linkfest – 01/11/15

Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense“Systems biology is largely based on the principal that the link between genotype and phenotype is deterministic, and, if we know enough, can be predicted with high accuracy. In contrast, recent work studying transcription within single celled organisms has shown that the genotype to phenotype link is stochastic, i.e. a single genotype actually makes a range of phenotypes even in a single environment. Further, natural variation within genes can lead to each allele displaying a different phenotypic distribution. To test if multi-cellular organisms also display natural genetic variation in the stochastic link between genotype and phenotype, we measured the metabolome, growth and defense metabolism within an Arabidopsis RIL population and mapped quantitative trait loci. We show that genetic variation in the nuclear and organeller genomes influence the stochastic variation in all measured traits. Further, each trait class has distinct genetics underlying the stochastic variance, showing that there are different mechanisms controlling the stochastic genotype to phenotype link for each trait.” – h/t kevin mitchell! who tweeted: Some genomes are ‘noisier’ than others – robustness of developmental outcome is itself a genetic trait.

Evolutionary pattern in the OXT-OXTR system in primates: Coevolution and positive selection footprints“It was previously believed that placental mammals present no variability in oxytocin (OXT). The present study reports novel data on the diversity of OXT and its receptor (OXTR) in primate species, including New World monkeys. Contrary to prior expectations, we found three novel OXT forms and several OXTR nonsynonymous changes not previously described. In the Cebidae family, signals of positive selection were found for an OXT variant at position 8, which is associated with larger litter sizes. We detected positive selection for OXTR forms and report a coevolutionary process between changes in OXT and OXTR.”

Effects of the demographic transition on the genetic variances and covariances of human life history traits“The recent demographic transitions to lower mortality and fertility rates in most human societies have led to changes and even quick reversals in phenotypic selection pressures. This can only result in evolutionary change if the affected traits are heritable, but changes in environmental conditions may also lead to subsequent changes in the genetic variance and covariance (the G matrix) of traits. It currently remains unclear if there have been concomitant changes in the G matrix of life history traits following the demographic transition. Using 300 years of genealogical data from Finland, we found that four key life history traits were heritable both before and after the demographic transition. The estimated heritabilities allow a quantifiable genetic response to selection during both time periods, thus facilitating continued evolutionary change. Further, the G matrices remained largely stable but revealed a trend for an increased additive genetic variance and thus evolutionary potential of the population after the transition.” – h/t ruben c. arslan!

Mapping granny: ancestry inference for admixed individuals“In the December issue of G3: Genes|Genomes|Genetics, Yang et al. describe a method for ancestry inference of admixed individuals that uses a geographic approach to explicitly model some of the messy realities of populations. Testing the new method on data from the Population Reference Sample project, the authors were able to localize the grandparents of admixed Europeans to within around 500 kilometres of their reported ancestry, while simultaneously identifying which segments of each person’s genome were inherited from each ancestor.”

Different neurodevelopmental symptoms have a common genetic etiology“Parents of all Swedish 9- and 12-year-old twin pairs born between 1992 and 2002 were targeted for interview regarding problems typical of autism spectrum disorders, ADHD and other neurodevelopmental conditions (response rate: 80 percent). Structural equation modeling was conducted on 6,595 pairs to examine the genetic and environmental structure of 53 neurodevelopmental problems. One general genetic factor accounted for a large proportion of the phenotypic covariation among the 53 symptoms. Three specific genetic subfactors identified ‘impulsivity,’ ‘learning problems,’ and ‘tics and autism,’ respectively.” – h/t jayman! who tweeted: More evidence for the p-factor. Common genetic factor underlies many mental disorders in study of all Swedish twins.”

Measuring missing heritability: Inferring the contribution of common variants“[T]he most reasonable hypothesis concerning ‘missing heritability’ is simply that larger sample size is required to find the many remaining alleles of small effect. Fisher’s infinitesimal model will turn out to be a good first approximation for most human traits.” – from steve hsu.

Self evident but unexplored – how genetic effects vary over time – from jason collins.

Mendelian and polygenic inheritance of intelligence: A common set of causal genes? Using next-generation sequencing to examine the effects of 168 intellectual disability genes on normal-range intelligence“Despite twin and family studies having demonstrated a substantial heritability of individual differences in intelligence, no genetic variants have been robustly associated with normal-range intelligence to date. This is largely ascribed to the high polygenicity of intelligence, i.e., to its being subject to the effects of a large number of genes of individually small effect. Intellectual disability, on the other hand, frequently involves large effects of single genetic mutations, many of which have been identified…. Using an existing pool of known intellectual disability genes, we constructed a set of 168 candidate genes for normal-range intelligence, and tested their association with intelligence in 191 individuals (aged 5–18) sampled from the high and low ends of the IQ distribution. In particular, we 1) employed exon sequencing to examine the possible effects of rare genetic variants in the 168 genes, and 2) used polygenic prediction to examine the overall effect of common genetic variants in the candidate gene set in a larger sample (N = 2125, mean age 20.4, SD = 14.1). No significant association between the candidate gene set and intelligence was detected.”

IQ and Birth Order Effects: Real? No – from jayman.

Educated parents more important than rich parents“Having a mobile phone, a video recorder and a game computer are associated with lower scholastic ability, and the only substantial positive correlation is with the number of books, and of course the cause may not be the books themselves, but the intellect and character of the families who choose to buy books.” – from dr. james thompson.

The inconsistency of studies of gender differences in cognitive abilities: due to using different methods? – from emil kirkegaard.

Familial Mediterranean fever – from greg cochran.

The etiologic role of genetic and environmental factors in criminal behavior as determined from full- and half-sibling pairs: an evaluation of the validity of the twin method“Heritability estimates for CB from full- and half-siblings closely approximated those found from twins in the same population, validating the twin method.” – h/t ben southwood! who tweeted: “N=1,005,471 study of Swedish siblings and half-siblings (reared together & apart) estimates criminal behaviour is 33-56% heritable.”

Genetic polymorphisms predict national differences in life history strategy and time orientation“Polymorphisms in three genes have been linked to aspects of life-history strategy. National frequencies of these polymorphisms form a strong single genetic factor. The genetic factor is strongly associated with national differences in life-history strategy. This association remains after controlling for national socioeconomic differences.”

Genetic clue points to most vulnerable children“Some children are more sensitive to their environments, for better and for worse. Now Duke University researchers have identified a gene variant that may serve as a marker for these children….” – h/t carlos esteban!

French lesson“Modern France is founded on Western principles of equality, human betterment, and universal morality. Anyone anywhere can become French. That view, the official one, seems more and more disconnected from reality.” – from peter frost.

Is Nothing Sacred? – thosewhocansee on the charlie hebdo killings.

Twin study suggests genetic factors contribute to insomnia in children, teens

Monkeys seem to recognize their reflections“Trained macaques studied themselves in mirrors, fuelling debate over animals’ capacity for self-recognition.”

Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data“Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach.”

A New Antibiotic That Resists Resistance

There is A Scientific Reason That Cold Weather Could Cause Colds“The rhinovirus that most commonly causes colds likes chillier temperatures, where the host’s immune system doesn’t fare so well…. [W]e now know that covering your nose might actually help it stay cold-free, in more than one way.” – yes! fiiiiinally!

Remains of long-dead viruses in our genomes aid our immune response

Skip Your Annual Physical“Regardless of which screenings and tests were administered, studies of annual health exams dating from 1963 to 1999 show that the annual physicals did not reduce mortality overall or for specific causes of death from cancer or heart disease…. [S]creening healthy people who have no complaints is a pretty ineffective way to improve people’s health. If you screen thousands of people, maybe you’ll find tens whose exams suggest they might have a disease. And then upon further tests, you’ll find it is really only a few individuals who truly have something. And of those individuals, maybe one or two actually gain a health benefit from an early diagnosis. The others may have discovered a disease, but one that either would never have become clinically evident and dangerous, or one that is already too advanced to treat effectively. For instance, early detection of most thyroid cancers leads to surgery, but in many cases those cancers would not have caused serious problems, much less death. Conversely, for individuals whose annual exams lead to the diagnosis of esophageal or pancreatic cancer, the early diagnosis might extend the time they know they have cancer but is unlikely to extend their lives.” – h/t jason collins!

Variation in cancer risk among tissues can be explained by the number of stem cell divisions“Some tissue types give rise to human cancers millions of times more often than other tissue types. Although this has been recognized for more than a century, it has never been explained. Here, we show that the lifetime risk of cancers of many different types is strongly correlated (0.81) with the total number of divisions of the normal self-renewing cells maintaining that tissue’s homeostasis. These results suggest that only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions. The majority is due to ‘bad luck,’ that is, random mutations arising during DNA replication in normal, noncancerous stem cells.”

Germs May Play Key Role in Wound-Induced Skin Cancer

Race and Police Killings: Additional Thoughts – from robert verbruggen who tweeted: “Three data sets now show that racial disparities in police shootings can be explained by violent crime rates.”

In Search of an Association Between Conception Risk and Prejudice [pdf] – h/t lars penke! who tweeted: “4 large studies (1 pre-reg) by @BrianNosek et al. fail to replicate menstrual cycle effects on racial biases.”

The Strange Inevitability of Evolution“Good solutions to biology’s problems are astonishingly plentiful…. [T]wo crucial things about the RNA sequence space. First, there are many, many possible sequences that will all serve the same function. If evolution is ‘searching’ for that function by natural selection, it has an awful lot of viable solutions to choose from. Second, the space, while unthinkably vast and multi-dimensional, is navigable: You can change the genotype neutrally, without losing the all-important phenotype. So this is why the RNAs are evolvable at all: not because evolution has the time to sift through the impossibly large number of variations to find the ones that work, but because there are so many that do work, and they’re connected to one another.” – h/t billare!

Skeptic’s Guide to Debunking Claims about Telomeres in the Scientific and Pseudoscientific Literature – h/t richard harper!

Mathematicians refute oft-cited ‘diversity trumps ability’ study“‘Diverse groups of people bring to organizations more and different ways of seeing a problem and, thus, faster/better ways of solving it,’ Page told The New York Times in 2008. ‘The reason: the diverse groups got stuck less often than the smart individuals, who tended to think similarly,’ Page said. ‘What the model showed was that diverse groups of problem solvers outperformed the groups of the best individuals at solving problems.’ But Thompson’s paper in the Notices of the American Mathematical Society systematically dismantles Page’s sophistic mathematics.”

Easter Island’s Demise May Have Surprising New Explanation“The downfall of Easter Island may have had more to do with preexisting environmental conditions than degradation by humans….”

13,000 Year Old Cosmic Impact Actually Just a Stone Age House Fire

bonus: Deep bacteria may evolve even without passing genes on“Bacteria living hundreds of metres below the seafloor carry more genetic changes than their peers nearer the surface – even though the deep microbes are unlikely to reproduce and undergo natural selection in its traditional sense…. The results show – for the first time, Briggs thinks – that the bacterial genomes change with depth: the micro-organisms at 554 metres carry more mutations in genes that code for energy-related processes like cell division and biosynthesis of amino acids than are seen in their shallower counterparts…. [I]f you take evolution in its broader sense to mean genetic changes across the population, then it might be occurring even without cell division, says Briggs. That’s because in theory, bacteria in these environments grow so slowly that they may survive for hundreds of thousands of years. Individual bacteria might have begun life at the seafloor before being gradually buried, over a period of thousands of years, as more sediment accumulated at the bottom of the sea. If so, perhaps the bacteria now at 554 metres were rare cells in the initial population that have now come to dominate because the other cells, which didn’t carry their genetic mutations, have all died.”

bonus bonus: Insights into the evolution of longevity from the bowhead whale genome“The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response.”

bonus bonus bonus: A Museum’s Butterfly Emerged Half Male, Half Female“The rarity is like a natural experiment that tells scientists how genes and hormones interact to produce different sexes.”

(note: comments do not require an email. bowhead whale!)


linkfest – 12/01/14

look! another linkfest! (^_^)

Our Cats, Ourselves“Which brings us to the genome of one critical tame animal: ourselves, humans. The Nobel Prize-winning zoologist Konrad Z. Lorenz once suggested that humans were subject to the same dynamics of domestication. Our brain and body sizes peaked during the end of the last ice age, and declined with the spread of agriculture…. Our cultural flexibility and creativity since the end of the ice age have not freed humans from evolutionary forces, but have opened up novel and startling paths. Thinking of domestication as an evolutionary process that occurs through ‘artificial’ selection creates a false dichotomy of nurture and nature that plays into a conceit of human exceptionalism. In fact, the idea that we are apart from nature, that it is ours to tame and exploit, is an outmoded approach. A more useful interpretation is that over the past 10,000 years, humans fashioned their own ecosystem. We were part of a natural process that altered the landscape…. The same forces that reshaped the genomes of our domesticates also reshaped ours.” – from razib. in the new york times! (^_^)

Ancient Easter Islanders Interbred With Native Americans“According to the recent study conducted by geneticists, the ancient inhabitants of Easter Island met and interbred with Native Americans long before Westerners arrived…. The recent genetic study is published on Thursday in the Current Biology journal. According to the study, these ancient people had significant contact with Native Americans hundreds of years ago, before the westerners reached the Island in 1722…. The finding of the study suggests that the intermixing occurred 19 to 23 generations ago. The researchers said that the Polynesian people (Rapa Nui’s) are not believed to have started mixing with Europeans until much later, the 19th century. Malaspinas said the genetic ancestry of today’s Rapa Nui people is roughly 75% Polynesian, 15% European and 10% Native American.”

Barley fuelled farmers’ spread onto Tibetan plateau“Cold-tolerant crop enabled high-altitude agriculture some 3,600 years ago”

Faster than Fisher“[M]igration and conquest, must explain the wide distribution of many geographically widespread selective sweeps and partial sweeps. They were adaptive, all right, but expanded much faster than possible from purely local diffusion.” – from greg cochran.

The Germ of Laziness – also from greg cochran.

Putting IBD to Bed – from razib.

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes – h/t mwpennell! who tweeted: “Recombination hotspots in humans appear to be young…evidence for Red Queen theory for evolution of recombination?”

Inclusive fitness and sexual conflict: How population structure can modulate the battle of the sexes – h/t rebecca sear!

Do Chinese people get bored less easily?“Advanced farming — intensive land use, task specialization, monoculture — has profoundly shaped East Asian societies, particularly China. This is particularly so for rice farming. Because the paddies need standing water, rice farmers must work collectively to build, dredge, and drain elaborate irrigation networks. Wheat farming, by comparison, requires no irrigation and only half as much work. Advanced farming seems to have favored a special package of predispositions and inclinations, including greater acceptance of monotony. This has been shown in two recent studies.” – from peter frost.

Culture and state boredom: A comparison between European Canadians and Chinese“European Canadians (vs. Chinese) are more likely to experience state boredom.” – h/t erwin schmidt!

Gender differences in preferences, choices, and outcomes: SMPY longitudinal study“The figures show significant gender differences in life and career preferences, which affect choices and outcomes *even after ability is controlled for*…. According to the results, SMPY men are more concerned with money, prestige, success, creating or inventing something with impact, etc. SMPY women prefer time and work flexibility, want to give back to the community, and are less comfortable advocating unpopular ideas. Some of these asymmetries are at the 0.5 SD level or greater.” – from steve hsu.

Are liberals and conservatives differently wired? – also from peter frost.

Detecting ‘polygenes’ using signals of polygenic selection. Tools for increasing the power of GWAS – from davide piffer who tweeted: “Watson and Venter’s genomes have higher frequency of intelligence polygenenes.”

Intelligence lost at 1.23 IQ points per decade“Michael Woodley of Menie spends much of his time tending his ancestral estate, pacing the linen-fold panelled rooms of the ancient house, warming his hands at the towering stone fireplace and meditating on the collapse of the aristocracy, the paucity of contemporary innovation and the lamentable and persistent downward drift of the national intellect. Now he sends me a barefoot runner with his latest manuscript, which I have read as the autumn mists creep across the Nadder valley, before penning this reply for the poor urchin to carry back to his master. Young Woodley avers that, not only are we going to hell in a handcart, but we are doing so at a pace which he can predict with some accuracy (1.23 IQ points per decade), composed as it is of two dysgenic effects: the dull have been reproducing with greater fecundity than the bright (.39), and increasing paternal age has increased the rate of deleterious mutations (.84).” – from dr. james thompson.

Gypsy intelligence – also from dr. james thompson.

Lower Body Symmetry and Running Performance in Elite Jamaican Track and Field Athletes – h/t keith laws! who tweeted: “More symmetrical knees & ankles in Elite Jamaican track and field athletes…Of course…”

Great Ape Origins of Personality Maturation and Sex Differences: A Study of Orangutans and Chimpanzees

The Case Against Early Cancer Detection“[C]ancer screening may harm more people than it helps.” – h/t jason collins!

In the U.S., Few Heavy Drinkers Are Actually Alcoholics“About 90 percent of people who drink excessively — more than eight drinks a week for women, 15 for men — are not alcohol dependent.” – h/t ray sawhill!

Genes tell new story: Alcohol in moderation only benefits 15% of population“An alcoholic beverage a day, especially wine, is widely believed to help keep heart disease risk low, but new research from the University of Gothenburg shows that only about 15% of the human population — those with a specific the form of the cholesteryl ester transfer protein (CETP) gene — actually gain this benefit from moderate alcohol consumption.”

The Real Roots of Midlife Crisis“What a growing body of research reveals about the biology of human happiness — and how to navigate the (temporary) slump in middle age.”

Despite its problems, the United States of America is still the best. Thing. Ever.“Other aspects of America’s story, though, seem less important now that the quest for racial equality has become almost a religious mission; this week I finally got around to watching the HBO series John Adams, which begins with the Massachusetts lawyer defending Captain Thomas Preston, the officer blamed for the Boston massacre. The mob wanted to avenge the deaths but, this being a colony where people passionately believed in their ancestral English liberties, ‘due process’ was followed – a term that dates back to the Parliament of Edward III but was obviously influenced by Clause 39 of the Magna Carta. Due process is what was followed in the Ferguson case, but maybe that’s just a boring old racist Anglo-Saxon idea that we can forget about now (grand juries are literally Anglo-Saxon, dating back to the reign of Ethelred II, or possibly the vibrant culturally-enriching Viking maniac King Canute).” – from ed west.

Children are not science projects“What do we tell to prospective adoptive parents? The first answer, and the only answer that ultimately counts, is that they are doing the Lord’s work. They have the opportunity to provide love and nurturing to a child who needs it. There are few better things that human beings can do with their time. The second answer is that they, like biological parents, are not miracle-workers. They will be unable to mold the child. Sometimes their adopted child will experience problems that are not the adoptive parents’ fault; sometimes they will reveal gifts of talent and character that are equally not to the adoptive parents’ credit. What is to the credit of good parents, adoptive and biological alike, is enfolding the child in love.” – from charles murray…who’s really just a big softie after all. (^_^) — see also: Adopt a child, but discard an illusion from dr. james thompson.

In Northern Ireland, a Wave of Immigrants Is Met With Fists – which came (or *should’ve* come) as a surprise to absolutely no one….

When exactly did the Industrial Revolution start?

Europe’s Bronze Age Collapse Not Caused by Climate Change

How Thanksgiving, the ‘Yankee Abolitionist Holiday,’ Won Over the South

Your Inner Feather“About 300 million years ago, our ancestors began to lay hard-shelled eggs. Those early animals would give rise to mammals, reptiles, and birds (collectively known as amniotes, named for the amniotic egg). Edwards and his colleagues found that the first amniotes already had the *entire* complement of feather patterning genes. That means you, as an amniote, have them too.” – cool!

Viruses as a Cure

Stop eating cats and dogs say animal rights campaigners in Switzerland“Cat appears on traditional Christmas menus in some areas of Switzerland.” – wait. what?!

bonus: Snakes are ‘righties’ — with their penis, that is

bonus bonus: Snakes Leave Identity Within Their Fang Marks“Getting a DNA swab from the fang marks of a snake bite can accurately identify the type of snake, a team working in Nepal has found.”

bonus bonus bonus: Monterey Bay researchers capture rare deep-sea anglerfish on video for first time – whoa!

bonus bonus bonus bonus: Ants Regularly Pack Up and Dig New Nests, and Nobody Knows Why

bonus bonus bonus bonus bonus: Red Baron’s WWI German Fokker triplane rebuilt by flying enthusiast – oooo! pretty. (^_^)

(note: comments do not require an email. a face only a mother could love. maybe.)