Evolution of Primate Regulation

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures:

Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes in which regulation has likely evolved under natural selection. To do so, we used a multi-species microarray to measure gene expression levels in livers, kidneys, and hearts from six humans, chimpanzees, and rhesus macaques. This comparative gene expression data allowed us to identify a large number of genes, as well as specific pathways, whose inter-species expression profiles are consistent with the action of stabilizing or directional selection on gene regulation. Among the latter set, we found an enrichment of genes involved in metabolic pathways, consistent with the hypothesis that shifts in diet underlie many regulatory adaptations in humans. In addition, we found evidence for tissue-specific selection pressures, as well as lower rates of protein evolution for genes in which regulation evolves under natural selection. These observations are consistent with the notion that adaptive circumscribed changes in gene regulation have fewer deleterious pleiotropic effects compared with changes at the protein sequence level.

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Another genetic map of Europe

I pointed to the paper at my other weblog, but since ScienceBlogs has a narrow page width, I’ve put the important charts below the fold.

Table 4 – Each horizontal line in the table shows the proportions of test samples originating from a given country that were assigned to each possible target country. I made a few edits, see paper for original.

PopulationsSpainFranceBelgiumUKNorwaySwedenRomaniaGermanyHungarySlovakiaCzechPolandRussia

Spain 0.945 0.055 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
France 0.085 0.515 0.270 0.105 0.000 0.000 0.004 0.014 0.007 0.000 0.000 0.000 0.000
Belgium 0.000 0.086 0.854 0.059 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
UK 0.000 0.009 0.027 0.947 0.000 0.000 0.000 0.017 0.000 0.000 0.000 0.000 0.000
Norway 0.000 0.000 0.000 0.000 0.991 0.010 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Sweden 0.000 0.000 0.000 0.000 0.099 0.901 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Romania 0.000 0.000 0.000 0.000 0.000 0.000 0.960 0.000 0.040 0.000 0.000 0.000 0.000
Germany 0.000 0.000 0.102 0.004 0.029 0.022 0.008 0.644 0.003 0.003 0.177 0.008 0.000
Hungary 0.000 0.000 0.000 0.000 0.000 0.000 0.022 0.051 0.546 0.292 0.090 0.000 0.000
Slovakia 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.077 0.220 0.453 0.250 0.000 0.000
Czech 0.000 0.000 0.000 0.000 0.000 0.000 0.038 0.052 0.161 0.205 0.484 0.062 0.000
Poland 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.002 0.009 0.025 0.021 0.802 0.134
Russia 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.008 0.008 0.000 0.040 0.944

Sex differences, ideology and IQ

The Audacious Epigone has two interesting posts up right now. Conservative men more intelligent than conservative women; Liberal women more intelligent than liberal men and Politics and IQ; Conservative Democrats and liberal Republicans least intelligent. The titles are self-evident, but, I would add that with hindsight it might make sense that liberal Republicans aren’t too bright. If you’re a liberal Republican you are probably just in denial, or, confused and dull. When I think liberal Republican I think Tom Campbell or Chris Shays, but these may simply be elite examples who don’t reflect the fact that most ideological outliers in parties are just individuals who don’t think deeply. For example, someone who was born into a “Republican family,” and doesn’t reflect much about ideology and so continues to vote Republican despite being liberal. I don’t feel I need to explain conservative Democrats, as it seems to me that political exemplars of this class are generally duller than liberal or moderate Democrats.

Note: I know this is kind of a political post, but I’m going to be strict about not letting the comment thread degenerate immediately. So don’t get offended if I don’t let you through the mod-queue even if I normally do.

Yankees, Catholics and Southerners

At my other weblog I have a post which presents dozens of charts gleaned from the GSS. The intent was to compare Catholics and Protestants of New England origin to whites from the McCain Belt, and adduce whether the various Catholic immigrant groups such as the Irish and Italians in New England absorbed the values of the Yankee natives.

Yankees, Irish Catholics and the McCain Belt

One of the implicit assumptions of a book like Albion’s Seed is the “First Settler Effect,” (FSE) whereby the groups which originally settle a region have a disproportionate effect on its cultural character in perpetuity. Obviously there are boundary conditions, the first settlers might be totally replaced demographically rapidly, or, superseded by a cultural complex which views itself as dominant and superior. But in the cased of the United States the best illustration of FSE is linguistic dialect. In New England the tendency to drop the final “r” in words like “car” (non-rhoticity) is a South English linguistic development, and is traced to the East Anglia bias of the original Puritan settlers. This tendency is today strongest in the regions around Boston. Of course, this is probably the area where the Irish Catholics overwhelmed the Yankee Protestants to the greatest extent, showing the strength of FSE (“r” was kept longer, or, is, in Irish and Scottish English, making the illustration of FSE symmetrically persuasive in this case).

But many of the arguments in favor of FSE are rather impressionistic. They are impressions filtered through the eyes of historians, though sometimes they are backed up by quantitative data (New England remains the smartest American region, as it was in 1700). Luckily for us, New England is one of the Census Divisions in the GSS, and so one can explore the differences between Protestants and Catholics, which would roughly map onto the division between original stock and later white ethnic immigrants, and compare them to the McCain Belt whites. Like New England, the East South Central Division of the GSS regions is nice and compact, and correspondences with a relatively homogeneous cultural area.

What are the religious breakdowns of New Englanders?

Religion %
Protestant 30.2
Catholic 53.8
Jewish 3.9
None 11.9

This looks about right checking with the Pew Religious Survey. I’m not totally sure about the representativeness of the GSS in terms of within New England balance, but since I’m interested in comparing New England Protestants and Catholics and McCain Belt whites I’m not too worried.

Earlier I said that the proportion of people with “No Religion” in New England probably was going to be disproportionately Yankee. I’m not so sure. The two tables below have rows which add up to 100% for religion and ancestry respectively.

% Protestant % Catholic % None
England & Wales 33.6 4.4 14.9
Germany 13.7 3.9 7.0
Ireland 9 24.1 19.1
Italy 3.7 21.1 9.5
Scotland 6.9 1.3 5.7
French Canada 4.9 17.8 5.8
% England & Wales % Ireland % Italy % Scotland % French Canada
Protestant 70.8 15.1 7.9 60.5 12.3
Catholic 17 73.4 82.3 20.1 81.9
None 11.1 11.3 2.7 17.5 5.2

If the Irish and English & Welsh are the canonical white ethnics vs. Yankees, it seems secularization hit them both to the same extent. Since 88% of whites in the East South Central Division are self-identified Protestant, I won’t even give a breakdown by religion for that region. From now on I’ll refer to Yankee for Protestant New Englander, and White Ethnic, for Catholic New Englander, and the McCain Belt. Remember that I’m excluding those who put religion down as “None” for New England.
Instead of an impression based on impressions, I went through the GSS and looked at a host of variables. Some of them might not be surprising to you (WORDSUM score), and some of them more so (# of sex partners since 18). The point was to collect a lot of disparate data, spanning explicit and implicit cultural markers. I tried excluding any question where N was smaller than 100 for any category, though some of the questions have N’s bigger than 1,000. On some characters New Englanders cluster together against McCain Belt Whites. On other characters Yankees and McCain Belt Whites custer together against White Ethnics. Finally, there are cases where White Ethnic cluster with McCain Belt whites against Yankees. In many (most it seems to me) cases the pattern seems to be McCain Belt Whites at one end, Yankees at the other, and White Ethnics in the middle, and more often than not, closer to Yankees than McCain Belt Whites.
The cases where the White Ethnics are outgroups can I think be chalked up to aspects of Roman Catholicism and the immigrant culture which make them unique vis-a-vis the other two groups, who are old line Protestant stock. Sometimes, as in abortion on demand, I suspect that the White Ethnics are more conservative than Yankees because of their Catholicism, but they still remain more liberal than McCain Belt conservatives. On the balance, I would say that FSE is plausible and supported by these data, even though Yankees did not turn White Ethnics into Catholic Yankees, they did change their outlook or standard reference point a considerable amount (i.e., they may be socially conservative and emphasize education to a lower extent than Yankees, but they are far more liberal and more educated than McCain Belters. In some cases it seems likely that White Ethnics and Yankees evolved together over time as one regional culture, so I don’t know if one can say that similarities are always due to FSE as such, though I would argue that contingency means that the original Yankee culture loaded the die in turns of future developmental paths.
A little history is warranted at this point. Around 30,000 whites settlers arrived in New England during the 17th century, but 75% arrived in the period between 1630-1640. Most of the derives from this decade and entered into a period of population growth unrivaled in the New World. The next major wave of immigrants were of course the Catholic Irish. Italians and Quebecois are also significant segments of the White Ethnic population. In sharp contrast to the Puritans, who were screened for education and skills to produce the world’s first universal literacy middle class society, the white ethnics came from contexts where they were much lower on the social ladder. The Irish and Italians were classical European peasant populations who lacked the bourgeois sensibilities of the Puritans.
In the McCain Belt the dominant ethnicity is Scots-Irish, broadly construed. They generally arrived in the 18th century into the port of Philadelphia and expanded through the Southern Uplan
ds, driving all the way to the Gulf of Mexico by the early 19th century. A secondary element consisted of migrants from the Southern lowlands, from the Tidewater down to the Carolinas. From these groups the small planter minority emerged. But demographically the former are more important, and represent the heart of the McCain Belt white culture.

Collecting these data was tedious. I expect comments to not be tedious.

Clicking on any of the phrases below will result in an image of the chart below

Abortion On Demand, Affirmative Action, Aged Should Live With Children, Drinks Alcohol, Allow Anti-Religion Book in Library, Allow Anti-Religionist To Speak, Allow Communist To Speak, Allow Doctors To Assist Death, Allow Racist Books In Library, Allow Racists To Speak, Amount Of Sex Within Last Year, Attendance (Religion), Ban Prayer In School, Beaten As Child Or Adult, Belief In Life After Death, Concern About Racial Issues, Confidence In Education, Confidence In Existence Of God, Confidence In Financial Institutions, Confidence In Military, Confidence In Organized Religion, Confidence In Science, Courts Dealing With Criminals, # Of Children, Disparate Racial Outcomes Inborn, Divorced, Educational Level, Ever Smoked, Extramarital Sex, Favor Law Against Interracial Marriage, Federal Income Tax Rate, Gun Permits, Had Affair While Married, Homosexuality Wrong, Hours Watching TV, How Fundamentalist, How Often Read Newspaper, How Often Spend Evenings With Relatives, How Often Spend Time With Neighbors, How Often You Pray, Human Evolution, Hunt?, Ideal Number Of Children, Life Exciting?, Liking For England, Liking For Israel, Birth Control For Teens, Make Divorce Laws Easier, Males Who Have Paid For Sex, Marijuana Legal, Marital Status, Marriage Happy, Money Spent On Blacks, Money Spent On Education, Money Spent On , Money Spent On Environment, Money Spent On Mass Transit, Money Spent On Military, Money Spent On National Parks, Money Spent On Roads, Money Spent On Space
Program
, Money Spent On , Mother Working Doesn’t Hurt Children, Own Or Rent, Owns Gun, People Can Be Trusted, People Are Selfish, Political Views, Vocab Score (rough proxy for intelligence), Seen Porn In Past Year, Sex Partners Since 18 Female, Sex Partners Since 18 Male, Spanking Appropriate, Threatened Within Gun Or Shot At, Warm Feelings Toward Jews, World Is Evil, Wrong To Cheat On Taxes, Years In Armed Forces

We have the technology; we can resurrect them!

Wooly_Mammoth-RBC.jpgRegenerating a Mammoth for $10 Million:

If the genome of an extinct species can be reconstructed, biologists can work out the exact DNA differences with the genome of its nearest living relative. There are talks on how to modify the DNA in an elephant’s egg so that after each round of changes it would progressively resemble the DNA in a mammoth egg. The final-stage egg could then be brought to term in an elephant mother, and mammoths might once again roam the Siberian steppes.
The same would be technically possible with Neanderthals, whose full genome is expected to be recovered shortly, but there would be several ethical issues in modifying modern human DNA to that of another human species.

In the age of $700 billion dollar bailouts, what’s $10 million to bring back megafauna? By the way, a pygmy mammoth survived on Wrangel Island until 3,650 years ago, as late as the end of the Egyptian Middle Kingdom

Should we know presidential candidates’ genomes?

That’s the question being asked at The Personal Genome. Over at Genetic Future Dan “The Man” MacArthur notes the difficulties which might emerge if we start engaging in widespread embryo screening. So how exactly is the average American voter going to interpret the myriad of genes responsible for only a small fraction of phenotypic variation?
I’m not sure that genetic data adds much value for the body politic. I would want to know, but, I would also take SAT scores and college transcripts before I’d be interested in a candidate’s genetic sequence. Our president elect has not, for example, released his academic record.

How predictive are known genetic factors for disease risk?

Two studies published today demonstrate what was immediately evident from genome-wide association studies of many common diseases: the genetic variants identified account for only a small fraction of risk.

In these cases, the authors try to predict whether an individual will get type II diabetes from a number of clinical variables, as well as recently identified genetic risk factors. The genetic factors only marginally improve the prediction of diabetes, likely to a clinically insignificant extent.

This was obvious, of course, from the initial studies themselves–you can’t expect variants responsible for a meager fraction of overall disease risk to function as effective predictors of the disease. But somewhat notable nonetheless.

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