Archives for posts with tag: identity by descent

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.)

*update below*

remember this map from ralph & coop [pdf]?:

coop et al - mean within-country ibd rates

those are the mean ibd (identity by descent) rates for various populations in europe. the bigger the circle, the greater the number of ibd blocks larger than 1cM in length shared in common between each populations’ members. so, the larger the circles, the more segments of dna the individuals within those population share in common — i.e. the more alike they are genetically.

well, i never added the hajnal line to that map like i usually like to do for any map of europe that lands on my desktop (see here and here for examples). how remiss of me! (recall that populations within the hajnal line have had a historic tendency to marry late.)

i thought i’d better rectify this situation … so, here it is! mean ibd rates for europe PLUS the hajnal line. enjoy!:

coop et al - mean within-country ibd rates + hajnal line

update: see also jayman’s More on Farming and Inheritance Systems – Part I: IQ.

previously: ibd and historic mating patterns in europe and behind the hajnal line and todd’s family systems and the hajnal line

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

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

(note: comments do not require an email. not out on a limb, am i?)

**update 08/03: post fixed to remove references to roh which i got wrong (roh≠blocks of ibd!) — see comments below (thanks, citrus!)**

princenuadha points me to this awesome pdf which i guess was a presentation given at a society for molecular biology and evolution (smbe) conference last weekend (thanks, prince!).

here is an interesting graphic from the presentation (pg. 21):

what this map shows are the means of runs of homozygosity (remember those?) blocks of identity by descent (ibd) that are greater than 1cM for each of these european populations. the longer the ibd blocks, the greater the identity by descent, and vice versa. small circles=fewer long blocks of ibd; large circles=more long blocks of ibd.

if a population has lots of short blocks of ibd, then its genetics are all mixed up, possibly due to outbreeding or because of a fairly recent mixing with another population. if a population has lots of long blocks of ibd, then its genetics are not so mixed up and the individuals within it share a lot of identity by descent. this can be an indicator of having been squeezed through a bottleneck or close inbreeding over time.

here are the mean numbers of long blocks of ibd for some of the countries on the map:

as you can see, my “core europeans” (english, french, germans, dutch, prolly some others) all have low means of blocks of ibd. the smallest circles are found right in the center of nw europe: england, france, belgium, germany. also italy (more about that below). in the immediate periphery around core europe, the circles are a bit larger, i.e. there are more long blocks of ibd: scotland, ireland, spain, portugal, switzerland, greece, scandinavians. eastern europeans have even larger circles/even more long blocks of ibd: poles, russians. and populations in the balkans, like the albanians, have enormous circles, i.e. LOTS of long blocks of ibd.

all of that fits the pattern i’ve been talking about here on the ol’ blog (see the mating patterns series below in the left-hand column): that the core europeans have been outbreeding the most and for the longest, with peripheral europeans lagging behind that trend, and eastern europeans really lagging behind the trend. i haven’t actually discussed the balkan populations (yet), but i do know that cousin/endogamous marriage rates are pretty high in the balkans.

i wonder if the numbers for italy may be unrepresentatively low, but it’s difficult to know. the data used are from popres and, like so much genetic data out there, have no provenance info attached to them. so, are the italian data from northern italy (which has a long history of outbreeding) or southern italy (which has a lot of inbreeding) or a combination of both? dunno.

this is a very cool study! i like it a lot. (^_^)

polish gen also has an interesting post about the presentation, btw.

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

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