped out of Africa: Tracing origins of malaria parasite“An international team has traced the origin of the second-worst malaria parasite of humans to Africa. The closest genetic relatives of human *Plasmodium vivax* were found only in Asian macaques, leading researchers to believe that *P. vivax* originated in Asia. This study overturns that, finding that wild-living apes in central Africa are widely infected with parasites that, genetically, are nearly identical to human *P. vivax*.” – h/t hbd bibliography!

Are Rich People Really That Selfish? – New Queendom.com Study Looks At Impact of Socio-Economic Status on Altruistic Tendencies“‘Our personality impacts every aspect of our life – the choices we make, the people we surround ourselves with, the career we pursue, the way we respond to life experiences, the way we manage our finances, and whether or not we share our good fortune,’ explains Dr. Jerabek, president of the company…. [H]ow individuals conduct themselves when they have money has everything to do with who they are as a person. Money doesn’t make a person more or less selfish. If you are a genuinely kind and giving person, you’ll continue to be that way no matter how many zeros are on your paycheck.'”

Babies born in England and Wales to non-UK born mothers infographic“Total Fertility Rate in England/Wales by where mother born: 4.3 Afghanistan, 3.8 Pakistan, 3.3 Nigeria, 2.4 India, 1.8 UK.”

The Tale of a CRISPR Clone – from razib.

Graft Probe in Scientific Community Widens in Southern China“A corruption probe has so far snared more than 50 scientists and research administrators in Guangdong, one of China’s wealthiest provinces.”

Quick Winter Olympics Digit Ratio Note – from sisyphean the mad contrarian.

Scientist proposes revolutionary naming system for all life on Earth“…a naming convention based on genome sequencing to enhance the way organisms are classified.” – h/t super mario!

Burials uncovered in Ireland reflect fusion of Paganism and Christianity“Excavations at Caherconnell in County Clare, Ireland, have uncovered ancient burials that reflect a fusion of Pagan practices with Christianity. Although it was initially believed that Christianity was well established in Ireland by the 5th Century, the latest finding reveals that Celtic Paganism was not quick to die out.” – h/t derek hopper!

The Society of Mutual Autopsy“The Society of Mutual Autopsy was an organisation formed in the late 1800s to advance neuroscience by examining dead members’ brains and to promote atheism by breaking sacred taboos.”

Heavy metal bands per 100,000 people – global map.

A Campus More Colorful Than Reality: Beware That College Brochure – h/t conrad hackett! who tweeted: “The whiter the college, the more diversity depicted in the brochures.”

bonus: Confirmed: Oldest Fragment of Early Earth is 4.4 Billion Years Old

bonus bonus: Hubble Finds Possible Oldest Object Ever Seen“The Hubble Telescope’s new set of Frontier Fields images includes a galaxy some 13-billion light-years away, which makes it a candidate for the most distant object ever seen.”

bonus bonus bonus: Rust Cohle, Guidance Counselor – heh. (~_^)

(note: comments do not require an email. rust cohle for president!)

(sorry. the dog ate my sunday linkfest….)

And Yet Another Tale of Two Maps – from jayman.

Why are girls and boys maturing earlier? – from peter frost.

When Did Humans Come to the Americas?

Large study shows substance abuse rates higher in teenagers with ADHD“When the adolescents were an average of 15 years old, 35 percent of those with ADHD histories reported using one or more substances, as compared to only 20 percent of teens without ADHD histories.”

Tribal societies and war – from mangan.

Crime and Twins – from dienekes.

HVGIQ: Cayman Islands – from jason malloy.

Evil Genes and the Long Dark Tea Time of the Soul – @bad data, bad!

Digging Deep in the DNA“‘I think I’m one of the few people,’ she said, ‘who have taken the rectal temperature of a grizzly bear.'”

Men are from Mars Earth, women are from Venus Earth“That men and women approach their social world similarly does not imply that there are no differences in average scores between the sexes. Average differences do exist, write the authors.” – yes, average differences do exist.

Exercise linked with reduced prostate cancer risk in Caucasians but not African-Americans“Studies have also revealed that African-American men have an increased risk of developing prostate cancer and of dying from the disease compared with Caucasians.”

Gene today, gone tomorrow: Genes for autism and schizophrenia only active in developing brains“Genes linked to autism and schizophrenia are only switched on during the early stages of brain development, according to a study in mice led by researchers at the University of Oxford.” – curioser and curioser….

The Lab Accident That Led to the Discovery of Supertasters“A cloud of chemicals. One researcher detects a smell. The other does not. What happens next? Science.”

So THAT’s why women’s feet and hands are always cold! Why they are slaves to their hormones

On Genteels – @bloody shovel.

Oral Mystery: Are Agriculture and Rats Responsible for Tooth Decay?“Tooth decay is a relatively modern problem. The bacteria feasting on your teeth might have originated in the mouth of a rodent, and found their way to our teeth, thanks to agriculture.”

bonus: ‘Google for spies’ draws ire from rights groups

bonus bonus: ‘It’s a boy!’ Monkey midwife delivers baby

bonus bonus bonus: What Are Dogs Saying When They Bark? [Excerpt]“Experiments have now shown that dogs use different barks and growls to communicate different things.” – see also: Your dog really does understand you… They’re more likely to steal food if they think you can’t see, research reveals.

bonus bonus bonus bonus: Pigeons Get a New Look“Pigeons, a Darwin favorite, carry new clues to evolution.”

bonus bonus bonus bonus bonus: Do plants ‘veto’ bad genes?“Latest evidence fails to quell doubt about whether plants can access “ancestral” genes outside their parents'”

bonus bonus bonus bonus bonus bonus: Face-to-face with the earliest ancestor of all placental mammals

bonus bonus bonus bonus bonus bonus bonus: Penicillin Mold Can Reproduce Sexually, Which Could Lead to Better Antibiotics“Penicillin-producing fungus, previously thought to be asexual, has a sexual side. The finding is the latest in a kind of sexual revolution in fungal genetics.”

bonus bonus bonus bonus bonus bonus bonus bonus: Fast Food Robot Builds the Perfect Burger – won’t need mexicans for flipping burgers anymore.

(note: comments do not require an email. two of earth’s moons in one picture.)

Racial differences in narcissistic tendencies“Study 1 (N = 367) found that Black individuals reported higher levels of narcissism than White individuals even when controlling for gender, self-esteem level, and socially desirable response tendencies.” – @steve sailer’s.

Genomics: The single life“‘In recent years we’ve learned that there is considerable variation in the recombination rate between different populations, between the sexes and even between individuals.'”

Moment Magazine’s great (Jewish) DNA experiment“Moment Magazine … wrote about their Great DNA Experiment, in which they look at the 23andMe results of 15 notable Americans of Jewish ancestry and make some interesting genetic connections…. The piece shows it’s not ‘six degrees’ that separates these individuals from each other, but, in all but one case, no degrees of separation.” – @race/history/evolution notes.

Are the cads outbreeding the dads?“Is natural selection now favoring the ‘cads’ over the ‘dads’?” – god, i hope not! – from peter frost.

Is there an upside to anxiety?“[S]ocial anxiety – the fear of interactions with strangers – may have evolved to enable a natural social ranking system in which some people feel most comfortable towards the bottom of the totem pole. This natural shuffling would have made for a less aggressive, more survivable living situation and reduced fighting for leadership.”

Young Children Are More Generous When Others Are Aware of Their Actions“Adults frequently employ reputation-enhancing strategies when engaging in prosocial acts, behaving more generously when their actions are likely to be witnessed by others and even more so when the extent of their generosity is made public…. Children were consistently generous only when the recipient was fully aware of the donation options; in all cases in which the recipient was not aware of the donation options, children were strikingly ungenerous…. These findings suggest that long before they develop a rich understanding of the social significance of reputation or are conscious of complex strategic reasoning, children behave more generously when the details of their prosocial actions are available to others.”

Evidence of Viking Outpost Found in Canada“Sharpeners may be smoking guns in quest for New World’s second Viking site.”

Archaeologists unearth 1,300-year-old Anglo Saxon feasting hall inches below village green in first major find of its kind in 30 years

bonus: NYU loses years of scientific research and thousands of mice to Hurricane Sandy – well that s*cks.

bonus bonus: darwin award winners – Celebratory gunfire at Saudi wedding cuts cable, 23 electrocuted – =/

bonus bonus bonus: Where Dragons Come From“The villains of countless stories, the mythical beasts have roots in Rome’s Pliny — and nature.”

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i’ve written before (here, here and here) about the hgdp samples and the fact that there is very little to no provenance info connected to them. the problem with this, afaics, is that it’s difficult to know whether or not the hgdp samples are truly representative, in all ways, of the populations from which they came.

i was particularly concerned initially about the french (and the japanese) hgdp samples — and then i got over that — but now i’m concerned about them again. here’s why:

the hgdp samples from france are described thusly:

“France – French/various regions (relatives) – This sample from various regions of France is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.”

great!

hang on — which regions?

auvergne? where, in some villages in the eighteenth century, groups of families regularly inbred with one another? lorraine? which, in some areas, had consanguinity rates of up to 50% between 1810 and 1910? burgundy or brittany, both of which had reportedly higher cousin marriage rates in the nineteenth and twentieth centuries than other regions of france? or were the hgdp samples collected in places like central france which, historically, had much lower rates (in the range of 1-3.5%) of close marriages?

the thing is: we don’t know.

what we do know is that the hgdp sampling seems kinda biased towards unique little groups like basques and orcadians, sardinians and the adygei. which is understandable ’cause these are all interesting, unusual groups and there’s legitimate concern that their unique genomes might sorta disappear in our modern, outbreeding world, and it would be a shame to miss out on the chance to at least keep a record of all that human biodiversity.

but then i have to wonder how representative of the majority of french people are the french hgdp samples? do they truly represent “the french,” or did the samples come from some of those crazy little villages way up in the mountains? i dunno. and neither does anybody else (afaik).

and the reason i wonder is: if teh scientists are gonna do really awesome genetic studies to check for the relatedness between the members of different human populations — like runs of homozygosity (roh) studies or identity by descent (ibd) studies — i think they need to know if the samples they’re looking at are representative or not. do the results for “the french” in studies like this or this or this truly represent the average french, or do they represent some special sub-groups of mountain dwelling french?

in the most recent roh study i posted about, the “french” don’t appear to be much more in- or out-bred than orcadians or the basques, something which strikes me as odd. perhaps — perhaps — that’s because the french hgdp samples are not truly representative of the broader french population. perhaps. i don’t know. nor do the researchers.

rinse and repeat above discussion for the other samples, too.

previously: hgdp samples and relatedness and more on the hgdp samples and why i care about the hgdp samples and meanwhile, in france… and runs of homozygosity and inbreeding (and outbreeding) and ibd and historic mating patterns in europe and runs of homozygosity again

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**update below**

here’s an exciting new paper!: Genomic Patterns of Homozygosity in Worldwide Human Populations. i don’t have access to the paper itself, but there are lots o’ neat figures and tables in the supplemental data [opens pdf] that relate to runs of homozygosity (roh). roh are identical stretches of dna within an individual’s genome (i.e. identical on each of the dna strands, paternally and maternally inherited). (roh shouldn’t be confused with blocks of identity by descent [ibd], which i did once! ibd blocks are identical stretches of dna as compared between different individuals, iiuc.)

recall that possessing lots of long roh indicates that one’s parents are/were quite similiar genetically speaking. that can be as a result of a couple of different genetic scenarios like (as greying wanderer has brought up a lot recently) simply being from a small sized population (i.e. having a small effective population size) and/or from regular inbreeding (consanguineous/endogamous mating). so, a population having a lot of long roh is either small and/or inbreeds a lot. populations having LOTS of short roh have probably been through some sort of bottleneck (see previous post).

in the paper i looked at in that previous post, the researchers had looked at the different roh lengths for large, regional populations like “europeans” or “east asians.” amongst other things, they had found that some of my regular inbreeders — the fbd marriage folks — had some of the highest numbers of medium and long roh, a state of genetic affairs which likely reflects their long-term close mating patterns. interestingly, the researchers had found that east asians had roh lengths similar to those of europeans across the board, something which surprised me since, at least according to what i’ve been reading, east asians (i.e. the chinese) have been inbreeding for a much longer time than europeans. one drawback of that previous study, though, was that, apart from the french, most of the european populations they looked at were peripheral groups who have had a tendency to inbreed more than my “core” europeans (see mating patterns in europe series below ↓ in left-hand column).

the new paper suffers from some of the same problems since the data come from the same sources (hgdp-ceph and hapmap phase 3 populations), so northern europeans — apart from the french — aren’t included in this paper either. (what can you do? it’s early days yet. i look forward to when there’s lots more genetic data available out there for teh scientists to work with! (^_^) )

what the researchers in this paper have done, though, is to look at both the different mean lengths of roh in each of the different populations sampled AND they looked at total numbers of roh within individuals for each population. this has, i think, drawn out some interesting differences between the populations.

first, here are two graphics from the supplmental data (linked to above). click on each for LARGER views (they should open in new tabs/windows — you might have to click on them again there to super-size them).

i’ve highlighted a handful of populations i want to focus on ’cause i know a little something about their historic mating patterns: the bedouin (as a proxy for the arabs — note that the bedouin have probably inbred more than more settled arabs); italians (not sure if they’re northern or southern italians or a mix of both — however, there are tuscans in the samples with which these “italians” can be compared); pathan or pastuns (more fbd marriage folks, like the bedouins/arabs); and han chinese (there are some northern han chinese with whom this groups can be compared). ok. here are the charts:

as you can see, the researchers have split up the roh into three classes (note that the short and medium classes here are a lot shorter than those in the paper looked at previously):

- A: 0.25-0.40 Mb (short)
– B: 0.6-1.2 Mb (medium)
– C: 0-35 Mb (long)

the interesting thing in the first chart above (Fig. S3 – Mean ROH Length for Each of the Three Size Classes in Each Population), is that the han chinese have lower means of roh length in all of the size classes compared to the other populations i’ve highlighted. in the previous study, the researchers found that east asians had similar means to europeans for all roh lengths. i found this surprising since, from what i’ve read, the han chinese have been inbreeding for a longer period of time than europeans. what might be confounding the results though, once again, is the fact that nw europeans (the outbreeders extraordinaire) are not really included in either of these studies apart from a handful of french samples.

in this latest study, both the bedouin and the pashtun, for instance, have higher means — and wider spreads — of long (class C) roh than the italians, which is what i would’ve expected since those two groups (the bedouins and the pashtuns) are, being fbd marriage folks, serious inbreeders. perhaps the reason the han chinese long roh mean is comparatively low is partly due to the fact that they historically practiced mother’s brother’s daughter (mbd) marriage which doesn’t push towards such close inbreeding as fbd marriage. still, i would’ve expected to see greater means of roh for the chinese than the italians — or, at least, around the same. not so much lower. (unless the italians practiced fbd marriage, too — or fzd marriage — but i don’t think so.)

if you look at the second chart (Fig. S4 – Total Number of ROH in Individual Genomes), however, you’ll see that, overall, the han chinese have more short, medium and long roh totally in individual genomes than any of the other three populations i’ve highlighted. both the bedouins and the pashtuns have greater numbers/wider total spread of long roh than the italians, but the han chinese have a much greater total number of long roh than any of the other three groups — three or four times as many.

but they’re, on average, shorter long roh don’t forget. (confusing, eh?!)

perhaps this is what you get when you have — as the chinese have had — a pretty good-sized effective population size for such a long time. there have been a LOT of han chinese for — wow — millennia.

so, it looks like this (in this order of inbrededness — i think):

- bedouins: highest mean, and very wide spread, of long roh; high total numbers, and widest spread, of long roh.
- pashtun: low mean, but widest spread, of long roh; low total number, but very wide spread, of long roh.
- han chinese: very low mean, and very narrow spread, of long roh; highest total numbers, and wide spread, of long roh.
- italians: low mean, and rather wide spread, of long roh; very low total number, and very small spread, of long roh.

other interesting points are that:

- the tuscans/tsi (toscani) appear to have lower short, medium and long mean roh than the generic “italian” category. however, the tuscans have lower total numbers of long roh than the “italians” while the toscani (tsi), on the other hand, appear to have a greater total number of long roh than the “italians.” while the tuscan samples and the toscani/tsi samples are from different studies (hgdp vs. hapmap), they are all supposed to be from tuscany, so it’s surprising that they’re so different. perhaps the individuals in the toscani/tsi sample were more closely related somehow?

- the northern han samples have lower short, medium and long mean roh than the generic “han” category. this would fit my general impression that historically inbreeding has been greater in southern china than in the north. however, the total number of long roh are greater in the northern han sample than in the “han” sample. not sure what that means.

don’t forget that there can be all sorts of reasons for differences in roh: inbreeding vs. outbreeding, yes, but also effective population size, population movement (migration in or out), bottlenecks, etc. i just happen to be interested in trying to pick out the effects of inbreeding/outbreeding — if possible.
_____

**update - here are a couple of excerpts from the article (thnx, b.b.!) [pgs. 277, 279-281]:

“Size Classification of ROH

“Separately in each population, we modeled the distribution of ROH lengths as a mixture of three Gaussian distributions that we interpreted as representing three ROH classes: (A) short ROH measuring tens of kb that probably reflect homozygosity for ancient haplotypes that contribute to local LD [linkage disequilibrium] patterns, (B) intermediate ROH measuring hundreds of kb to several Mb that probably result from background relatedness owing to limited population size, and (c) long ROH measuring multiple Mb that probably result from recent parental relatedness….

“In each population, the size distribution of ROH appears to contain multiple components (Figure 2A). Using a three-component Gaussian mixture model, we classified ROH in each population into three size classes (Figure 2B): short (class A), intermediate (class B), and long (class C). Size boundaries between different classes vary across populations (Table S1); however, considering all populations, all A-B boundaries are strictly smaller than all B-C boundaries (Figure 2C). The mean sizes of class A and B ROH are similar among populations from the same geographic region (Figure S3), with the exception that Africa and East Asia have greater variability. The class C mean is generally largest in the Middle East, Central/South Asia, and the Americas and smallest in East Asia (Figure S3), with the exception that the Tujia population has the largest values. In the admixed Mexican population (MXL), mean ROH sizes are similar to those in European populations. In the admixted African American population (ASW), however, mean ROH sizes are among the smallest in our data set, notably smaller than in most Africans and Europeans.

“Geographic Pattern of ROH

Several patterns emerge from a comparison of the per-individual total lengths of ROH across populations (Figure 3). First, the total lengths of class A (Figure 3A) and class B (Figure 3B) ROH generally increase with distance from Africa, rising in a stepwise fashion in successive continental groups. This trend is similar to the observed reduction in haplotype diversity with increasing distance from Africa. Second, total lengths of class C ROH (Figure 3C) do not show the stepwise increase. Instead, they are higher and more variable in most populations from the Middle East, Central/South Asia, Oceania, and the Americas than in most populations from Africa, Europe, and East Asia. This pattern suggests that a larger fraction of individuals from the Middle East, Central/South Asia, Oceanis, and the Americas tend to have higher levels of parental relatedness, in accordance with demographic estimates of high levels of consanguineous marriage particularly in populations from the Middle East and central/South Asia, and it is similar to that observed for inbreeding-coefficient and identity-by-descent estimates. Third, in the admixed ASW and MXL individuals, total lengths of ROH in each size class are similar to those observed in populations from Africa and Europe, respectively (Figure 3).

“The total numbers of ROH per individual (Figure S4) show similar patterns to those observed for total lengths (Figure 3). However, in East Asian populations, total numbers of class B and class C ROH per individual are notably more variable across populations than are ROH total lengths.”

previously: runs of homozygosity and inbreeding (and outbreeding) and ibd and historic mating patterns in europe

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The genetic history of Europeans – from dienekes.

The DNA Olympics — Jamaicans Win Sprinting ‘Genetic Lottery’ — and Why We Should All Care – in which jon entine sneaks the phrase “human biodiveristy” into forbes online. (^_^)

Neandertal ancestry “Iced”“The genome of this Neolithic-era individual [Ötzi] shows a substantially higher degree of Neandertal ancestry than living Europeans.” – from john hawks.

Analysis Of China’s PISA 2009 Results – anatoly concludes that china’s pisa-derived iq is ≈ 102.5.

What predicts college grades better than IQ score?“At the university level, introversion predicts academic performance better than cognitive ability.” – from barking up the wrong tree, via foseti.

Parents also choose“[I]n many if not most societies, men, i.e. fathers, decide which man is allowed to mate with his daughter or other female relative.” – @the breviary.

A GPS in Your DNA“Using a probabilistic model of genetic traits for every coordinate on the globe, the researchers have developed a method for determining more precisely the geographical location of a person’s ancestral origins.”

Early birds have the best temperament profile – but night owls have higher iqs. (~_^) – from the inductivist.

Fertile Gals Have All the Right Dance Moves“Women in the fertile phase of their menstrual cycle are judged as more attractive dancers by men than are women in a less-fertile phase, a new study finds.”

Genetically engineering ‘ethical’ babies is a moral obligation, says Oxford professor“‘Indeed, when it comes to screening out personality flaws, such as potential alcoholism, psychopathy and disposition to violence, you could argue that people have a moral obligation to select ethically better children.'” – hmmm. who’s going to go first? mightn’t their kids be at a disadvantage in some situations? see also: The wrongs, and rights, of genetic screening for children.

Sporting aggression more common in opponents of a similar ability than in contests between unequal teams“The same is also true of aggressive contests between individuals in the animal kingdom, whether it is rutting deer stags or quarrelsome Siamese fighting fish. Now scientists believe they have found evidence for the same trait in competing groups of sportsmen.”

bonus: ‘Who’s Your Daddy’ Truck Rolls Through NYC, Offers Answers With DNA Tests

bonus bonus: Gorillas certainly show emotion – but what do they feel?

bonus bonus bonus: What you don’t know can hurt you“In 1972, the U.S. passed the Clean Water Act, despite a presidential veto by Richard Nixon. Did this act also end an era of unusually high estrogen levels in the environment?” – from peter frost.

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